Contacts of the helix formed by residues 13 - 22 (chain B) in PDB entry 2VGL
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 GLY 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B LYS* 1.3 79.8 - - - +
14B GLU* 1.3 65.9 + - - -
15B ILE 3.3 3.3 + - - -
16B PHE* 3.5 0.9 + - - +
17B GLU* 3.1 28.3 + - - +
99S CYS* 3.6 26.6 - - - -
101S LEU* 4.1 13.2 - - - -
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 2.6 34.5 + - - +
13B GLY* 1.3 71.8 - - - -
15B ILE* 1.3 64.8 + - + +
17B GLU* 3.5 7.1 + - + +
18B LEU* 3.1 41.9 + - + +
40B ALA* 5.9 3.1 - - - -
45B LYS* 2.8 39.2 + - - +
100S GLU* 5.6 0.9 - - - +
101S LEU* 3.8 18.3 - - + +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.2 35.7 - - - +
12B LYS 5.8 0.9 - - - +
13B GLY 3.3 0.8 - - - -
14B GLU* 1.3 82.4 - - + +
16B PHE* 1.3 60.0 - - - +
18B LEU* 3.2 8.8 + - + +
19B LYS* 2.9 24.1 + - + -
40B ALA* 5.8 1.1 - - + -
45B LYS* 5.4 8.7 - - + -
46B ASP 3.8 23.6 - - - +
47B VAL* 3.9 21.5 - - + -
49B SER* 3.8 11.0 - - - +
50B LEU* 3.4 22.9 - - + +
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.8 17.7 - - - +
11B LYS* 3.5 27.8 - - - -
12B LYS* 3.7 31.5 + - - +
13B GLY 3.8 3.1 - - - +
15B ILE* 1.3 76.8 - - - +
17B GLU* 1.3 72.6 + - + +
19B LYS* 3.4 16.6 + - + +
20B ALA* 3.3 22.6 + - + +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 4.4 8.3 + - - -
13B GLY 3.1 23.7 + - - +
14B GLU* 3.6 7.3 - - - +
15B ILE 3.2 0.2 - - - -
16B PHE* 1.3 83.7 - - + +
18B LEU* 1.3 65.7 + - + +
19B LYS 3.2 0.5 + - - -
20B ALA* 3.2 8.8 + - - +
21B GLU* 3.2 28.7 + - - +
101S LEU* 3.7 26.6 - - - +
105S PHE* 5.6 1.6 - - - -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.1 34.2 + - + +
15B ILE* 3.2 12.3 + - + +
17B GLU* 1.3 76.9 - - + +
19B LYS* 1.3 52.5 + - - +
21B GLU* 3.4 10.0 + - - +
22B LEU* 2.8 38.9 + - + +
33B ALA* 4.3 7.3 - - - +
36B LYS* 4.0 42.4 - - + +
37B VAL* 3.9 33.4 - - + +
40B ALA* 5.2 7.0 - - + -
47B VAL* 5.3 0.4 - - + -
50B LEU* 3.8 15.5 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 5.9 2.0 - - - +
15B ILE* 2.9 13.7 + - + +
16B PHE* 3.4 22.2 - - + +
18B LEU* 1.3 74.0 - - - +
20B ALA* 1.3 65.6 + - - +
22B LEU* 3.3 4.2 + - - +
23B ASN* 3.0 30.1 + - - -
49B SER* 4.3 12.2 + - - +
50B LEU* 3.6 19.7 - - + +
52B PRO* 6.2 0.4 - - - +
53B ASP* 3.0 33.8 + - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.3 13.5 + - + +
17B GLU* 3.2 10.4 + - - +
19B LYS* 1.3 76.9 - - - +
21B GLU* 1.3 59.3 + - + +
23B ASN* 2.9 22.3 + - - +
24B ASN* 2.9 14.0 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 3.2 15.1 + - - +
18B LEU* 3.6 16.4 - - - +
19B LYS 3.3 0.2 - - - -
20B ALA* 1.3 81.4 - - + +
22B LEU* 1.3 59.5 + - - +
23B ASN 3.2 0.9 + - - -
24B ASN* 3.5 19.6 + - + +
29B LYS* 3.9 19.5 - - + +
30B ARG* 3.7 14.9 - - - +
32B GLU* 5.3 0.7 - - - +
33B ALA* 3.9 15.2 - - + -
36B LYS* 2.4 34.4 + - - -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU 2.8 24.6 + - - +
19B LYS 3.8 5.2 - - - +
20B ALA 3.3 0.6 - - - -
21B GLU* 1.3 72.7 - - - +
23B ASN* 1.3 61.2 + - - +
30B ARG* 3.7 19.8 - - - +
33B ALA* 3.6 15.0 - - + -
34B VAL* 3.2 37.2 - - + +
37B VAL* 4.3 3.6 - - + -
50B LEU* 4.0 22.4 - - + -
53B ASP* 3.7 32.3 - - + +
54B VAL* 3.8 22.9 - - + -
56B ASN* 6.0 1.0 - - - +
57B CYS* 3.9 15.8 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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