Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 1G4C
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 SER 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 3.3 1.0 - - - -
12A ALA* 1.3 79.8 - - - +
14A PRO* 1.3 75.0 - - - +
15A LEU* 3.2 2.9 - - - -
16A GLU* 2.8 28.6 + - - +
17A GLN* 3.0 9.0 + - - +
308B THR 4.0 4.1 + - - -
309B GLU 3.5 8.7 + - - -
310B ARG 3.6 5.3 + - - -
311B LEU* 3.3 14.4 + - - -
312B THR* 2.9 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.5 40.4 + - - +
10A ASN* 3.9 16.8 - - - -
11A LEU 4.2 2.9 - - - +
12A ALA 3.9 0.2 - - - -
13A SER* 1.3 87.5 - - - +
15A LEU* 1.3 55.8 - - - +
17A GLN* 3.1 1.8 + - - +
18A VAL* 2.8 32.1 + - - +
51A PRO* 6.4 0.2 - - + -
52A ASP 4.6 1.8 - - - +
54A LEU* 3.8 19.9 - - + +
158A TRP* 4.1 14.8 - - + -
309B GLU* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.2 2.0 - - - -
14A PRO* 1.3 78.6 - - - +
16A GLU* 1.3 63.6 + - - +
18A VAL* 3.2 7.3 - - - +
19A ASN* 3.2 32.8 + - - +
39A PHE* 3.6 37.9 - - + -
54A LEU* 3.8 10.9 - - + +
158A TRP* 4.4 8.1 - - + +
366A CL 3.8 26.7 - - + -
274B GLN* 3.9 24.7 - - - +
309B GLU 5.2 1.0 + - - +
310B ARG 6.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 4.5 2.9 - - - +
13A SER* 2.8 25.2 + - - +
15A LEU* 1.3 79.6 - - - +
17A GLN* 1.3 65.7 + - + +
19A ASN* 3.3 7.2 + - - +
20A ALA* 3.0 25.2 + - - +
296B LEU 5.2 0.2 - - - +
297B ASP* 2.9 6.4 - - - +
310B ARG 5.8 1.8 - - - +
315B HIS* 3.3 25.9 + - + +
316B TYR* 6.5 0.7 - - + -
362B MG 2.0 32.1 - - - -
363B MG 3.9 6.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.4 20.4 - - - +
11A LEU 3.5 19.3 - - - +
12A ALA* 2.9 31.9 + - - +
13A SER 3.0 7.4 + - - +
14A PRO 3.1 1.8 + - - +
16A GLU* 1.3 78.0 - - - +
18A VAL* 1.3 64.4 + - - +
20A ALA* 3.4 2.2 + - - +
21A ALA* 3.0 12.5 + - - +
80A GLN* 3.0 46.4 + - - +
93A THR* 3.5 24.8 - - - +
94A LEU* 4.5 2.9 - - + +
316B TYR* 3.5 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.8 33.9 - - + -
9A SER* 5.1 3.1 - - - -
14A PRO 2.8 19.0 + - - +
15A LEU* 3.2 16.6 - - - +
17A GLN* 1.3 73.2 - - - +
19A ASN* 1.3 63.6 + - - +
21A ALA* 3.3 6.0 + - - +
22A LEU* 2.9 29.7 + - + +
39A PHE* 3.6 45.5 - - + -
54A LEU* 4.1 19.7 - - + -
56A ALA* 4.4 2.7 - - + -
94A LEU* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.2 39.9 + - - +
16A GLU* 3.8 7.0 - - - +
17A GLN 3.2 0.6 - - - -
18A VAL* 1.3 85.3 - - - +
20A ALA* 1.3 61.3 + - - +
22A LEU* 3.4 14.2 + - - +
23A LYS* 3.1 27.0 + - - +
39A PHE* 4.1 8.9 - - - -
290B GLY 4.8 7.6 - - - +
291B PRO* 6.0 0.2 - - - +
292B ALA* 5.7 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.0 18.0 + - - +
17A GLN* 3.8 2.0 - - - +
19A ASN* 1.3 76.5 - - - +
21A ALA* 1.3 57.6 + - - +
23A LYS* 3.3 17.1 + - - +
24A ALA* 3.0 28.2 + - - +
80A GLN* 3.4 22.8 - - + +
321B ARG* 5.8 6.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
7A ILE* 4.4 8.3 - - + -
17A GLN 3.0 18.4 + - - +
18A VAL* 3.6 6.5 - - - +
19A ASN 3.3 0.2 - - - -
20A ALA* 1.3 76.8 - - - +
