Contacts of the helix formed by residues 9 - 22 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 1.3 87.3 - - + +
10H ARG* 1.3 57.1 + - - +
11H ARG* 4.3 5.2 - - + +
12H ILE* 2.7 49.7 + - + +
13H ILE* 3.5 5.1 + - - +
37H ARG* 3.3 28.0 - - - +
64H GLU 6.1 0.4 - - - +
66H TYR 5.5 4.9 - - - +
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Residues in contact with ARG 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU 3.3 1.5 + - - +
9H PRO* 1.3 68.6 - - - +
11H ARG* 1.3 71.7 + - - +
12H ILE 2.7 3.9 + - - -
13H ILE* 3.0 21.4 + - + +
14H LYS* 2.9 65.3 + - - +
17H GLN* 5.9 0.4 + - - -
228T ILE* 3.6 23.2 - - - +
238T PHE 5.9 0.2 - - - -
239T GLU* 3.8 44.8 - - + +
301T VAL* 5.6 11.8 - - - +
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Residues in contact with ARG 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PRO* 3.1 5.6 - - + +
10H ARG* 1.3 81.0 - - - +
12H ILE* 1.4 71.8 + - + +
14H LYS* 3.5 3.6 + - - +
15H GLU* 2.9 42.2 + - + +
66H TYR* 3.5 10.9 + - - -
67H PRO* 3.5 28.7 - - + +
101H PRO 3.0 21.2 + - - -
102H ALA 4.7 0.6 + - - -
103H LEU 2.9 27.9 + - - -
104H GLN* 3.6 7.5 - - - +
236T ILE* 3.4 27.9 + - - +
237T SER 3.6 15.7 + - - +
238T PHE* 3.6 40.2 - - + -
239T GLU* 4.6 2.0 + - - +
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Residues in contact with ILE 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 4.2 15.9 - - + -
9H PRO* 2.7 36.2 + - + +
10H ARG 2.7 1.6 + - - -
11H ARG* 1.4 81.8 - - + +
13H ILE* 1.4 54.3 + - - +
15H GLU* 2.6 34.4 + - + +
16H THR* 2.8 21.2 + - - +
36H ALA 5.0 8.7 - - - +
37H ARG* 3.9 19.3 - - + +
39H PHE* 5.3 3.4 - - + -
62H LEU* 3.3 37.5 - - + -
66H TYR* 3.8 22.2 - - + +
105H ILE* 5.8 0.2 - - + -
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Residues in contact with ILE 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ALA 4.0 9.9 - - - +
8H LEU* 3.3 53.1 - - + +
9H PRO 3.5 10.0 + - - +
10H ARG* 3.5 20.0 - - + +
12H ILE* 1.4 74.0 - - - +
14H LYS* 1.3 68.5 + - + +
16H THR* 3.0 19.5 + - - -
17H GLN* 3.2 38.7 + - + +
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Residues in contact with LYS 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ARG* 2.9 33.5 + - - +
11H ARG* 4.0 5.6 - - - +
12H ILE 2.9 1.8 - - - -
13H ILE* 1.3 86.7 - - + +
15H GLU* 1.3 60.4 + - - +
17H GLN* 4.0 7.2 + - - +
18H ARG* 3.1 70.2 + - - +
228T ILE* 3.0 47.8 + - - +
230T ASP* 4.4 4.6 + - - -
233T CYS* 4.6 5.7 - - - -
238T PHE* 3.7 34.3 + - + +
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Residues in contact with GLU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ARG* 2.9 28.6 + - - +
12H ILE* 2.6 20.3 + - - +
14H LYS* 1.3 71.4 - - - +
16H THR* 1.4 47.9 - - - +
18H ARG* 3.6 5.8 + - - +
19H LEU* 2.8 38.4 + - - +
66H TYR* 2.2 33.5 + - - -
104H GLN* 3.0 24.5 + - - +
105H ILE* 2.7 45.0 + - + +
106H ARG 3.9 2.3 + - - -
238T PHE* 4.1 19.7 - - + -
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Residues in contact with THR 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 2.8 28.6 + - - +
13H ILE* 3.0 11.5 + - - -
15H GLU* 1.4 70.7 - - - +
17H GLN* 1.4 54.7 + - - +
18H ARG 3.2 0.7 - - - -
19H LEU* 2.9 10.0 + - - +
20H LEU* 2.6 46.5 + - + +
31H PRO* 4.0 24.0 - - + -
36H ALA 5.2 2.5 + - - +
39H PHE* 3.9 32.6 - - + -
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Residues in contact with GLN 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ILE* 3.2 36.6 + - + +
14H LYS* 4.1 9.3 - - - +
16H THR* 1.4 69.1 - - - +
18H ARG* 1.3 62.0 + - - +
20H LEU* 4.7 8.4 - - + +
21H ALA* 2.6 42.3 + - + +
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Residues in contact with ARG 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LYS* 3.1 68.5 + - - +
15H GLU* 3.8 5.4 - - - +
16H THR 3.2 1.0 - - - -
17H GLN* 1.3 83.3 - - - +
19H LEU* 1.3 64.5 + - - +
21H ALA* 4.8 2.9 - - - -
22H GLU* 3.1 27.8 + - - +
106H ARG* 3.9 6.3 + - - +
230T ASP* 3.1 34.1 + - - -
238T PHE* 5.6 5.4 - - - -
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H GLU 2.8 20.5 + - - +
16H THR* 2.9 7.0 + - - +
18H ARG* 1.3 76.0 - - - +
20H LEU* 1.4 58.9 + - + +
23H PRO* 2.8 70.8 - - + +
24H VAL* 3.7 17.0 - - + -
27H ILE* 5.5 1.1 - - + -
29H ALA* 4.2 18.2 - - + +
39H PHE* 5.8 7.0 - - + -
105H ILE* 3.8 20.4 - - + -
106H ARG* 3.7 26.2 - - + +
109H LEU* 3.7 28.0 - - + -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H THR* 2.6 28.7 + - + +
17H GLN* 4.0 5.6 - - + +
19H LEU* 1.4 72.5 - - + +
21H ALA* 1.3 54.1 - - - +
22H GLU* 2.2 25.4 + - - -
23H PRO* 3.2 12.6 - - - +
29H ALA 3.5 14.6 - - - +
30H GLU* 3.4 35.0 - - + +
31H PRO* 3.7 20.6 - - + -
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Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLN* 2.6 26.2 + - + +
18H ARG* 4.0 3.4 - - - +
20H LEU* 1.3 71.2 - - - +
22H GLU* 1.4 60.0 + - - +
23H PRO* 4.4 0.2 - - - -
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Residues in contact with GLU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ARG* 3.1 9.9 + - - +
19H LEU 3.1 4.3 - - - -
20H LEU 2.2 12.9 + - - -
21H ALA* 1.4 72.6 - - - +
23H PRO* 1.3 67.4 - - + +
106H ARG* 2.6 36.4 + - - -
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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