Contacts of the helix formed by residues 3 - 29 (chain H) in PDB entry 1VF5
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 ILE 3 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASP* 1.3 93.3 + - + +
5H VAL* 3.2 26.9 - - + +
6H LEU* 4.4 2.7 - - - +
7H GLY* 3.5 15.3 + - - -
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Residues in contact with ASP 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G GLY* 5.3 8.5 - - - +
16G ALA* 4.5 3.6 - - - +
3H ILE* 1.3 105.9 - - + +
5H VAL* 1.3 63.5 + - - +
6H LEU 3.1 0.4 - - - -
7H GLY* 3.6 9.9 - - - +
8H TRP* 2.5 54.5 - - + +
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Residues in contact with VAL 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 4.1 27.4 - - + -
15F LEU* 6.1 1.8 - - + -
16G ALA* 4.9 5.5 - - - +
3H ILE* 3.9 19.0 - - + +
4H ASP 1.3 80.5 - - - +
6H LEU* 1.3 56.9 + - + +
9H VAL* 2.5 50.2 + - + +
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Residues in contact with LEU 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE 4.4 3.2 - - - +
4H ASP 4.1 0.6 - - - +
5H VAL* 1.3 83.4 - - + +
7H GLY* 1.3 55.6 + - - +
8H TRP 2.4 16.8 + - - -
9H VAL* 3.8 17.7 - - + -
10H ALA* 2.8 38.2 + - + +
11H LEU* 4.5 0.2 - - - +
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Residues in contact with GLY 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE 3.5 20.0 + - - -
4H ASP* 3.6 5.8 - - - +
6H LEU* 1.3 77.5 - - - +
8H TRP* 1.3 53.5 + - - +
11H LEU* 2.8 32.3 - - - +
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Residues in contact with TRP 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU 5.5 3.7 + - - -
12G GLY* 5.4 1.8 - - - +
13G LEU* 4.0 49.1 - - + +
16G ALA* 4.2 11.0 - - + -
4H ASP* 2.5 42.9 + - + +
6H LEU 2.4 9.9 + - - -
7H GLY* 1.3 77.5 - - - +
9H VAL* 1.3 64.4 + - - +
10H ALA 3.2 1.1 - - - -
11H LEU* 2.9 27.8 + - + +
12H LEU* 2.8 35.0 + - + +
15H PHE* 3.9 10.8 - + - -
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Residues in contact with VAL 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 5.2 9.0 - - + -
16G ALA* 4.2 14.0 - - + +
19G GLY* 4.2 6.1 - - - +
20G GLY* 3.7 25.8 - - - +
5H VAL* 2.5 44.1 + - + +
6H LEU* 3.8 17.7 - - + -
8H TRP* 1.3 68.5 - - - +
10H ALA* 1.3 68.6 + - - +
11H LEU 2.7 15.0 + - - -
12H LEU* 4.5 1.6 - - - +
13H VAL* 2.8 49.9 + - + +
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Residues in contact with ALA 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 2.8 31.8 + - + +
9H VAL* 1.3 84.5 - - + +
11H LEU* 1.3 64.8 + - + +
13H VAL* 4.7 2.5 - - - -
14H VAL* 2.8 35.0 - - + +
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Residues in contact with LEU 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU 4.5 1.6 - - - +
7H GLY* 2.8 32.1 - - - +
8H TRP* 2.9 30.3 - - + +
9H VAL 2.7 1.0 + - - -
10H ALA* 1.3 81.1 - - + +
12H LEU* 1.3 71.1 + - - +
13H VAL 2.7 2.6 + - - -
14H VAL 2.8 13.3 + - - -
15H PHE* 2.9 40.8 - - + -
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ILE* 5.0 1.3 - - + -
262C ILE* 5.3 1.3 - - + -
263C CYS* 4.1 28.7 - - - -
266C MET* 4.5 14.8 - - + -
13G LEU* 4.0 22.7 - - + -
