Contacts of the helix formed by residues 4 - 26 (chain A) in PDB entry 1A7C
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 PRO 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A HIS* 3.5 25.7 - - + +
3A HIS* 1.3 84.5 - - + +
5A PRO* 1.4 70.5 - - + +
7A TYR* 3.2 9.8 + - + +
8A VAL* 3.0 28.5 + - + +
70A GLY 5.6 1.3 - - - +
74A ALA* 3.8 20.0 - - + -
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Residues in contact with PRO 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.4 30.7 - - + +
4A PRO* 1.4 97.4 - - + +
6A SER* 1.3 56.2 + - - +
8A VAL* 3.6 3.1 + - + +
9A ALA* 3.1 26.5 + - - +
74A ALA* 3.8 22.2 - - + +
77A HIS* 3.8 28.5 - - + +
78A LEU* 3.8 24.4 - - + +
81A GLU* 4.8 5.2 - - + +
367A THR* 5.3 1.1 - - + -
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Residues in contact with SER 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.0 34.0 + - - +
5A PRO* 1.3 76.4 - - - +
7A TYR* 1.3 67.5 + - - +
9A ALA* 3.2 2.8 + - - +
10A HIS* 2.9 41.5 + - - -
366A PRO 3.7 18.5 + - - -
367A THR* 3.8 18.5 - - - +
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Residues in contact with TYR 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS* 4.1 32.1 - + + +
3A HIS 3.1 11.2 + - - +
4A PRO* 3.2 9.2 + - + +
6A SER* 1.3 77.0 - - - +
8A VAL* 1.3 71.2 + - + +
10A HIS* 3.4 11.0 + - + +
11A LEU* 3.2 57.2 + - + +
63A GLY 5.0 3.1 + - - -
64A PHE* 5.5 1.1 - - + +
71A MET* 5.1 12.1 - - + -
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.0 16.1 + - + +
5A PRO* 4.0 4.7 - - + +
7A TYR* 1.3 81.3 - - + +
9A ALA* 1.3 65.9 + - - +
11A LEU* 3.3 7.1 + - + +
12A ALA* 3.0 25.0 + - + +
64A PHE* 4.5 19.7 - - + -
71A MET* 3.9 29.8 - - + -
74A ALA* 4.3 13.7 - - + +
75A LEU* 3.7 28.3 - - + -
78A LEU* 4.4 8.5 - - + -
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO 3.1 18.9 + - - +
6A SER 3.2 1.3 + - - +
8A VAL* 1.3 78.6 - - - +
10A HIS* 1.3 58.3 + - - +
12A ALA* 3.5 4.5 + - - +
13A SER* 2.8 35.4 + - - -
37A TYR* 6.4 0.4 - - - -
78A LEU* 4.0 15.2 - - + +
367A THR* 3.4 20.0 - - - +
368A GLY 4.6 0.2 - - - -
369A THR* 3.3 27.0 - - - +
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Residues in contact with HIS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 2.9 31.9 + - - +
7A TYR* 3.8 9.5 - - + +
8A VAL 3.3 0.4 - - - -
9A ALA* 1.3 74.1 - - - +
11A LEU* 1.3 60.4 + - + +
13A SER* 3.4 4.8 + - - -
14A ASP* 2.9 30.3 + - - +
256A ALA* 4.6 2.9 - - - +
260A SER* 5.8 2.9 - - - -
363A ARG* 5.4 3.4 + - - -
367A THR 3.0 29.5 + - - -
368A GLY* 3.9 15.5 - - - -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.2 53.4 + - + +
8A VAL* 3.8 6.7 - - + +
10A HIS* 1.3 74.8 - - + +
12A ALA* 1.3 65.6 + - - +
14A ASP* 3.3 8.6 + - + +
