Contacts of the helix formed by residues 10 - 21 (chain D) in PDB entry 2V5P
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 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D CYS* 1.3 72.5 - - - +
11D GLY* 1.3 63.5 + - - -
12D GLU 3.2 2.5 + - - -
13D LEU* 3.4 13.7 + - - +
14D VAL* 3.6 13.7 - - - +
47D CYS* 4.8 1.6 - - - -
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Residues in contact with GLY 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569A GLN* 6.6 0.2 - - - -
1570A THR* 4.3 12.5 - - - +
10D GLY* 1.3 69.6 - - - -
12D GLU* 1.3 59.9 + - - +
13D LEU 3.2 1.1 - - - -
14D VAL* 3.2 11.8 + - - +
15D ASP* 2.9 36.3 + - - +
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570A THR* 3.7 32.2 - - + +
1572A ILE* 4.0 17.6 - - + +
8D LEU* 5.2 6.4 - - - +
9D CYS 3.4 17.0 + - - +
10D GLY 3.2 0.8 - - - -
11D GLY* 1.3 78.4 - - - +
13D LEU* 1.3 52.3 + - - +
15D ASP 4.4 0.9 - - - -
16D THR* 2.6 28.9 + - - -
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.4 33.2 + - + +
9D CYS* 3.7 3.9 + - - -
10D GLY 3.4 11.3 + - - +
11D GLY 3.2 0.6 - - - -
12D GLU* 1.3 79.3 - - - +
14D VAL* 1.3 59.7 + - + +
15D ASP 3.4 0.2 - - - -
16D THR* 3.4 6.5 + - - -
17D LEU* 3.1 39.1 + - + +
28D PHE* 5.2 4.7 - - + -
42D ILE* 4.8 11.0 - - + -
43D VAL* 4.5 30.7 - - + -
46D CYS* 3.8 23.8 - - + -
47D CYS* 4.8 4.0 - - + -
56D LEU* 4.2 16.6 - - + +
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Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLY 3.6 16.2 - - - +
11D GLY* 3.2 11.8 + - - +
13D LEU* 1.3 77.7 - - + +
15D ASP* 1.3 64.9 + - - +
17D LEU* 3.2 26.3 + - + +
18D GLN* 3.5 19.2 + - - +
26D PHE* 4.4 15.0 - - + -
28D PHE* 5.1 12.6 - - + -
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Residues in contact with ASP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542A TYR* 4.4 8.0 + - - +
1567A PHE* 5.1 9.3 - - + -
1568A GLY* 4.6 6.1 - - - +
1569A GLN* 3.6 26.0 + - - +
1570A THR* 2.6 42.0 + - - +
1572A ILE* 4.2 11.0 - - + -
11D GLY* 2.9 15.8 + - - +
14D VAL* 1.3 77.3 - - - +
16D THR* 1.3 61.4 + - - +
18D GLN* 3.3 32.2 + - - +
19D PHE* 3.4 12.0 + - - +
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567A PHE* 6.0 3.4 - - + -
1572A ILE* 4.1 10.2 - - - +
1599A PRO* 5.2 4.5 - - + -
1606A TYR* 4.0 20.7 + - - +
12D GLU 2.6 22.8 + - - -
13D LEU* 3.4 10.9 + - - -
14D VAL 3.2 0.6 - - - -
15D ASP* 1.3 77.0 - - - +
17D LEU* 1.3 64.0 + - - +
19D PHE* 3.3 11.7 + - + +
20D VAL* 3.2 25.1 + - + +
53D LEU* 4.2 8.5 - - + -
56D LEU* 3.8 21.8 - - + -
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.1 31.3 + - + +
14D VAL* 3.2 16.1 + - - +
16D THR* 1.3 75.4 - - - +
18D GLN* 1.3 51.0 + - - +
20D VAL* 3.1 3.5 + - - +
21D CYS* 2.7 43.9 + - - +
26D PHE* 3.7 50.3 - - + -
27D TYR 4.4 3.4 - - - +
28D PHE* 3.8 21.8 - - + -
42D ILE* 3.8 26.7 - - + -
56D LEU* 4.8 16.4 - - + +
59D TYR* 5.0 1.6 - - + -
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542A TYR* 4.1 14.2 + - + +
1543A SER* 3.7 16.8 + - - +
1545A LYS 5.9 2.3 - - - -
1569A GLN* 5.5 1.6 + - - -
14D VAL* 3.5 21.2 + - - +
15D ASP* 3.3 36.7 + - - +
17D LEU* 1.3 75.3 - - - +
19D PHE* 1.3 61.8 + - - +
20D VAL 3.2 0.4 - - - -
22D GLY* 3.0 33.4 + - - +
26D PHE* 3.6 21.0 - - + -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542A TYR* 3.9 22.6 - + + +
1548A VAL* 5.7 1.1 - - + -
1567A PHE* 3.2 43.1 - + + -
1606A TYR* 4.8 13.0 - + - -
1626A LEU* 4.3 18.1 - - + +
1629A LEU* 3.7 38.1 - - + +
1636A LEU* 3.8 24.9 - - + -
15D ASP 3.4 15.1 + - - +
16D THR* 3.3 17.7 + - + +
17D LEU 3.2 0.2 - - - -
18D GLN* 1.3 80.8 - - - +
20D VAL* 1.3 68.3 + - + +
22D GLY* 5.7 0.2 - - - -
53D LEU* 6.1 2.7 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629A LEU* 5.3 9.6 - - + -
1631A LYS* 5.3 8.1 - - + -
16D THR* 3.3 15.3 - - + +
17D LEU 3.1 5.2 + - - +
19D PHE* 1.3 91.9 - - + +
21D CYS* 1.3 63.3 + - - +
24D ARG* 3.2 15.1 + - - -
53D LEU* 4.5 16.2 - - + +
56D LEU* 3.9 19.7 - - + -
57D GLU* 3.7 42.2 - - + +
60D CYS* 4.0 3.8 - - - -
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Residues in contact with CYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 2.7 26.6 + - - +
20D VAL* 1.3 78.8 - - - +
22D GLY* 1.3 64.5 + - - +
23D ASP 3.4 0.9 + - - -
24D ARG* 3.3 24.9 + - - +
25D GLY 3.3 22.0 - - - +
26D PHE* 3.5 18.6 - - + -
56D LEU* 4.8 2.2 - - - -
59D TYR 4.4 0.4 - - - -
60D CYS* 2.0 57.4 - - + -
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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