16G ALA 3.7 24.5 - - - +
17G THR* 4.1 15.7 - - + +
20G GLY* 5.2 2.2 - - - -
8H TRP* 2.8 19.9 + - + +
9H VAL* 4.2 1.3 - - - +
11H LEU* 1.3 77.2 - - - +
13H VAL* 1.3 64.2 + - + +
15H PHE* 3.0 27.3 + - + +
16H THR* 3.2 25.1 + - + +
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Residues in contact with VAL 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C MET* 5.1 3.6 - - + -
15F LEU* 6.4 0.2 - - + -
18F VAL* 6.0 3.1 - - + -
22F LEU* 4.0 28.3 - - + -
20G GLY* 4.3 17.0 - - - +
23G TYR* 5.2 6.6 - - + -
26G TYR* 5.0 11.0 - - + +
9H VAL* 2.8 45.7 + - + +
10H ALA* 4.4 3.6 - - - +
11H LEU 2.7 3.4 + - - -
12H LEU* 1.3 73.9 - - - +
14H VAL* 1.3 69.3 + - + +
15H PHE 3.3 0.3 + - - -
16H THR* 3.4 7.1 + - - -
17H TRP* 3.1 20.4 + - + +
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Residues in contact with VAL 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ALA* 2.8 28.5 - - + +
11H LEU 2.8 6.5 + - - +
13H VAL* 1.3 78.4 - - + +
15H PHE* 1.3 57.0 + - + +
17H TRP* 3.6 29.6 - - + -
18H SER* 2.5 37.4 + - - +
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Residues in contact with PHE 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H TRP* 3.9 13.0 - + - -
11H LEU* 2.9 54.5 - - + -
12H LEU* 3.0 21.3 - - + +
13H VAL 3.2 0.4 - - - -
14H VAL* 1.3 78.3 - - + +
16H THR* 1.3 64.1 + - + +
17H TRP 2.9 4.5 + - - -
18H SER* 3.1 8.4 + - - -
19H ILE* 3.0 29.6 + - + +
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Residues in contact with THR 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C CYS* 4.8 11.7 - - + +
266C MET* 3.7 35.1 - - + +
267C LEU* 4.8 14.8 - - + +
270C LEU* 4.2 3.0 - - + +
23G TYR* 4.1 19.8 + - - -
12H LEU* 3.2 20.8 + - + +
13H VAL 3.4 6.1 + - - -
15H PHE* 1.3 78.2 - - + +
17H TRP* 1.3 56.3 + - - +
19H ILE* 3.5 19.5 - - + +
20H ALA* 3.0 23.2 + - - +
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Residues in contact with TRP 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 5.0 17.3 - - + +
25F LEU* 3.8 37.2 - - + -
26F LEU* 2.9 36.0 - - + +
29F ILE* 4.1 11.7 - - + -
23G TYR* 5.2 9.2 - + + -
13H VAL* 3.1 18.3 + - + +
14H VAL* 3.1 36.3 - - + +
15H PHE 2.9 0.4 - - - -
16H THR* 1.3 75.1 - - - +
18H SER* 1.3 53.5 + - - +
19H ILE 3.1 0.9 - - - -
20H ALA* 2.7 28.7 + - + +
21H MET* 2.7 55.2 + - + +
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Residues in contact with SER 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H VAL* 2.5 18.7 + - - -
15H PHE* 3.5 11.0 - - - -
17H TRP* 1.3 72.9 - - - +
19H ILE* 1.3 54.9 + - - +
20H ALA 3.0 0.2 + - - -
21H MET* 3.2 17.3 + - - +
22H VAL* 2.7 51.5 + - - +
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Residues in contact with ILE 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.4 20.4 - - + -
270C LEU* 3.9 11.4 - - + -
271C MET* 5.4 1.8 - - + -
15H PHE* 3.0 16.4 + - + +
16H THR* 3.5 20.6 - - + +
18H SER* 1.3 76.5 + - - +
20H ALA* 1.3 51.5 + - - +
22H VAL* 4.5 4.3 - - - -
23H VAL* 2.6 60.8 + - + +
26H ARG* 5.2 9.9 - - - +
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Residues in contact with ALA 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 3.2 35.7 - - + -
