Contacts of the helix formed by residues 10 - 21 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C CYS* 1.3 72.7 - - - +
11C GLY* 1.3 65.8 + - - -
13C LEU* 3.2 21.8 + - - +
14C VAL* 3.4 13.3 + - - +
47C CYS* 4.5 3.2 - - - -
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Residues in contact with GLY 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569B GLN* 6.5 0.4 - - - -
1570B THR* 3.6 15.7 - - - +
9C CYS 3.6 0.6 + - - -
10C GLY* 1.3 70.3 - - - -
12C GLU* 1.3 60.1 + - - +
14C VAL* 3.1 9.9 + - - -
15C ASP* 2.8 37.7 + - - +
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570B THR* 3.5 29.1 - - + +
1571B ARG 6.5 0.2 - - - -
1572B ILE* 3.7 20.8 - - + +
8C LEU* 5.4 9.1 - - + +
9C CYS 3.4 16.2 - - - +
10C GLY 3.2 0.4 - - - -
11C GLY* 1.3 78.7 - - - +
13C LEU* 1.3 56.8 + - - +
16C THR* 2.8 30.5 + - - -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.6 30.7 - - + +
9C CYS 3.6 5.7 + - - +
10C GLY 3.2 15.9 + - - +
12C GLU* 1.3 78.3 - - - +
14C VAL* 1.3 65.5 + - + +
16C THR* 3.6 4.3 + - - -
17C LEU* 3.3 33.3 + - + +
28C PHE* 4.5 16.4 - - + -
42C ILE* 4.5 7.4 - - + -
43C VAL* 4.4 19.7 - - + +
46C CYS* 4.3 13.5 - - + -
47C CYS* 4.3 13.7 - - + -
56C LEU* 4.3 22.3 - - + +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLY 3.4 16.2 - - - +
11C GLY* 3.1 10.3 + - - +
13C LEU* 1.3 77.3 - - + +
15C ASP* 1.3 69.2 + - - +
17C LEU* 3.0 24.0 + - - +
18C GLN* 3.5 12.9 + - - +
26C PHE* 4.2 21.6 - - + -
28C PHE* 4.4 17.9 - - + -
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Residues in contact with ASP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542B TYR* 4.0 6.5 + - - +
1567B PHE* 4.9 6.3 - - + -
1568B GLY* 3.6 6.5 + - - +
1569B GLN* 2.8 45.6 + - - +
1570B THR* 2.8 33.0 + - - +
1572B ILE* 3.9 10.8 - - + -
11C GLY* 2.8 20.0 + - - +
14C VAL* 1.3 75.1 - - - +
16C THR* 1.3 61.2 + - - +
18C GLN* 3.5 18.7 + - - +
19C PHE* 3.4 18.7 + - - +
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567B PHE* 5.5 4.6 - - + -
1572B ILE* 3.5 15.0 - - - +
1599B PRO* 5.8 2.0 - - + -
1606B TYR* 4.0 20.5 + - - +
8C LEU* 6.1 4.4 - - + +
12C GLU 2.8 19.3 + - - -
13C LEU* 4.0 4.9 - - - -
14C VAL 3.2 0.8 - - - -
15C ASP* 1.3 75.1 - - - +
17C LEU* 1.3 63.5 + - - +
19C PHE* 3.2 15.0 + - + +
20C VAL* 3.0 25.2 + - + +
53C LEU* 4.3 9.2 - - + -
56C LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.3 23.8 + - + +
14C VAL* 3.0 11.3 + - - +
16C THR* 1.3 77.7 - - - +
18C GLN* 1.3 58.0 + - - +
20C VAL* 3.2 3.5 + - + +
21C CYS* 2.8 36.4 + - - -
26C PHE* 3.7 48.0 - - + -
27C TYR 5.0 0.7 - - - +
28C PHE* 3.9 19.1 - - + -
42C ILE* 3.6 33.7 - - + -
56C LEU* 4.2 26.0 - - + +
59C TYR* 4.6 2.9 - - + -
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542B TYR* 4.1 16.4 + - + +
1543B SER* 3.2 14.4 + - - +
1545B LYS* 5.7 4.6 + - - +
1546B GLY* 5.7 3.6 - - - -
1569B GLN* 4.4 14.6 + - - -
14C VAL* 3.5 10.6 + - - +
15C ASP* 3.5 28.3 + - - +
17C LEU* 1.3 75.0 - - - +
19C PHE* 1.3 63.3 + - - +
20C VAL 3.3 0.2 - - - -
21C CYS 3.8 0.2 - - - -
22C GLY* 3.0 36.9 + - - +
26C PHE* 3.5 22.3 - - + -
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542B TYR* 3.5 32.9 - + + +
1543B SER* 5.4 0.9 - - - -
1548B VAL* 5.0 2.0 - - + -
1567B PHE* 3.3 42.8 - + + -
1606B TYR* 5.5 5.2 - + - -
1626B LEU* 4.1 24.4 - - + +
1629B LEU* 3.5 44.2 - - + -
1636B LEU* 4.3 8.3 - - + -
15C ASP 3.4 13.7 + - - +
16C THR* 3.2 19.0 + - + +
17C LEU 3.2 0.6 - - - -
18C GLN* 1.3 80.6 - - - +
20C VAL* 1.3 67.7 + - + +
53C LEU* 6.1 2.0 - - + -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1631B LYS* 5.8 4.9 - - + -
16C THR* 3.0 16.8 + - + +
17C LEU* 3.7 5.4 - - - +
19C PHE* 1.3 86.0 - - + +
21C CYS* 1.3 61.1 + - - +
24C ARG* 3.2 14.4 + - - -
53C LEU* 4.2 19.1 - - + +
56C LEU* 4.0 21.8 - - + -
57C GLU* 3.6 43.3 - - + +
60C CYS* 3.8 5.2 - - - -
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Residues in contact with CYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543B SER* 5.2 0.6 - - - -
17C LEU* 2.8 28.8 + - - +
18C GLN 3.8 0.9 - - - -
20C VAL* 1.3 76.6 - - - +
22C GLY* 1.3 63.4 + - - +
23C ASP* 3.3 3.6 + - - +
24C ARG* 3.7 18.6 + - - +
25C GLY 3.2 24.0 - - - +
26C PHE* 3.6 15.0 - - + -
56C LEU 4.8 0.4 - - - -
60C CYS* 2.0 56.3 - - + -
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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