Contacts of the helix formed by residues 8 - 30 (chain A) in PDB entry 4C48
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 ARG 8 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.0 69.6 + - + +
5A PHE* 2.8 19.0 + - + +
7A ASP* 1.3 85.1 - - + +
9A PRO* 1.4 67.6 - - - +
10A ILE 3.5 1.9 + - - -
11A PHE* 3.7 23.0 + - + +
12A ALA 3.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE 3.3 7.3 - - - +
6A ILE 4.6 2.5 - - - +
7A ASP 3.0 14.8 - - - +
8A ARG* 1.4 82.9 - - - +
10A ILE* 1.3 76.7 + - + +
12A ALA* 3.4 14.4 - - - +
13A TRP* 3.0 22.4 + - - +
491A ALA* 4.0 8.7 - - + +
495A THR* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG 3.5 0.2 - - - -
9A PRO* 1.3 85.2 - - + +
11A PHE* 1.3 60.0 + - - +
13A TRP* 2.4 43.9 + - + +
14A VAL* 2.9 21.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.5 15.3 - + - -
5A PHE* 3.6 29.2 - + - -
8A ARG* 3.7 20.9 + - + +
9A PRO 3.4 0.6 - - - -
10A ILE* 1.3 80.7 - - - +
12A ALA* 1.3 61.5 + - - +
14A VAL* 3.2 23.3 + - + +
15A ILE* 3.1 35.7 + - + +
2038A LMT 4.8 17.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
5A PHE* 4.1 6.0 - - + -
8A ARG 3.9 2.8 + - - -
9A PRO 3.4 13.2 + - - +
10A ILE 3.0 0.2 - - - -
11A PHE* 1.3 77.6 - - - +
13A TRP* 1.3 66.5 + - - +
15A ILE* 2.9 5.4 + - - +
16A ALA* 2.9 23.2 + - - +
487A ILE* 3.6 41.5 - - + +
488A LEU* 4.0 11.5 - - + +
491A ALA* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 3.0 32.8 + - - +
10A ILE* 2.4 39.3 + - + +
12A ALA* 1.3 73.3 - - + +
14A VAL* 1.3 55.5 + - + +
16A ALA* 3.3 7.0 + - + +
17A ILE* 2.8 53.8 + - + +
370A ILE* 5.1 18.6 - - + -
488A LEU* 4.5 7.0 - - + -
491A ALA* 5.7 2.2 - - - +
492A LEU* 3.3 34.0 - - + +
495A THR* 5.5 3.8 + - - -
496A MET* 4.2 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 2.9 21.4 + - + +
11A PHE* 3.3 28.7 - - + +
13A TRP* 1.3 76.4 - - + +
15A ILE* 1.3 67.3 + - + +
17A ILE* 4.0 5.8 - - + +
18A ILE* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.7 2.7 - - + -
11A PHE* 3.1 38.6 + - + +
12A ALA* 2.9 11.2 + - - +
14A VAL* 1.3 78.7 - - + +
16A ALA* 1.3 66.5 + - - +
18A ILE* 3.4 12.0 + - + +
19A ILE* 3.0 45.4 + - + +
484A VAL* 6.0 3.6 - - + -
487A ILE* 4.5 21.3 - - + -
2038A LMT 5.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 2.9 13.8 + - - +
13A TRP* 3.6 7.0 - - + +
15A ILE* 1.3 80.6 - - - +
17A ILE* 1.3 59.3 + - + +
19A ILE* 3.1 8.2 + - - +
20A MET* 2.9 31.6 + - - +
374A VAL* 4.0 27.9 - - + +
484A VAL* 6.3 0.2 - - - -
488A LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 2.8 41.7 + - + +
14A VAL* 4.0 5.6 - - + +
16A ALA* 1.3 74.8 - - + +
18A ILE* 1.3 61.4 + - + +
20A MET* 2.6 41.5 + - + +
21A LEU* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 2.9 41.9 + - + +
15A ILE* 3.6 12.8 - - + +
17A ILE* 1.3 77.6 - - + +
19A ILE* 1.3 61.6 + - + +
21A LEU* 3.5 9.0 + - + +
22A ALA* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.0 34.0 + - + +
16A ALA* 3.3 11.9 - - - +
17A ILE 3.0 0.8 - - - -
