Contacts of the helix formed by residues 7 - 36 (chain A) in PDB entry 3M0V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 7 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.6 4.2 + - - -
5A ARG 4.1 2.0 + - - -
6A ILE* 1.3 74.6 - - - +
8A GLN* 1.3 66.0 + - - +
9A ASP* 3.9 24.0 - - - +
10A VAL* 3.0 25.2 + - + +
11A VAL* 3.3 10.0 + - - +
409A SER* 5.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 2.9 57.3 - - + +
6A ILE 3.3 1.8 + - - +
7A ALA* 1.3 72.0 - - - +
9A ASP* 1.3 57.8 + - - +
11A VAL* 3.2 9.0 + - - +
12A ALA* 2.8 30.9 + - - +
90A GLN* 5.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 3.9 13.4 - - - +
8A GLN* 1.3 77.8 - - - +
10A VAL* 1.3 85.7 + - - +
12A ALA* 3.8 6.8 - - - +
13A ARG* 2.9 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.6 3.1 - - + -
7A ALA* 3.0 20.8 + - + +
9A ASP* 1.3 93.2 + - - +
11A VAL* 1.3 60.3 + - - +
13A ARG* 3.3 15.4 + - - +
14A GLU* 2.9 31.9 + - + +
405A THR* 4.0 25.4 - - + +
408A ALA* 4.3 13.0 - - + +
409A SER* 4.1 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.9 19.1 - - + -
7A ALA 3.7 11.9 - - - +
8A GLN* 3.2 9.3 + - - +
10A VAL* 1.3 76.4 - - - +
12A ALA* 1.3 63.8 + - - +
14A GLU* 3.9 0.3 - - - -
15A ASN* 3.0 36.2 + - - +
90A GLN* 4.0 16.4 - - + +
91A LEU* 4.1 7.2 - - + -
397A GLY 4.4 8.7 - - - +
398A GLY 3.7 28.3 - - - +
399A ALA* 4.4 5.8 - - + +
405A THR* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN 2.8 16.8 + - - +
9A ASP* 3.8 8.7 - - - +
11A VAL* 1.3 79.3 - - - +
13A ARG* 1.3 56.8 + - - +
15A ASN* 3.3 4.4 + - - +
16A ASP* 2.9 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 2.9 41.7 + - - +
10A VAL* 3.7 20.3 - - - +
12A ALA* 1.3 75.7 - - - +
14A GLU* 1.3 62.3 + - - +
16A ASP* 3.3 9.0 + - - +
17A ARG* 3.0 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 2.9 21.4 + - + +
11A VAL 4.2 1.3 - - - +
13A ARG* 1.3 83.8 + - - +
15A ASN* 1.3 66.0 - - - +
17A ARG* 3.1 32.7 + - - -
18A ARG* 2.8 64.0 + - - +
401A ASP 6.3 0.2 - - - -
404A ALA 5.2 0.2 - - - +
405A THR* 3.4 29.6 - - + +
408A ALA* 3.9 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.0 26.7 + - - +
12A ALA* 3.7 5.2 - - - +
14A GLU* 1.3 75.0 - - - +
16A ASP* 1.3 65.1 + - - +
18A ARG* 3.0 4.3 + - - +
19A ALA* 2.8 29.8 + - - +
394A ARG* 4.7 12.5 - - + +
398A GLY 3.1 19.3 - - - +
399A ALA* 3.4 9.3 - - - +
400A VAL* 2.8 47.1 - - + +
401A ASP 4.7 0.8 - - - +
405A THR* 4.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 2.9 33.2 + - - +
13A ARG* 3.7 6.8 - - - +
15A ASN* 1.3 80.3 - - - +
17A ARG* 1.3 61.6 + - - +
18A ARG 3.1 1.2 + - - -
19A ALA* 3.3 19.9 + - - +
