Contacts of the helix formed by residues 7 - 24 (chain A) in PDB entry 1VZS
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 VAL 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP* 2.6 23.2 + - + +
6A PRO* 1.3 79.0 - - + +
8A GLN* 1.3 74.1 + - + +
9A LYS* 3.0 10.4 - - - +
10A LEU* 2.7 57.0 + - + +
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Residues in contact with GLN 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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3A GLU 3.9 9.6 + - - +
4A LEU* 3.4 35.9 - - + +
5A ASP* 3.4 11.0 + - + +
7A VAL* 1.3 86.6 - - + +
9A LYS* 1.3 61.9 - - - +
11A PHE* 2.9 34.8 + - + +
12A VAL* 3.5 16.6 + - + +
47A LYS* 5.3 15.6 - - + +
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Residues in contact with LYS 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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4A LEU* 2.9 33.7 - - + +
5A ASP 3.9 13.0 - - - +
6A PRO* 4.7 5.8 - - + -
7A VAL* 3.9 14.8 - - - +
8A GLN* 1.3 78.2 - - - +
10A LEU* 1.3 78.7 + - - +
11A PHE 3.0 1.2 + - - -
12A VAL* 3.2 17.2 + - - +
13A ASP* 3.2 12.6 + - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 2.7 48.7 + - + +
9A LYS* 1.3 94.6 - - - +
11A PHE* 1.3 67.0 + - + +
13A ASP* 3.3 11.6 + - - +
14A LYS* 3.2 41.7 + - + +
61A PHE* 4.3 15.9 - - + -
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Residues in contact with PHE 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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8A GLN* 2.9 27.0 + - + +
10A LEU* 1.3 82.6 - - + +
12A VAL* 1.3 50.2 + - + +
13A ASP 2.9 3.8 - - - -
14A LYS* 2.5 31.9 + - + +
15A ILE* 2.7 41.2 + - + +
46A LEU* 5.0 1.6 - - + -
47A LYS* 5.0 16.4 - - + -
50A TYR* 4.0 31.6 - + + -
55A MET* 5.9 4.9 - - + -
61A PHE* 3.4 55.9 - + + -
63A PHE* 4.7 5.2 - + - -
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.9 1.1 - - + -
8A GLN* 4.2 22.7 - - - +
9A LYS* 3.2 10.8 + - - +
11A PHE* 1.3 74.5 - - - +
13A ASP* 1.3 57.1 + - - +
14A LYS 3.2 2.3 + - - -
15A ILE* 3.6 14.2 - - - +
16A ARG* 3.5 29.3 - - - +
40A ASP* 4.4 17.7 - - - +
43A LEU* 4.9 5.8 - - + -
47A LYS* 4.6 16.2 - - - +
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 3.2 11.3 + - - +
10A LEU* 3.3 15.5 - - - +
11A PHE 2.9 1.4 + - - -
12A VAL* 1.3 76.1 - - - +
14A LYS* 1.3 61.4 + - - +
16A ARG* 4.3 13.0 + - - +
17A GLU* 3.8 16.6 + - - +
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Residues in contact with LYS 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 LEU* 3.5 24.3 - - + +
11A PHE* 2.5 24.4 + - + +
13A ASP* 1.3 79.2 - - - +
15A ILE* 1.3 59.5 + - + +
16A ARG 3.1 1.6 - - - -
17A GLU* 3.1 50.2 + - - +
18A TYR* 3.3 14.2 + - - +
61A PHE* 3.5 38.4 - - + -
63A PHE* 6.3 0.7 - - - -
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Residues in contact with ILE 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 PHE* 2.7 51.4 + - + +
12A VAL* 3.6 9.9 - - - +
14A LYS* 1.3 74.9 - - - +
16A ARG* 1.3 55.9 + - - +
17A GLU 3.1 0.4 - - - -
18A TYR* 2.5 54.7 - - + +
19A ARG* 3.1 12.6 + - - +
39A LEU* 3.8 1.7 - - - +
43A LEU* 3.3 42.8 - - + +
46A LEU* 3.5 21.8 - - + -
47A LYS* 4.5 6.3 - - - -
63A PHE* 4.2 8.3 - - + -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.5 27.8 + - - +
13A ASP* 4.7 12.1 + - - +
14A LYS 3.1 0.8 - - - -
