Contacts of the helix formed by residues 9 - 22 (chain B) in PDB entry 2C2V
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 PRO 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B GLY 4.6 2.2 - - - +
8B LEU* 1.4 78.6 - - + +
10B ARG* 1.3 57.0 + - - +
11B ARG* 4.4 6.1 - - + +
12B ILE* 2.9 25.8 + - + +
13B ILE* 2.8 35.7 + - - +
37B ARG* 3.3 30.5 - - - +
64B GLU 5.7 2.2 - - - +
66B TYR 5.4 5.2 - - - +
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Residues in contact with ARG 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 3.6 1.2 + - - -
9B PRO* 1.3 69.6 - - - +
11B ARG* 1.3 68.2 + - - +
13B ILE* 2.9 40.9 + - + +
14B LYS* 2.9 45.6 + - - +
17B GLN* 4.9 4.2 - - - +
239S GLU* 4.2 31.6 - - - +
300S TRP* 3.2 44.4 - - + -
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Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 4.4 6.0 - - + +
10B ARG* 1.3 77.8 - - - +
12B ILE* 1.4 65.0 + - + +
14B LYS* 3.1 5.5 + - - +
15B GLU* 2.8 41.6 + - - +
66B TYR* 3.4 19.3 + - + -
67B PRO* 2.6 45.0 - - + +
101B PRO 3.1 15.3 + - - -
103B LEU 2.8 28.5 + - - -
104B GLN* 3.4 7.3 - - - +
236S ILE* 3.1 21.2 + - - +
237S SER* 4.1 13.1 + - - +
238S PHE* 3.8 37.5 - - + -
239S GLU* 5.0 3.2 + - - +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.9 21.8 - - + -
9B PRO* 2.9 42.4 + - + +
11B ARG* 1.4 75.1 - - + +
13B ILE* 1.4 60.7 + - - +
15B GLU* 3.3 6.3 + - - +
16B THR* 2.4 42.9 + - - +
36B ALA 4.7 7.2 - - - +
37B ARG* 3.9 22.9 - - + +
39B PHE* 5.1 0.4 - - + -
62B LEU* 4.0 23.8 - - + -
66B TYR* 3.9 34.3 - - + +
105B ILE* 5.6 0.7 - - + -
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA* 4.6 11.0 - - + -
8B LEU* 3.5 33.0 - - + +
9B PRO 2.8 28.2 + - - +
10B ARG* 2.9 37.0 + - + +
12B ILE* 1.4 76.7 - - - +
14B LYS* 1.3 66.7 + - - +
16B THR* 3.2 8.3 + - - -
17B GLN* 3.2 47.7 + - - +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 2.9 31.4 + - - +
11B ARG* 3.4 9.4 - - - +
13B ILE* 1.3 78.8 - - - +
15B GLU* 1.4 64.5 + - - +
17B GLN* 2.9 9.2 + - - +
18B ARG* 2.9 69.8 + - + +
228S ILE* 3.8 25.0 + - - +
230S ASP* 5.1 1.0 + - - -
233S CYS* 4.5 12.1 - - - -
238S PHE* 3.3 37.7 + - + +
239S GLU* 5.3 4.1 - - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 2.8 38.9 + - + +
12B ILE* 3.3 6.7 + - - +
14B LYS* 1.4 71.1 - - - +
16B THR* 1.3 64.2 + - - +
18B ARG* 3.3 7.3 + - - +
19B LEU* 2.9 30.1 + - + +
66B TYR* 2.5 27.0 + - - -
104B GLN* 2.8 43.4 - - - +
105B ILE* 3.0 28.1 + - + +
238S PHE* 4.3 15.9 - - + -
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 5.7 0.7 - - - +
12B ILE* 2.4 28.8 + - - +
13B ILE* 3.4 8.8 - - - -
14B LYS 3.0 0.2 - - - -
15B GLU* 1.3 78.3 - - - +
17B GLN* 1.3 61.3 + - + +
19B LEU* 3.6 6.3 + - - +
20B LEU* 3.1 33.7 + - + +
31B PRO* 4.0 29.6 - - + -
36B ALA 5.2 1.1 + - - +
39B PHE* 3.9 26.6 - - + -
105B ILE* 5.6 0.4 - - - +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 4.9 6.1 - - - +
13B ILE* 3.2 40.1 + - - +
14B LYS* 2.9 7.1 + - - +
16B THR* 1.3 81.2 - - + +
18B ARG* 1.4 66.9 + - - +
20B LEU* 3.5 8.8 + - + +
21B ALA* 3.3 22.4 + - - +
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 2.9 61.6 + - + +
15B GLU* 3.8 6.2 - - - +
17B GLN* 1.4 76.6 - - - +
19B LEU* 1.4 55.2 + - - +
21B ALA* 2.9 7.5 + - - -
22B GLU* 2.5 36.2 + - - +
106B ARG* 4.2 10.9 + - - +
228S ILE* 5.0 6.7 + - - +
230S ASP* 3.1 32.7 + - - -
238S PHE* 4.6 14.8 - - - -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 2.9 22.3 + - + +
16B THR* 3.9 4.5 - - - +
18B ARG* 1.4 74.7 - - - +
20B LEU* 1.3 71.6 + - + +
23B PRO* 3.1 26.4 - - + +
24B VAL* 4.3 20.2 - - + +
29B ALA* 5.3 12.7 - - + +
39B PHE* 5.0 13.9 - - + -
104B GLN* 6.1 0.7 - - - +
105B ILE* 3.8 32.5 - - + -
106B ARG* 3.9 33.2 - - + +
109B LEU* 5.3 11.4 - - + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B THR* 3.1 27.8 + - + +
17B GLN* 3.5 10.1 + - + +
18B ARG 3.4 0.2 - - - -
19B LEU* 1.3 82.9 - - + +
21B ALA* 1.3 59.7 + - - +
23B PRO* 3.8 11.4 - - - +
29B ALA 3.5 25.1 - - - +
30B GLU* 4.1 17.0 - - + +
31B PRO* 4.3 18.2 - - + -
39B PHE* 6.5 0.2 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN 3.3 12.9 + - - +
18B ARG* 2.9 13.1 + - - +
20B LEU* 1.3 78.7 - - - +
22B GLU* 1.3 66.2 + - + +
23B PRO* 2.9 10.4 - - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 2.5 11.9 + - - -
19B LEU 3.6 2.7 - - - -
21B ALA* 1.3 78.0 - - - +
23B PRO* 1.4 65.3 - - + +
106B ARG* 2.7 56.8 + - - +
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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