20A SER 4.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.0 34.7 + - - +
14A GLU* 3.1 40.0 + - - +
15A ASN 3.2 0.2 - - - -
16A ASP* 1.3 77.0 - - - +
18A ARG* 1.3 72.8 + - + +
19A ALA 3.7 0.2 - - - -
20A SER* 5.4 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.8 64.0 + - - +
15A ASN 3.0 4.6 + - - +
17A ARG* 1.3 95.9 - - + +
19A ALA* 1.3 62.6 + - - +
20A SER 3.4 2.2 + - - -
21A ALA* 3.5 11.4 + - + +
22A LEU* 3.1 22.8 + - - +
400A VAL* 4.0 20.1 - - + +
401A ASP* 3.5 32.4 + - - +
404A ALA* 3.3 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN 2.8 14.2 + - - +
16A ASP* 3.3 16.8 + - - +
18A ARG* 1.3 74.1 - - - +
20A SER* 1.3 66.3 + - - +
22A LEU* 3.3 8.6 + - - +
23A LYS* 2.9 25.5 + - - +
394A ARG* 6.1 4.9 - - - +
400A VAL* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP 4.7 2.0 + - - -
17A ARG 5.4 1.7 + - - -
18A ARG 3.4 0.4 - - - -
19A ALA* 1.3 78.9 - - - +
21A ALA* 1.3 65.3 + - - +
23A LYS* 3.3 9.4 + - - +
24A GLU* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.5 11.9 + - + +
19A ALA 3.4 0.2 - - - -
20A SER* 1.3 78.2 - - - +
22A LEU* 1.3 63.9 + - - +
24A GLU* 3.3 2.9 + - - +
25A ASP* 2.9 35.5 + - - +
35D ARG* 4.4 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 3.1 18.1 + - - +
19A ALA* 3.7 7.6 - - - +
21A ALA* 1.3 73.4 - - - +
23A LYS* 1.3 58.6 + - - +
25A ASP* 4.6 4.5 - - + -
26A TYR* 2.7 43.6 + - + +
387A PRO* 3.6 34.3 - - + +
390A ALA* 3.8 13.2 - - + +
391A GLU* 4.1 28.3 - - + +
394A ARG* 4.5 9.0 - - - -
400A VAL* 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.9 17.4 + - - +
20A SER* 3.4 9.6 - - - +
22A LEU* 1.3 78.1 - - - +
24A GLU* 1.3 71.0 + - - +
26A TYR* 4.0 3.7 - - - +
27A GLU* 2.8 68.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 3.1 19.9 + - - +
21A ALA* 3.6 7.0 - - - +
23A LYS* 1.3 95.0 - - - +
25A ASP* 1.3 56.5 + - - +
27A GLU* 4.0 9.6 - - - +
28A ALA* 3.0 29.7 + - - +
35D ARG* 3.7 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 2.9 27.9 + - - +
22A LEU* 3.9 5.0 - - + +
24A GLU* 1.3 74.1 - - - +
26A TYR* 1.3 61.0 + - - +
28A ALA* 3.4 5.9 + - - +
29A LEU* 2.9 30.0 + - - +
387A PRO* 3.8 21.9 - - + +
32D ASN* 3.0 25.7 + - - +
35D ARG* 3.0 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.7 26.7 + - + +
23A LYS* 4.0 3.6 - - - +
25A ASP* 1.3 73.7 - - - +
27A GLU* 1.3 66.6 + - + +
29A LEU* 3.3 3.1 + - - +
30A GLY* 2.8 25.5 + - - -
40A ILE* 3.5 33.4 - - + +
41A GLU* 2.7 33.8 + - - -
44A THR* 3.0 23.7 + - - -
387A PRO* 3.6 30.2 - - + +
388A ILE* 4.1 4.7 - - - -
391A GLU* 3.6 30.7 - - + -
395A ARG* 3.5 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 2.8 59.4 + - + +
24A GLU* 4.1 9.8 - - - +
26A TYR* 1.3 81.5 - - + +