15A PHE* 3.0 24.4 + - - +
18A ARG* 5.2 0.3 + - - -
62A MET 4.2 11.6 - - - +
63A GLY* 4.1 9.9 - - - +
64A PHE* 3.7 40.4 - - + -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.0 21.1 + - + +
9A ALA* 3.8 6.1 - - - +
11A LEU* 1.3 76.9 - - - +
13A SER* 1.3 56.6 + - - +
15A PHE* 3.4 5.0 + - - +
16A GLY* 2.9 24.4 + - - -
36A PRO 4.3 1.4 - - - +
37A TYR* 5.1 14.6 - - + -
40A ALA* 3.7 30.1 - - + +
62A MET* 5.7 0.2 - - - -
64A PHE* 4.3 13.4 - - + -
78A LEU* 6.0 0.7 - - + -
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 2.8 21.7 + - - -
10A HIS* 3.8 4.7 - - - -
12A ALA* 1.3 74.4 - - - +
14A ASP* 1.3 59.6 + - - +
16A GLY* 3.3 1.9 + - - +
17A VAL* 2.9 35.5 + - - +
36A PRO* 4.5 5.1 - - - +
37A TYR* 5.8 1.0 - - - +
256A ALA* 4.1 7.9 - - - -
368A GLY 3.2 9.4 + - - -
369A THR* 3.5 5.0 - - - +
370A VAL* 3.0 45.1 + - - -
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS 2.9 19.2 + - - +
11A LEU* 3.3 11.1 + - + +
13A SER* 1.3 76.0 - - - +
15A PHE* 1.3 63.5 + - - +
17A VAL* 3.4 3.2 + - - +
18A ARG* 3.1 53.9 + - - +
255A SER* 4.9 6.4 - - - -
256A ALA* 3.7 25.4 + - + +
257A GLN* 4.9 2.8 + - - +
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 3.0 16.4 + - - +
12A ALA* 3.6 3.6 - - - +
14A ASP* 1.3 78.0 + - - +
16A GLY* 1.3 63.6 + - - +
18A ARG* 3.2 22.3 + - - +
19A VAL* 3.0 46.9 + - + +
39A VAL* 4.3 5.2 - - + -
40A ALA* 4.2 20.6 - - + -
43A LEU* 3.8 36.8 - - + -
61A ALA* 3.6 26.7 - - + -
62A MET* 4.0 24.2 - - + -
64A PHE* 6.2 0.2 - - + -
290A LEU* 4.3 2.9 - - + -
293A LEU* 4.3 4.0 - - + -
295A MET* 3.9 26.7 - - + -
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Residues in contact with GLY 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 2.9 11.2 + - - -
13A SER 3.7 2.7 - - - -
15A PHE* 1.3 78.4 - - - +
17A VAL* 1.3 55.8 + - - +
19A VAL* 3.3 1.6 + - - +
20A PHE* 3.0 22.2 + - - +
34A PHE* 3.5 12.1 - - - -
36A PRO* 3.7 32.5 - - - -
39A VAL* 3.9 11.0 - - - -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 2.9 23.8 + - - +
14A ASP 3.9 4.0 - - - +
16A GLY* 1.3 73.1 - - - +
18A ARG* 1.3 62.2 + - + +
20A PHE* 3.3 6.4 + - - +
21A GLN* 3.0 26.7 + - - +
36A PRO* 4.5 0.7 - - + -
254A LEU* 4.2 15.9 - - + +
255A SER* 3.9 29.6 - - - +
256A ALA* 4.3 8.7 - - - +
259A ILE* 4.4 14.8 - - + -
370A VAL* 4.5 13.9 - - + -
373A MET* 3.9 26.2 - - + -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU 5.2 0.4 + - - -
14A ASP* 3.1 39.4 + - - +
15A PHE* 3.2 29.2 + - - +
17A VAL* 1.3 77.4 - - + +
19A VAL* 1.3 62.4 + - - +
21A GLN* 3.5 19.5 - - - +
22A GLN* 3.4 26.2 + - - +
61A ALA* 2.8 34.9 + - - +
62A MET 4.6 5.1 + - - -
63A GLY* 5.9 0.2 - - - -
254A LEU 5.9 1.1 - - - +
255A SER* 6.4 2.2 - - - -