22A LEU* 1.3 56.9 + - - +
24A ALA* 3.3 4.5 + - - +
25A LEU* 2.8 36.0 + - - +
76A ILE* 4.9 1.5 - - - +
80A GLN* 3.2 10.5 + - - +
94A LEU* 3.7 28.9 - - + -
96A LEU* 4.6 8.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
7A ILE* 3.7 10.1 - - + -
18A VAL* 2.9 23.3 + - + +
19A ASN* 3.7 15.5 - - - +
20A ALA 3.3 0.2 - - - -
21A ALA* 1.3 76.3 - - - +
23A LYS* 1.3 58.7 + - - +
25A LEU* 3.4 3.6 + - + +
26A GLY* 2.9 23.6 + - - -
33A ILE* 3.5 20.1 - - + +
36A VAL* 4.0 26.0 - - + -
39A PHE* 4.0 26.0 - - + -
58A VAL* 3.4 33.4 - - + -
289B TRP* 6.1 0.2 - - + -
290B GLY* 4.9 14.8 - - - +
291B PRO* 5.5 5.1 - - + +
----------------------------------------------------------
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 ASN* 3.1 16.8 + - - +
20A ALA* 3.5 15.0 - - - +
22A LEU* 1.3 77.9 - - - +
24A ALA* 1.3 63.7 + - - +
26A GLY* 3.2 2.6 + - - -
27A ASP* 3.2 38.3 + - - +
253B TYR* 4.0 31.7 + - + +
291B PRO* 5.4 12.9 - - + +
292B ALA 5.1 10.3 + - - +
295B ASP* 5.4 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.0 15.7 + - - +
21A ALA 3.6 4.9 - - - +
22A LEU 3.3 0.2 - - - -
23A LYS* 1.3 77.7 - - + +
25A LEU* 1.3 62.9 + - - +
27A ASP* 3.2 18.5 + - - +
28A ILE* 3.5 13.2 + - - +
75A ARG* 4.9 4.2 + - - +
76A ILE* 3.8 35.6 - - + +
80A GLN* 4.8 2.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
5A ILE* 3.8 31.0 - - + -
7A ILE* 4.0 25.4 - - + -
21A ALA 2.8 20.8 + - - +
22A LEU* 3.7 5.6 - - - +
23A LYS 3.3 0.2 - - - -
24A ALA* 1.3 76.0 - - - +
26A GLY* 1.3 62.3 + - - +
28A ILE* 3.3 45.3 + - + +
31A SER* 5.0 0.2 - - - -
33A ILE* 4.5 8.5 - - + -
58A VAL* 4.5 11.2 - - + -
60A LEU* 4.0 14.3 - - + +
73A THR* 4.1 10.8 - - + -
76A ILE* 4.1 11.7 - - + -
96A LEU* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 2.9 10.6 + - - -
23A LYS* 3.6 4.9 - - - -
24A ALA 3.2 0.4 - - - -
25A LEU* 1.3 77.8 - - - +
27A ASP* 1.3 61.1 + - - +
28A ILE 3.4 2.6 + - - +
31A SER 4.3 7.3 - - - +
32A HIS* 5.4 1.4 - - - -
33A ILE* 3.6 24.7 - - - +
60A LEU* 5.3 1.3 - - - -
361A MG 4.0 11.6 - - - -
250B GLN* 5.2 0.9 + - - -
291B PRO* 6.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 3.3 26.8 - - - +
24A ALA* 3.2 12.2 + - - +
25A LEU 3.2 1.0 - - - -
26A GLY* 1.3 75.8 - - - +
28A ILE* 1.3 65.9 + - - +
29A PRO* 3.3 3.6 - - - +
75A ARG* 6.1 0.4 - - - -
244B PRO* 5.7 0.2 - - - +
245B LEU* 3.8 36.5 + - + +
246B GLY* 4.5 1.6 - - - -
247B PRO* 3.6 19.1 - - - +
250B GLN* 3.0 34.7 + - - +
253B TYR* 5.0 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.5 7.8 + - - +
25A LEU* 3.3 45.6 + - + +
26A GLY 4.3 0.9 - - - +
27A ASP* 1.3 78.4 - - - +
29A PRO* 1.3 81.2 - - + +
30A GLU 3.6 0.2 + - - -
31A SER* 3.4 36.7 + - - +
60A LEU* 4.4 2.9 - - + -
64A LEU* 3.5 17.3 - - + -
69A LEU* 4.1 15.3 - - + -
72A HIS* 3.9 29.8 - - + +
73A THR* 4.8 1.6 - - + -
75A ARG* 4.7 4.0 - - - +
76A ILE* 4.1 6.3 - - + -
----------------------------------------------------------
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