28A ALA* 1.3 65.2 + - - +
30A GLY* 3.7 1.9 - - - +
31A ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 3.0 19.7 + - - +
25A ASP* 3.6 7.6 - - - +
27A GLU* 1.3 77.6 - - - +
29A LEU* 1.3 61.7 + - - +
31A ALA* 3.3 6.9 + - - +
32A ASN* 3.1 22.6 + - - +
35A ARG* 4.9 1.9 + - - -
28D ALA* 4.0 28.3 - - + +
35D ARG* 6.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP 2.9 19.0 + - - +
26A TYR 3.6 3.8 - - - +
28A ALA* 1.3 77.1 - - - +
30A GLY* 1.3 58.5 + - - +
32A ASN* 3.2 10.5 + - + +
33A LEU* 2.8 45.7 + - + +
40A ILE* 3.9 7.6 - - + -
383A THR* 3.7 28.0 - - + -
384A ASP 3.6 21.5 - - - +
385A VAL* 4.3 1.3 - - - -
387A PRO* 4.1 14.4 - - + -
388A ILE* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR 2.8 17.5 + - - -
27A GLU* 3.7 3.6 - - - -
28A ALA 3.2 0.2 - - - -
29A LEU* 1.3 76.7 - - - +
31A ALA* 1.3 56.2 + - - +
33A LEU* 3.8 2.0 - - - +
34A ALA* 2.9 29.5 + - - +
38A VAL 4.7 0.9 - - - +
40A ILE* 3.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 3.0 16.6 + - - +
28A ALA* 3.7 5.6 - - - +
29A LEU 3.3 0.4 - - - -
30A GLY* 1.3 73.6 - - - +
32A ASN* 1.3 64.8 + - - +
34A ALA* 3.3 7.2 + - - +
35A ARG* 3.1 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 3.1 13.8 + - - +
29A LEU* 3.2 14.7 + - + +
31A ALA* 1.3 77.1 - - - +
33A LEU* 1.3 64.1 + - - +
35A ARG* 3.3 27.8 + - - +
36A ARG* 2.8 49.6 + - - +
383A THR* 5.2 0.2 - - - +
25D ASP* 3.0 31.3 + - - +
384D ASP* 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.8 42.8 + - + +
30A GLY* 3.8 3.6 - - - +
32A ASN* 1.3 76.1 - - - +
34A ALA* 1.3 59.4 + - - +
36A ARG* 2.8 47.7 + - - +
37A GLY 3.0 0.2 + - - -
38A VAL* 2.8 41.9 + - + +
40A ILE* 4.0 26.7 - - + +
355A LEU* 4.1 33.9 - - + -
383A THR* 4.5 0.2 - - + -
388A ILE* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY 2.9 18.2 + - - +
31A ALA* 3.6 8.5 - - - +
32A ASN 3.3 0.2 - - - -
33A LEU* 1.3 76.3 - - - +
35A ARG* 1.3 57.4 + - + +
37A GLY* 2.9 19.1 + - - -
38A VAL 3.3 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 4.9 1.4 + - - -
31A ALA* 3.1 34.3 + - - +
32A ASN* 3.5 24.0 - - - +
33A LEU 3.2 0.2 - - - -
34A ALA* 1.3 77.0 - - + +
36A ARG* 1.3 60.1 + - + +
37A GLY 3.3 1.4 + - - -
21D ALA* 4.1 27.4 - - + +
24D GLU* 3.7 33.4 + - - +
25D ASP* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 2.8 44.3 + - - +
33A LEU* 2.8 26.8 + - - +
35A ARG* 1.3 80.0 - - + +
37A GLY* 1.3 62.0 + - - +
38A VAL* 3.4 12.2 + - + +
355A LEU* 4.5 10.9 + - - +
357A ASP* 5.3 5.0 - - - +
379A ARG* 3.1 23.0 + - - +
380A ALA* 4.2 5.5 - - - +
383A THR* 2.9 32.9 + - - +
384D ASP* 5.4 4.2 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il