274C LEU* 4.4 3.8 - - + +
26F LEU* 5.0 10.1 - - + -
23G TYR* 4.5 2.2 - - + +
30G LYS* 5.8 0.4 - - - +
16H THR 3.0 11.3 + - - +
17H TRP* 2.7 26.8 + - + +
19H ILE* 1.3 72.9 - - - +
21H MET* 1.3 63.8 + - - +
22H VAL 3.0 0.9 - - - -
23H VAL* 2.9 19.1 - - - +
24H TRP* 3.1 8.8 + - - +
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Residues in contact with MET 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 5.1 4.2 - - - +
29F ILE* 4.3 24.0 - - + -
14H VAL* 6.1 0.2 - - + -
17H TRP* 2.7 63.6 + - + +
18H SER* 3.2 23.3 - - - +
20H ALA* 1.3 73.5 - - - +
22H VAL* 1.3 70.2 + - - +
24H TRP* 2.9 37.0 - - + +
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Residues in contact with VAL 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H SER* 2.7 33.8 + - - +
19H ILE* 4.0 4.0 - - - +
21H MET* 1.3 85.6 - - - +
23H VAL* 1.3 55.3 + - - +
24H TRP* 2.6 16.0 + - - -
25H GLY* 2.7 14.4 + - - +
26H ARG* 2.9 45.0 + - + +
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Residues in contact with VAL 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 3.9 3.6 - - + -
271C MET* 5.1 9.0 - - + -
274C LEU* 3.2 33.4 - - + -
19H ILE* 2.6 53.4 + - + +
20H ALA* 2.9 19.5 - - - +
22H VAL* 1.3 73.2 - - - +
24H TRP* 1.3 57.6 + - - +
26H ARG* 3.5 30.3 - - - +
27H ASN* 2.4 39.6 + - - +
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Residues in contact with TRP 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.9 10.8 - - + -
29F ILE 4.9 17.5 + - - -
30F GLN* 5.2 11.3 - - + +
30G LYS* 6.3 0.4 - - - +
20H ALA 3.1 11.3 + - - +
21H MET* 2.9 30.5 - - + +
22H VAL* 2.6 1.4 + - - -
23H VAL* 1.3 76.2 - - - +
25H GLY* 1.3 80.5 - - - +
27H ASN* 3.1 5.2 + - - +
28H GLY* 2.7 46.6 + - - -
29H LEU* 6.1 4.3 - - + -
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Residues in contact with GLY 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H VAL* 2.7 10.5 + - - -
24H TRP* 1.3 106.5 - - - +
26H ARG* 1.3 54.5 + - - -
28H GLY* 2.7 20.6 + - - -
29H LEU* 2.9 27.0 + - - +
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Residues in contact with ARG 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ILE* 5.2 9.5 - - - +
22H VAL* 2.9 40.8 + - + +
23H VAL* 3.5 38.1 - - - +
24H TRP 3.2 0.2 - - - -
25H GLY* 1.3 74.1 - - - +
27H ASN* 1.3 64.9 + - - +
29H LEU* 3.3 22.2 - - - +
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Residues in contact with ASN 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 5.6 3.8 - - - +
19D MET* 4.7 26.8 - - - +
23H VAL* 2.4 35.3 + - - +
24H TRP* 3.1 3.1 + - - +
26H ARG* 1.3 81.0 - - - +
28H GLY* 1.3 57.2 + - - +
29H LEU* 2.8 17.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TRP* 2.7 29.1 + - - -
25H GLY* 2.7 8.0 + - - -
27H ASN* 1.3 76.2 - - - +
29H LEU* 1.3 70.2 + - - +
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Residues in contact with LEU 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TRP* 6.1 4.3 - - + -
25H GLY* 2.9 22.8 + - - +
26H ARG* 3.3 17.3 - - - +
27H ASN* 2.8 9.7 - - - +
28H GLY 1.3 92.1 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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