Contacts of the helix formed by residues 6 - 19 (chain A) in PDB entry 1VFQ
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 ASP 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE* 1.3 69.4 - - - +
7A LYS* 1.3 58.0 + - - +
8A GLU* 3.5 10.0 + - - +
9A ALA* 3.2 31.8 + - + +
10A CYS* 2.9 28.9 + - - +
35A THR* 3.9 6.1 - - + +
36A ILE 3.0 16.4 + - - +
37A VAL* 4.3 15.6 - - + +
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Residues in contact with LYS 7 (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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5A ILE* 3.2 30.5 + - + +
6A ASP* 1.3 73.9 + - - +
8A GLU* 1.3 53.8 + - - +
10A CYS* 4.5 0.4 - - - -
11A ARG* 2.7 75.8 + - - +
100A LEU* 5.4 1.6 - - - +
103A GLU* 3.3 35.8 + - - -
104A VAL* 4.1 17.2 - - + +
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Residues in contact with GLU 8 (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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6A ASP* 3.3 7.8 + - - +
7A LYS* 1.3 78.5 - - - +
9A ALA* 1.3 66.1 + - - +
11A ARG* 3.9 9.1 - - - +
12A ALA* 3.1 23.4 + - + +
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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
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6A ASP* 3.2 27.1 + - - +
8A GLU* 1.3 82.9 - - + +
10A CYS* 1.3 63.7 + - - +
12A ALA* 3.3 7.9 + - - +
13A ALA* 3.2 16.6 + - - +
38A PRO* 3.3 28.9 - - + +
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Residues in contact with CYS 10 (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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5A ILE* 3.9 12.6 - - + -
6A ASP 2.9 21.7 + - - +
7A LYS 4.1 2.2 - - - +
9A ALA* 1.3 78.6 - - - +
11A ARG* 1.3 61.4 + - - +
13A ALA* 3.2 3.6 + - - +
14A TYR* 3.0 23.2 + - - +
29A PHE* 3.6 33.5 - - + -
36A ILE* 3.6 24.5 - - - -
37A VAL* 4.0 2.0 - - - -
38A PRO* 3.9 12.3 - - - -
104A VAL* 3.7 17.4 - - + +
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Residues in contact with ARG 11 (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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7A LYS* 2.7 64.0 + - - +
8A GLU* 3.9 8.8 - - - +
10A CYS* 1.3 72.2 - - - +
12A ALA* 1.3 59.0 + - - +
14A TYR* 3.4 6.1 + - + +
15A ASN* 2.9 43.0 + - - +
103A GLU 4.8 7.7 + - - -
104A VAL* 3.5 26.3 - - + +
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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
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8A GLU 3.1 15.6 + - - +
9A ALA* 3.6 7.9 - - - +
10A CYS 3.2 0.2 - - - -
11A ARG* 1.3 81.2 - - - +
13A ALA* 1.3 55.8 + - - +
15A ASN* 3.8 7.8 - - - +
16A LEU* 3.0 28.1 + - - +
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Residues in contact with ALA 13 (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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9A ALA 3.2 9.1 + - - +
10A CYS 3.2 8.5 + - - +
12A ALA* 1.3 77.6 - - - +
14A TYR* 1.3 63.9 + - - +
16A LEU* 3.1 22.3 - - - +
17A VAL* 3.4 5.2 + - - +
27A VAL* 3.6 18.9 - - + +
29A PHE* 3.9 16.6 - - + -
38A PRO* 4.2 9.0 - - + -
41A GLN* 3.7 25.4 - - - +
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Residues in contact with TYR 14 (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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10A CYS 3.0 15.6 + - - +
11A ARG* 3.6 8.1 - - + +
13A ALA* 1.3 76.7 - - - +
15A ASN* 1.3 83.6 + - - +
17A VAL 3.2 9.5 + - - -
18A ARG* 2.9 49.8 + - - +
27A VAL* 4.8 0.2 - - - -
29A PHE* 4.3 10.1 - - + -
61A PHE* 3.5 39.7 - + - -
104A VAL* 3.6 28.0 - - + -
105A VAL* 3.7 26.0 - - + -
106A GLN* 3.6 5.2 + - + +
107A ASN* 3.0 28.6 + - - +
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Residues in contact with ASN 15 (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 ARG* 2.9 32.3 + - - +
12A ALA* 3.8 8.2 - - - +
14A TYR* 1.3 96.1 - - - +
16A LEU* 1.3 57.4 + - - +
18A ARG* 2.9 10.6 + - - +
19A ASP* 2.9 33.5 + - - +
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Residues in contact with LEU 16 (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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12A ALA 3.0 15.1 + - - +
13A ALA* 3.1 13.7 - - - +
15A ASN* 1.3 76.1 - - - +
17A VAL* 1.3 59.3 + - - +
18A ARG 3.4 0.2 + - - -
19A ASP* 3.5 7.3 + - + -
22A SER* 2.8 47.4 + - - +
24A VAL* 3.8 31.0 - - + -
27A VAL* 4.4 1.8 - - + -
41A GLN* 3.6 33.4 - - - +
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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
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13A ALA 3.8 3.1 - - - +
14A TYR 3.2 1.4 + - - +
15A ASN 3.2 0.6 - - - -
16A LEU* 1.3 77.0 - - - +
18A ARG* 1.3 57.2 + - - +
19A ASP 4.2 1.4 - - - +
22A SER* 5.0 0.2 + - - -
24A VAL 3.6 16.2 - - - +
25A ILE 3.7 13.5 - - - +
27A VAL* 3.5 33.7 - - + -
61A PHE* 3.5 41.7 - - + +
62A VAL 4.2 0.2 - - - -
63A ARG* 3.2 52.7 + - + +
76A PHE* 3.7 2.2 - - + -
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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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14A TYR* 2.9 49.6 + - - +
15A ASN* 2.9 13.1 + - - +
17A VAL* 1.3 77.4 - - - +
19A ASP* 1.3 62.4 - - - +
20A ASP* 3.6 5.2 + - - +
61A PHE* 3.5 14.9 - - + -
63A ARG* 3.3 9.8 + - - -
76A PHE* 3.9 36.3 - - + -
107A ASN* 2.6 46.7 + - - +
108A PHE 3.9 0.6 - - - +
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Residues in contact with ASP 19 (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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15A ASN* 2.9 16.8 + - - +
16A LEU* 3.6 12.4 - - + +
17A VAL 3.4 1.1 - - - +
18A ARG* 1.3 77.1 - - - +
20A ASP* 1.3 64.6 + - - +
21A GLY* 2.7 32.8 + - - -
22A SER* 3.2 23.5 + - - +
63A ARG* 3.8 7.2 + - - -
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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