Contacts of the helix formed by residues 7 - 20 (chain A) in PDB entry 2P5V
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 3.9 2.9 + - + +
6A LEU* 1.3 72.8 - - - +
8A LYS* 1.3 67.8 + - + +
9A THR* 3.2 15.3 + - - -
10A ASP* 2.9 50.0 + - - +
11A ILE* 3.0 17.6 + - - +
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Residues in contact with LYS 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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7A ASP* 1.3 74.6 - - + +
9A THR* 1.3 61.5 + - - +
11A ILE* 3.3 3.8 + - - +
12A LYS* 3.0 29.0 + - + +
158A LEU* 4.1 27.9 - - + +
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Residues in contact with THR 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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7A ASP* 3.1 15.2 + - - -
8A LYS* 1.3 77.6 - - - +
10A ASP* 1.3 62.2 + - - +
12A LYS* 3.4 7.4 + - - +
13A ILE* 3.0 34.0 + - + +
32A VAL* 3.4 27.2 + - + +
33A ALA* 4.6 6.3 + - - +
34A LEU* 3.8 33.4 - - + -
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Residues in contact with ASP 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 THR 3.5 0.9 - - - +
6A LEU* 3.3 18.0 - - + -
7A ASP* 2.9 41.9 + - - +
9A THR* 1.3 75.5 - - - +
11A ILE* 1.3 68.1 + - - +
13A ILE* 3.3 9.3 + - - +
14A LEU* 3.1 28.1 + - - +
34A LEU* 5.5 0.2 - - - +
42A ARG* 2.8 57.1 + - - +
46A LEU* 4.6 5.0 - - + +
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Residues in contact with ILE 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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6A LEU* 4.0 23.8 - - + +
7A ASP 3.0 15.3 + - - +
8A LYS 3.5 6.7 - - - +
10A ASP* 1.3 74.7 - - - +
12A LYS* 1.3 59.1 + - - +
14A LEU* 3.1 10.9 + - + +
15A GLN* 2.8 55.2 + - - +
154A LEU* 4.0 16.8 - - + +
157A LEU* 3.7 40.2 - - + +
158A LEU* 4.1 26.5 - - + -
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Residues in contact with LYS 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 LYS* 3.0 14.3 + - + +
9A THR* 3.6 11.4 - - - +
10A ASP 3.3 0.2 - - - -
11A ILE* 1.3 75.7 - - - +
13A ILE* 1.3 58.3 + - - +
15A GLN* 3.6 17.7 + - + +
16A VAL* 2.9 52.6 + - + +
31A ARG* 2.5 41.4 + - - +
32A VAL* 4.1 16.8 - - + +
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Residues in contact with ILE 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 THR* 3.0 22.0 + - + +
10A ASP* 3.4 10.5 - - - +
11A ILE 3.2 0.2 - - - -
12A LYS* 1.3 76.5 - - - +
14A LEU* 1.3 58.3 + - + +
16A VAL* 3.4 1.7 + - - +
17A LEU* 3.0 50.3 + - + +
28A LEU* 4.3 10.7 - - + +
32A VAL* 3.8 27.4 - - + -
34A LEU* 4.1 24.9 - - + -
39A CYS* 4.7 10.8 - - - +
42A ARG* 4.3 19.7 - - + -
43A LEU* 4.6 4.3 - - + +
46A LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 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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6A LEU* 4.5 9.9 - - + -
10A ASP 3.1 19.9 + - - +
11A ILE* 3.1 20.8 + - + +
13A ILE* 1.3 77.2 - - + +
15A GLN* 1.3 56.9 + - - +
17A LEU* 4.0 4.2 - - + +
18A GLN* 2.9 37.3 + - - +
46A LEU* 4.1 17.7 - - + -
51A ILE* 3.9 26.7 - - + -
52A VAL* 3.9 14.8 - - + -
154A LEU* 3.6 20.9 - - + -
59B LEU* 3.8 29.5 - - + +
64B VAL* 4.6 4.0 - - + -
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Residues in contact with GLN 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 ILE* 2.8 31.9 + - - +
12A LYS* 3.6 27.1 + - + +
14A LEU* 1.3 75.7 - - - +
16A VAL* 1.3 67.2 + - + +
18A GLN* 3.6 9.8 + - - +
19A GLU* 3.4 27.4 + - - +
154A LEU* 4.1 22.9 - - + +
155A ASN* 5.1 5.7 - - - +
158A LEU* 4.6 11.8 - - - +
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Residues in contact with VAL 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 LYS* 2.9 42.6 + - + +
13A ILE 3.7 3.1 - - - +
15A GLN* 1.3 75.5 - - + +
17A LEU* 1.3 57.8 + - - +
19A GLU* 3.3 2.3 + - - -
20A ASN* 2.7 38.1 + - - +
23A LEU* 3.4 31.4 - - + -
28A LEU* 3.7 16.4 - - + -
31A ARG* 3.6 33.4 - - + +
32A VAL* 4.6 4.5 - - + -
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Residues in contact with LEU 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 ILE* 3.0 31.4 + - + +
14A LEU* 4.3 4.3 - - + +
16A VAL* 1.3 71.4 - - - +
18A GLN* 1.3 65.3 + - - +
19A GLU 3.1 2.0 - - - -
20A ASN 3.6 16.4 - - - +
21A GLY 3.2 16.1 + - - +
23A LEU* 4.5 5.4 - - + -
28A LEU* 4.0 22.7 - - + -
43A LEU* 3.7 34.8 - - + -
52A VAL* 5.4 3.4 - - + -
55A TYR* 4.5 7.0 - - + +
22B ARG* 3.9 24.0 - - - +
57B ALA* 2.8 33.5 + - + -
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Residues in contact with GLN 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 LEU 2.9 21.2 + - - +
15A GLN* 3.9 9.0 - - - +
17A LEU* 1.3 76.2 - - - +
19A GLU* 1.3 57.5 + - - +
150A THR* 4.0 3.5 + - - +
151A SER* 3.4 27.2 + - - +
152A LEU* 2.8 49.2 + - - +
154A LEU* 3.9 14.8 - - - +
54B GLN* 3.6 2.8 - - - +
56B ALA* 3.3 22.3 - - - +
57B ALA* 3.5 22.2 - - - +
59B LEU* 3.5 33.8 + - + +
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Residues in contact with GLU 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 GLN 3.4 13.7 + - - +
16A VAL 3.3 2.3 + - - +
17A LEU 3.1 0.4 - - - -
18A GLN* 1.3 78.6 + - - +
20A ASN* 1.3 81.7 + - - +
149A THR* 4.7 3.3 + - - -
151A SER* 2.7 32.3 + - - -
54B GLN* 2.8 30.9 + - - +
55B TYR 3.3 5.0 - - - +
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Residues in contact with ASN 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 VAL* 2.7 34.8 + - - +
17A LEU* 3.3 20.8 - - - +
19A GLU* 1.3 93.8 - - - +
21A GLY* 1.3 62.9 + - - +
22A ARG 3.2 4.4 + - - -
23A LEU* 3.6 28.8 + - + +
31A ARG* 4.2 12.5 - - - +
55B TYR* 3.6 1.8 - - - -
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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