Contacts of the helix formed by residues 7 - 21 (chain A) in PDB entry 2CVP
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 ASN 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA 3.1 14.0 + - - +
4A LEU* 3.2 15.2 + - - +
6A ARG* 1.3 77.2 - - - +
8A PRO* 1.3 71.2 - - - +
9A GLN* 2.8 33.8 + - - +
10A PHE* 3.1 13.5 + - + +
11A GLN* 3.2 22.1 + - - +
71A LEU* 3.3 9.4 - - - +
74A SER* 2.8 37.5 + - - -
75A ARG* 3.9 13.6 - - - +
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Residues in contact with PRO 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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6A ARG 3.4 8.0 - - - +
7A ASN* 1.3 89.1 - - - +
9A GLN* 1.3 83.1 + - - +
11A GLN* 3.5 7.7 + - + +
12A LYS* 3.0 27.5 + - - +
74A SER* 5.1 0.7 - - - +
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 2.8 13.3 + - - +
8A PRO* 1.3 93.2 - - - +
10A PHE* 1.3 57.2 + - - +
12A LYS* 3.5 13.7 + - + +
13A LEU* 3.0 27.2 + - - +
67A MET* 5.1 4.8 - - - +
70A GLU* 4.4 20.0 - - + +
71A LEU* 4.1 21.0 - - + +
74A SER* 2.7 33.1 + - - -
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Residues in contact with PHE 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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4A LEU* 3.3 48.7 - - + +
5A THR* 3.9 16.6 - - + -
7A ASN* 3.1 8.0 + - - +
9A GLN* 1.3 75.8 - - - +
11A GLN* 1.3 81.9 + - - +
13A LEU* 3.2 7.8 + - + +
14A LEU* 2.9 54.7 + - + +
71A LEU* 3.7 27.7 - - + +
325A ILE* 5.0 2.2 - - + -
329A ASN* 3.8 31.2 - - + -
330A CYS* 4.5 12.3 - - - -
373A HIS* 5.7 2.0 - - + -
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Residues in contact with GLN 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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5A THR* 2.7 39.8 + - - +
6A ARG 5.3 1.1 - - - +
7A ASN 3.2 9.4 + - - +
8A PRO* 3.5 9.4 + - + +
9A GLN 3.4 0.2 - - - -
10A PHE* 1.3 92.9 - - - +
12A LYS* 1.3 57.4 + - - +
14A LEU* 3.5 17.4 + - - +
15A GLU* 3.0 30.1 + - - +
18A ARG* 5.1 5.2 + - - -
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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 PRO 3.0 18.3 + - - +
9A GLN* 3.6 14.6 - - + +
10A PHE 3.2 0.2 - - - -
11A GLN* 1.3 72.9 - - - +
13A LEU* 1.3 58.8 + - - +
15A GLU* 3.3 5.8 + - - +
16A TRP* 2.9 29.1 + - + +
67A MET* 4.2 30.3 - - + +
70A GLU* 4.4 10.4 + - - +
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Residues in contact with LEU 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 GLN 3.0 13.6 + - - +
10A PHE* 3.2 13.2 + - + +
12A LYS* 1.3 76.9 - - - +
14A LEU* 1.3 56.1 + - - +
16A TRP* 3.3 3.8 + - - +
17A HIS* 2.8 28.1 + - - +
64A VAL* 4.3 2.2 - - + +
67A MET* 3.7 43.2 - - + +
68A LEU* 3.6 36.8 - - + +
71A LEU* 4.1 17.0 - - + -
325A ILE* 5.3 2.5 - - + -
326A TRP* 3.8 22.9 - - + -
330A CYS* 3.8 21.1 - - - -
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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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10A PHE* 2.9 35.4 + - + +
11A GLN* 3.8 22.4 - - - +
13A LEU* 1.3 76.2 - - - +
15A GLU* 1.3 57.4 + - - +
17A HIS* 3.2 8.5 + - + +
18A ARG* 2.9 49.5 + - - +
329A ASN 3.4 25.8 - - - +
330A CYS* 3.7 22.6 - - + +
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Residues in contact with GLU 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 GLN 3.0 19.2 + - - +
12A LYS* 3.7 6.7 - - - +
14A LEU* 1.3 72.9 - - - +
16A TRP* 1.3 65.5 + - - +
18A ARG* 2.8 42.2 + - - +
19A ALA* 3.0 30.8 + - - +
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Residues in contact with TRP 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 14.5 + - + +
13A LEU 3.5 7.4 - - - +
15A GLU* 1.3 76.7 - - - +
17A HIS* 1.3 60.1 + - - +
19A ALA* 3.2 1.0 + - - -
20A ASN* 2.8 70.9 + - + +
21A SER 4.2 3.8 - - - -
24A LEU* 4.0 26.0 - - + -
61A SER* 4.3 7.9 - - - -
63A GLU* 3.5 26.7 + - + -
64A VAL* 3.5 28.7 - - + -
67A MET* 3.5 30.4 - - + +
326A TRP* 3.9 19.3 - + - -
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Residues in contact with HIS 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 LEU 2.8 13.8 + - - +
14A LEU* 3.2 11.4 + - + +
16A TRP* 1.3 84.1 - - - +
18A ARG* 1.3 67.0 + - - +
21A SER* 2.8 59.0 + - - -
326A TRP* 3.8 13.7 - + + -
330A CYS* 3.2 39.8 + - + -
331A TYR* 3.4 43.3 - + - -
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Residues in contact with ARG 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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11A GLN* 5.1 4.4 + - - -
14A LEU* 2.9 33.8 + - - +
15A GLU* 2.8 49.2 + - - +
17A HIS* 1.3 81.2 + - - +
19A ALA* 1.3 61.7 + - - +
21A SER* 5.0 0.7 + - - -
22A ALA* 5.8 1.9 + - - +
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Residues in contact with ALA 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 GLU* 3.0 26.3 + - - +
16A TRP* 4.7 0.4 - - - -
18A ARG* 1.3 78.0 - - - +
20A ASN* 1.3 75.3 + - - +
22A ALA* 5.6 2.1 - - - +
23A ASN* 4.2 7.8 - - - +
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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
----------------------------------------------------------
16A TRP* 2.8 75.5 + - + +
19A ALA* 1.3 89.4 - - - +
21A SER* 1.3 57.8 + - - +
22A ALA* 3.2 3.1 - - - -
23A ASN* 2.9 37.1 + - + +
24A LEU* 3.9 4.7 + - - +
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.0 3.4 + - - -
17A HIS* 2.8 59.5 + - - -
18A ARG 4.9 0.5 + - - -
20A ASN* 1.3 77.6 - - - +
22A ALA* 1.3 58.3 + - - +
23A ASN 3.0 0.2 - - - -
24A LEU* 3.0 39.9 + - - +
326A TRP* 5.0 0.4 - - - -
331A TYR* 3.6 19.8 + - - -
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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