293A LEU* 4.3 26.4 - - + +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.0 38.7 + - + +
16A GLY 3.5 6.7 - - - +
17A VAL 3.2 0.2 - - - -
18A ARG* 1.3 74.9 - - - +
20A PHE* 1.3 63.6 + - - +
22A GLN* 3.1 7.3 + - - +
23A VAL* 3.1 20.5 + - + +
34A PHE* 3.7 21.1 - - + -
39A VAL* 4.3 9.4 - - + -
286A LEU* 4.0 18.4 - - + -
289A PRO* 4.4 11.7 - - + -
290A LEU* 4.4 9.6 - - + -
293A LEU* 3.7 22.4 - - + -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 3.0 9.8 + - - +
17A VAL 3.5 7.9 - - - +
19A VAL* 1.3 78.0 - - - +
21A GLN* 1.3 56.8 + - - +
23A VAL* 3.0 7.0 + - + +
24A ALA* 2.8 51.6 + - + +
32A VAL* 4.0 24.5 - - + -
34A PHE* 3.7 38.5 - + + -
251A THR* 4.7 5.2 - - + -
254A LEU* 4.0 22.9 - - + -
359A LEU* 4.6 4.5 - - + -
373A MET* 3.7 28.7 - - + -
374A GLY* 4.0 32.1 - - - -
375A GLN* 4.3 9.9 - - + -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL 3.0 10.8 + - - +
18A ARG* 3.5 25.1 - - - +
19A VAL 3.2 0.4 - - - -
20A PHE* 1.3 81.1 - - + +
22A GLN* 1.3 66.3 + - + +
24A ALA* 3.5 5.0 + - - +
25A GLN* 3.1 45.6 + - - +
251A THR* 3.0 23.0 + - - +
252A ASN* 2.9 30.5 + - - +
253A ILE 4.3 0.2 - - - -
254A LEU* 3.6 25.5 + - + +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 3.4 14.5 + - - +
19A VAL 3.1 8.6 + - - +
21A GLN* 1.3 82.2 + - - +
23A VAL* 1.3 62.5 + - - +
25A GLN* 3.5 20.2 + - - +
26A ALA* 3.2 21.5 + - - +
289A PRO* 3.7 33.3 - - + +
292A ASN* 3.1 35.7 + - - +
293A LEU* 4.3 17.6 - - + +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL 3.1 16.4 + - - +
20A PHE* 3.0 10.7 + - + +
22A GLN* 1.3 77.2 - - - +
24A ALA* 1.3 61.5 + - - +
26A ALA* 3.2 15.4 + - - +
27A SER* 3.2 19.8 + - - +
32A VAL* 3.9 25.6 - - + -
34A PHE* 4.4 13.5 - - + -
284A VAL* 3.5 35.9 - - + -
286A LEU* 4.5 3.1 - - + -
289A PRO* 4.0 18.4 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 2.8 38.0 + - + +
21A GLN* 3.8 4.7 - - - +
23A VAL* 1.3 74.4 - - - +
25A GLN* 1.3 62.5 + - + +
27A SER* 3.2 5.1 - - - +
28A LYS* 3.2 26.5 + - - +
32A VAL* 5.1 2.7 - - - -
251A THR* 4.4 16.4 - - - +
375A GLN* 3.8 26.6 + - - +
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.1 38.1 + - + +
22A GLN* 3.9 24.5 + - - +
24A ALA* 1.3 75.1 - - + +
26A ALA* 1.3 63.2 + - - +
28A LYS* 3.4 31.1 - - - +
251A THR* 5.3 3.4 - - - +
252A ASN* 3.2 28.8 - - - +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 3.2 12.1 + - - +
23A VAL* 3.2 12.3 + - - +
25A GLN* 1.3 81.1 - - - +
27A SER* 1.3 60.1 + - - +
28A LYS 3.6 2.4 + - - -
30A ARG* 4.3 5.2 + - - -
289A PRO* 5.9 3.8 - - + -
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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) + - + + + + + -
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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