Contacts of the helix formed by residues 2 - 16 (chain A) in PDB entry 1WZV
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 ALA 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 1.3 69.0 + - - +
4A MET* 3.1 7.4 + - - +
5A ARG* 3.1 9.2 + - - +
6A VAL* 2.9 25.7 + - + +
32A LEU* 4.1 13.9 - - + -
57A PRO 3.9 11.9 - - - +
58A PRO* 3.2 30.5 + - + +
60A TYR* 3.8 21.3 - - + +
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Residues in contact with SER 3 (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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2A ALA* 1.3 78.7 - - - +
4A MET* 1.3 61.3 + - - +
6A VAL* 3.9 0.9 - - - +
7A VAL* 2.9 35.5 + - - +
31A VAL* 3.2 29.1 - - - +
32A LEU* 3.8 16.2 - - - +
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Residues in contact with MET 4 (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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2A ALA 3.1 4.3 + - - +
3A SER* 1.3 81.9 - - - +
5A ARG* 1.3 62.8 + - - +
7A VAL* 4.0 5.2 - - - +
8A LYS* 3.3 21.3 + - - +
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Residues in contact with ARG 5 (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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2A ALA* 3.1 11.4 + - - +
4A MET* 1.3 80.1 - - - +
6A VAL* 1.3 58.3 + - - +
8A LYS* 3.2 9.8 + - - +
9A GLU* 3.0 42.1 + - - +
60A TYR* 3.7 26.5 - - + +
61A PRO* 3.4 37.2 - - - +
62A PHE* 4.8 9.1 - - - -
96A PRO 5.2 3.0 + - - -
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Residues in contact with VAL 6 (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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2A ALA* 2.9 20.7 + - + +
3A SER 3.9 3.1 - - - +
5A ARG* 1.3 76.8 - - - +
7A VAL* 1.3 52.9 + - - +
9A GLU* 3.1 7.5 + - - +
10A LEU 2.7 32.1 + - - -
31A VAL 3.2 25.8 - - - +
32A LEU* 3.8 16.8 - - + -
34A TRP* 3.3 32.3 - - + +
56A PHE* 3.8 20.0 - - + -
60A TYR* 3.7 26.9 - - + -
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Residues in contact with VAL 7 (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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3A SER 2.9 21.1 + - - +
4A MET* 4.0 6.3 - - - +
6A VAL* 1.3 74.1 - - - +
8A LYS* 1.3 59.2 + - - +
10A LEU* 3.7 13.3 - - + +
11A GLU* 2.9 43.9 + - + +
31A VAL* 3.9 31.0 - - + +
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Residues in contact with LYS 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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4A MET 3.3 14.3 + - - +
5A ARG* 3.2 12.5 + - - +
7A VAL* 1.3 78.3 - - - +
9A GLU* 1.3 62.5 + - + +
11A GLU* 3.5 13.1 - - - +
12A ASP* 3.1 40.9 + - - +
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Residues in contact with GLU 9 (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 ARG* 3.0 27.7 + - + +
6A VAL* 3.4 9.9 - - - +
8A LYS* 1.3 75.3 - - + +
10A LEU* 1.3 54.8 + - - +
12A ASP* 3.3 7.7 + - - +
13A LEU* 3.0 31.9 + - + +
34A TRP* 3.9 10.3 - - + -
56A PHE* 5.4 0.2 - - - -
60A TYR* 2.4 35.9 + - - -
61A PRO* 5.6 0.2 - - - +
98A THR 5.0 0.2 - - - +
99A LYS* 3.9 26.4 - - - +
100A THR* 2.8 37.4 + - - -
101A CYS 4.6 1.0 + - - -
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Residues in contact with LEU 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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6A VAL 2.7 13.7 + - - +
7A VAL* 3.7 16.6 - - + +
9A GLU* 1.3 71.4 - - - +
11A GLU* 1.3 54.4 + - - +
13A LEU* 3.2 3.1 + - - +
14A GLN* 2.8 61.4 + - - +
24A LEU* 3.6 30.5 - - + -
26A SER* 3.4 35.2 - - - +
31A VAL* 5.3 1.1 - - + +
34A TRP* 3.1 43.2 - - + +
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Residues in contact with GLU 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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7A VAL* 2.9 27.0 + - + +
8A LYS* 3.5 17.1 - - - +
10A LEU* 1.3 74.5 - - - +
12A ASP* 1.3 69.2 + - - +
14A GLN* 3.5 12.1 + - - +
15A LYS* 3.2 59.8 + - - +
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Residues in contact with ASP 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 LYS* 3.1 32.6 + - - +
9A GLU* 3.6 6.2 - - - +
11A GLU* 1.3 82.4 - - - +
13A LEU* 1.3 57.2 + - - +
15A LYS* 3.4 9.7 + - - +
16A LYS* 2.9 32.9 + - - +
99A LYS* 5.7 4.2 + - - -
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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 GLU* 3.0 13.3 + - + +
10A LEU 3.2 4.2 + - - +
12A ASP* 1.3 76.2 - - + +
14A GLN* 1.3 56.7 + - - +
16A LYS 4.2 6.7 - - - +
17A PRO* 3.0 34.3 - - - +
18A PRO* 3.9 29.6 - - + -
21A LEU* 4.6 5.2 - - + -
24A LEU* 3.4 17.3 - - + +
34A TRP* 3.8 28.7 - - + -
100A THR* 4.5 2.2 - - - -
101A CYS* 4.1 36.6 - - + +
104A LEU* 3.8 20.0 - - + -
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Residues in contact with GLN 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 LEU* 2.8 45.7 + - + +
11A GLU* 4.0 11.0 - - - +
12A ASP 3.4 0.4 - - - -
13A LEU* 1.3 73.3 - - - +
15A LYS* 1.3 60.7 + - + +
17A PRO* 3.6 12.7 - - - +
24A LEU* 2.8 38.9 + - + +
25A SER* 3.8 10.5 - - - +
26A SER 4.8 0.2 - - - +
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Residues in contact with LYS 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 GLU* 3.2 51.9 + - - +
12A ASP* 3.9 8.5 + - - +
14A GLN* 1.3 79.6 - - + +
16A LYS* 1.3 83.9 + - + +
17A PRO* 3.2 9.0 - - - +
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Residues in contact with LYS 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 ASP 2.9 15.4 + - - +
13A LEU* 3.2 12.4 - - - +
15A LYS* 1.3 95.9 + - + +
17A PRO* 1.3 63.9 - - - +
18A PRO* 3.7 3.6 - - - +
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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