15A ILE* 1.3 78.3 - - - +
17A GLU* 1.3 50.2 + - - +
20A THR* 2.7 30.2 - - - +
36A GLN* 3.7 31.9 + - - +
39A LEU* 4.2 21.8 - - + +
40A ASP* 4.4 10.3 + - - +
43A LEU* 4.2 13.5 - - + -
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Residues in contact with GLU 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 ASP 3.8 10.2 - - - +
14A LYS* 3.1 43.4 + - + +
16A ARG* 1.3 79.3 - - - +
18A TYR* 1.3 55.9 + - + +
20A THR* 2.8 11.5 - - - +
21A LYS* 2.7 50.2 + - - +
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Residues in contact with TYR 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 LYS 3.3 6.5 + - - +
15A ILE* 2.5 68.0 - - + +
17A GLU* 1.3 82.1 - - + +
19A ARG* 1.3 111.4 + - + +
20A THR 3.3 0.4 - - - -
21A LYS* 3.7 13.3 + - - +
22A ARG* 3.7 17.8 + - - +
42A GLU 5.0 0.9 + - - -
43A LEU* 4.2 5.2 - - - -
46A LEU* 4.2 7.7 - - + +
62A THR 4.8 1.3 - - - +
63A PHE* 3.5 47.6 - + + -
64A GLU* 4.6 19.4 - - + +
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Residues in contact with ARG 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 ILE 3.1 14.3 + - - +
18A TYR* 1.3 125.2 + - + +
20A THR* 1.3 65.8 + - - +
21A LYS 3.1 2.0 - - - -
22A ARG* 3.1 40.6 + - + +
23A GLN* 3.1 31.8 + - - +
39A LEU* 3.3 43.7 - - + +
42A GLU* 2.8 47.0 + - - +
43A LEU* 4.7 0.9 - - - +
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Residues in contact with THR 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 ARG* 2.7 29.2 + - - +
17A GLU* 2.8 33.0 - - - +
19A ARG* 1.3 80.2 - - - +
21A LYS* 1.3 64.7 + - + +
23A GLN* 3.2 23.4 - - - +
24A THR 3.7 2.9 + - - -
35A TYR* 5.1 1.6 - - - -
39A LEU* 4.6 5.7 - - - +
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Residues in contact with LYS 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 GLU* 2.7 45.0 + - - +
18A TYR* 3.7 10.1 + - - +
19A ARG 3.1 0.6 - - - -
20A THR* 1.3 86.4 - - + +
22A ARG* 1.3 60.6 + - + +
24A THR* 2.8 30.1 - - - +
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Residues in contact with ARG 22 (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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18A TYR* 3.7 11.5 + - - +
19A ARG* 3.1 50.6 + - + +
21A LYS* 1.3 77.9 - - + +
23A GLN* 1.3 69.0 + - - +
24A THR* 3.5 6.5 + - - +
26A GLY 4.3 7.8 - - - +
27A GLY* 5.2 2.4 - - - -
63A PHE* 5.0 13.2 + - - +
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Residues in contact with GLN 23 (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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19A ARG* 3.1 27.7 + - - +
20A THR* 3.2 13.9 - - - +
21A LYS 3.1 0.2 - - - -
22A ARG* 1.3 81.5 - - - +
24A THR* 1.3 70.5 + - - +
25A SER* 2.5 10.8 + - - -
26A GLY 3.1 14.0 + - - +
27A GLY* 4.6 2.5 + - - +
28A PRO* 4.5 16.9 - - - +
29A VAL* 5.1 0.3 - - - +
31A ALA* 4.0 17.4 - - + +
35A TYR* 3.2 43.9 - - + +
39A LEU* 3.4 17.6 - - - +
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Residues in contact with THR 24 (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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20A THR 3.7 3.6 + - - -
21A LYS 2.8 28.5 + - - +
22A ARG* 3.5 6.1 + - - +
23A GLN* 1.3 85.5 + - - +
25A SER* 1.3 73.7 + - - -
26A GLY 3.9 6.2 + - - -
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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