18A ILE* 1.3 79.1 - - + +
20A MET* 1.3 58.0 + - - +
22A ALA* 3.7 9.1 - - + +
23A GLY 2.9 22.7 + - - -
374A VAL* 3.6 14.8 - - + +
377A LEU* 3.1 5.1 - - + +
378A GLY* 3.5 26.9 - - - +
381A ALA* 5.6 1.1 - - + -
480A LEU* 6.2 3.6 - - + -
484A VAL* 4.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 2.9 18.6 + - - +
17A ILE* 2.6 38.9 + - - +
19A ILE* 1.3 70.9 - - - +
21A LEU* 1.3 65.4 + - + +
24A GLY* 2.9 27.4 + - - -
370A ILE* 6.6 0.2 - - - -
373A PRO* 5.8 5.8 - - + -
374A VAL* 4.4 20.6 - - + -
377A LEU* 3.3 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 2.9 37.3 + - + +
18A ILE* 4.0 6.3 - - - +
20A MET* 1.3 83.2 - - + +
22A ALA* 1.3 58.5 + - - +
24A GLY* 4.9 1.1 - - - -
25A LEU* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 2.9 22.1 + - + +
19A ILE* 3.7 9.0 - - + +
21A LEU* 1.3 76.5 - - - +
23A GLY* 1.3 56.6 + - - +
25A LEU* 3.9 4.9 - - - +
26A ALA* 3.0 27.9 + - - +
381A ALA* 3.9 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 2.9 14.2 + - - -
22A ALA* 1.3 74.5 - - - +
24A GLY* 1.3 59.4 + - - +
26A ALA* 2.9 22.0 + - - +
27A ILE* 3.1 15.8 + - - +
377A LEU* 3.2 33.7 - - - -
380A PHE* 3.8 5.9 - - - +
381A ALA* 3.9 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET 2.9 22.4 + - - -
21A LEU* 3.8 1.3 - - - -
23A GLY* 1.3 68.7 - - - +
25A LEU* 1.3 59.5 + - - +
27A ILE* 3.0 29.0 - - - +
28A LEU* 3.4 15.3 - - - +
377A LEU* 4.6 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 2.8 21.6 + - + +
22A ALA* 3.9 5.4 - - - +
24A GLY* 1.3 76.7 - - - +
26A ALA* 1.3 60.2 + - - +
28A LEU* 2.9 28.4 + - + +
29A LYS* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 3.0 19.8 + - - +
23A GLY 2.9 8.5 + - - +
25A LEU* 1.3 73.5 - - - +
27A ILE* 1.3 59.8 + - - +
29A LYS* 4.0 6.3 - - - +
30A LEU* 3.0 33.4 + - - +
380A PHE* 3.6 11.0 - - + +
381A ALA* 3.6 26.0 - - - +
384A ALA* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.1 7.3 + - - +
24A GLY* 3.0 24.7 - - - +
26A ALA* 1.3 74.5 - - - +
28A LEU* 1.3 83.2 + - + +
29A LYS 3.0 5.6 + - - -
30A LEU* 3.2 18.7 + - - +
32A VAL* 5.2 4.0 - - - +
380A PHE* 3.6 44.9 - - + -
390A ILE* 4.2 17.3 - - + +
2044A LMT 4.3 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY 3.4 18.4 - - - +
25A LEU* 2.9 13.3 + - + +
27A ILE* 1.3 98.2 - - + +
29A LYS* 1.3 58.0 + - + +
30A LEU 5.0 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.0 36.3 + - + +
26A ALA* 4.8 4.0 - - - -
27A ILE 3.0 0.6 - - - -
28A LEU* 1.3 80.4 - - - +
30A LEU* 1.3 60.6 + - - +
31A PRO* 4.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.0 20.4 + - - +
27A ILE 3.2 11.3 + - - +
28A LEU 5.0 0.9 - - - +
29A LYS* 1.3 80.3 - - - +
31A PRO* 1.4 79.1 - - + +
32A VAL* 3.7 8.0 + - - +
380A PHE* 4.7 7.6 - - + +
383A LEU* 4.0 14.1 - - + -
384A ALA* 3.6 30.3 - - + +
387A GLY* 5.8 0.7 - - - -
388A PHE 3.5 22.2 - - - +
390A ILE* 3.7 36.1 - - + +
----------------------------------------------------------
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