Contacts of the helix formed by residues 3 - 15 (chain C) in PDB entry 2AXV
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 LYS 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C PHE* 1.3 76.7 - - + +
4C ILE* 1.3 60.4 + - - +
5C GLY 3.3 2.7 - - - -
6C SER* 2.8 37.3 + - - +
7C VAL* 3.5 14.8 + - - +
10C GLN* 5.7 4.5 - - - +
38C ASP* 3.5 15.3 - - - +
64C ARG 3.3 26.4 + - - -
65C ALA* 3.5 15.4 - - - +
66C GLY* 4.3 4.9 - - - +
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Residues in contact with ILE 4 (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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2C PHE* 3.4 17.6 + - - +
3C LYS* 1.3 76.5 - - - +
5C GLY* 1.3 58.6 + - - +
7C VAL* 3.1 5.0 + - - +
8C LEU* 2.9 29.2 + - + +
38C ASP* 3.5 1.2 + - - -
42C ILE* 4.2 20.2 - - + -
47C LEU* 3.5 32.3 - - + -
61C ILE* 4.6 5.8 - - + -
62C LEU* 4.0 11.7 - - + -
65C ALA* 3.3 26.2 - - + -
67C MET* 6.4 0.7 - - + -
44D VAL* 3.7 40.6 - - + -
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Residues in contact with GLY 5 (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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4C ILE* 1.3 79.3 - - - +
6C SER* 1.3 61.4 + - - +
8C LEU* 3.2 11.0 + - - +
9C LYS 3.0 18.9 + - - -
35C VAL* 3.5 21.0 + - - +
36C GLU* 3.4 20.9 - - - +
38C ASP* 2.8 13.8 + - - -
42C ILE* 5.7 1.0 - - - +
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Residues in contact with SER 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS* 2.8 40.4 + - - +
5C GLY* 1.3 75.4 - - - +
7C VAL* 1.3 57.9 + - - +
9C LYS* 3.3 7.3 + - - +
10C GLN* 2.9 31.8 + - - +
36C GLU 3.6 5.4 + - - -
38C ASP* 3.3 16.7 + - - -
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS* 3.5 23.6 - - - +
4C ILE* 3.1 7.7 + - - +
6C SER* 1.3 74.6 + - - +
8C LEU* 1.3 66.3 + - - +
10C GLN* 3.2 18.4 + - - +
11C ILE* 2.9 44.6 + - + +
61C ILE* 4.2 13.7 - - + -
64C ARG* 3.7 26.9 - - + +
65C ALA* 3.7 25.6 - - + -
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 2.9 18.2 + - + +
5C GLY* 3.4 12.8 - - - +
7C VAL* 1.3 77.9 - - - +
9C LYS* 1.3 56.8 + - - +
11C ILE* 3.8 4.4 - - + +
12C ARG* 2.8 31.0 + - - +
22C LEU* 4.9 1.7 - - + +
32C TYR* 4.1 16.6 - - + +
35C VAL* 4.4 11.2 - - + -
36C GLU* 4.1 3.1 - - + +
42C ILE* 4.1 13.7 - - + -
47C LEU* 4.1 12.8 - - + -
50C PHE* 3.5 43.1 - - + -
54C LEU* 3.8 25.7 - - + +
61C ILE* 4.7 9.6 - - + -
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Residues in contact with LYS 9 (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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5C GLY 3.0 8.5 + - - +
6C SER* 3.6 10.1 - - - +
8C LEU* 1.3 75.5 - - - +
10C GLN* 1.3 67.5 + - - +
12C ARG* 3.1 4.1 + - - +
13C GLN* 2.9 58.4 + - - +
36C GLU* 3.3 38.7 + - + +
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Residues in contact with GLN 10 (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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3C LYS* 5.7 4.0 - - - +
6C SER* 2.9 17.3 + - - +
7C VAL* 3.5 28.3 - - - +
9C LYS* 1.3 78.5 - - - +
11C ILE* 1.3 60.3 + - - +
13C GLN* 4.0 4.6 - - - +
14C GLU* 3.0 29.1 + - + +
64C ARG* 4.2 19.2 + - - +
147D THR* 5.7 4.7 - - + +
149D PHE* 5.5 3.2 - - + -
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Residues in contact with ILE 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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7C VAL* 2.9 37.9 + - + +
8C LEU* 4.0 3.4 - - - +
10C GLN* 1.3 79.0 - - - +
12C ARG* 1.3 66.9 + - - +
14C GLU* 3.3 7.0 + - - +
15C LEU* 3.1 41.2 + - + +
54C LEU* 3.9 16.4 - - + -
56C VAL* 3.6 37.7 - - + -
61C ILE* 4.0 13.5 - - + -
64C ARG* 4.8 6.3 - - - -
149D PHE* 3.7 23.8 - - + -
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Residues in contact with ARG 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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8C LEU 2.8 19.1 + - - +
9C LYS* 3.5 7.5 - - - +
11C ILE* 1.3 76.7 - - - +
13C GLN* 1.3 92.2 + - - +
15C LEU* 3.2 3.6 + - - +
16C ASN 3.2 3.8 + - - -
17C TYR* 3.0 57.8 + - + -
18C HIS* 3.8 15.0 + - - +
19C GLN* 3.4 30.6 - - - +
22C LEU* 3.8 18.2 - - + -
32C TYR* 4.2 7.4 - - - +
36C GLU* 2.9 35.0 + - - -
54C LEU* 3.7 11.2 - - + +
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Residues in contact with GLN 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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9C LYS* 2.9 54.8 + - - +
10C GLN* 4.1 4.7 - - - +
12C ARG* 1.3 98.5 + - - +
14C GLU* 1.3 68.1 + - - +
16C ASN* 2.9 18.6 + - - +
17C TYR 4.6 4.7 - - - +
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Residues in contact with GLU 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 GLN* 3.0 21.1 + - + +
11C ILE 3.5 7.2 - - - +
12C ARG 3.2 0.2 - - - -
13C GLN* 1.3 77.8 - - - +
15C LEU* 1.3 58.6 + - - +
16C ASN* 3.2 6.6 + - - -
144D LYS 4.5 3.5 - - - +
145D ARG* 2.9 27.5 + - - +
146D THR* 2.8 46.5 + - - +
147D THR* 3.0 16.7 - - - +
149D PHE* 3.7 30.3 - - + -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.1 31.7 + - + +
12C ARG 3.8 0.7 - - - +
13C GLN 3.1 0.8 - - - -
14C GLU* 1.3 78.1 - - - +
16C ASN* 1.3 73.5 + - - +
17C TYR* 3.7 27.6 - - + -
54C LEU* 3.2 28.9 - - + +
56C VAL* 4.5 3.8 - - + -
107D LEU* 4.3 13.5 - - + -
145D ARG* 3.7 38.8 - - - +
149D PHE* 3.8 14.1 - - + -
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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