Contacts of the helix formed by residues 2 - 11 (chain A) in PDB entry 2GWU
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 ASP 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 70.4 - - - +
3A ILE* 1.3 65.3 + - - +
4A GLU* 3.1 3.6 - - + +
5A ALA* 3.2 30.3 + - + +
6A TYR 3.3 6.6 + - - -
56A PHE* 2.7 44.7 - - - +
60A VAL* 4.5 2.9 - - - +
61A ARG* 5.2 7.1 + - - +
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Residues in contact with ILE 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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1A MET* 3.0 28.8 + - + +
2A ASP* 1.3 72.1 - - - +
4A GLU* 1.3 70.6 + - + +
6A TYR* 3.1 6.5 + - - +
7A LEU* 2.8 39.0 + - + +
16A ARG* 3.8 35.7 - - - +
78A ALA* 5.5 1.8 - - + -
81A THR* 3.3 35.0 - - + +
82A ILE* 5.0 7.2 - - + -
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Residues in contact with GLU 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 ASP* 3.1 2.7 - - + -
3A ILE* 1.3 87.5 - - + +
5A ALA* 1.3 63.8 + - - +
7A LEU* 3.2 3.5 + - - +
8A GLU* 2.9 22.4 + - + +
14A LYS* 3.1 50.3 + - + +
16A ARG* 4.1 21.1 - - - +
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Residues in contact with ALA 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 ASP* 3.2 34.6 + - + +
4A GLU* 1.3 79.5 - - - +
6A TYR* 1.3 62.5 + - - +
8A GLU* 3.2 13.2 + - - +
9A ARG* 3.0 25.3 + - - +
60A VAL* 3.7 13.9 - - + -
61A ARG* 4.7 12.7 + - - +
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Residues in contact with TYR 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 ASP 3.3 2.4 + - - +
3A ILE* 3.1 10.0 + - - +
5A ALA* 1.3 77.0 - - - +
7A LEU* 1.3 80.9 + - + +
9A ARG* 3.1 5.5 + - + +
10A ILE* 3.0 46.8 + - + +
27A ILE* 4.1 14.2 - - + +
31A GLN* 2.7 37.2 + - - +
35A VAL* 5.6 1.3 - - + -
56A PHE* 3.8 19.7 - + + -
60A VAL* 4.0 16.8 - - + +
74A LEU* 3.3 39.7 - - + +
75A LEU* 4.1 9.9 - - + +
78A ALA* 4.3 21.1 - - + -
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Residues in contact with LEU 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 ILE* 2.8 39.8 + - + +
4A GLU* 3.7 6.1 - - - +
6A TYR* 1.3 90.8 - - + +
8A GLU* 1.3 56.1 + - - +
10A ILE* 2.7 14.3 - - + +
11A GLY 2.8 2.3 + - - -
12A TYR* 2.7 83.6 + - + +
13A LYS 4.9 0.9 - - - +
14A LYS* 5.8 0.9 - - - +
15A SER 4.9 0.2 - - - +
16A ARG* 4.2 17.0 - - - +
17A ASN* 4.6 9.2 - - - +
27A ILE* 5.0 13.5 - - + -
78A ALA* 6.0 1.6 - - + -
82A ILE* 5.3 10.3 - - + -
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Residues in contact with GLU 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 GLU* 2.9 14.4 + - + +
5A ALA* 3.5 12.1 - - - +
7A LEU* 1.3 77.8 - - - +
9A ARG* 1.3 65.1 + - - +
11A GLY* 3.0 13.8 + - - +
12A TYR 3.9 6.0 + - - +
14A LYS* 5.2 19.9 - - + -
61A ARG* 4.1 18.2 + - - -
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Residues in contact with ARG 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 ALA 3.0 8.4 + - - +
6A TYR* 3.1 9.8 + - + +
8A GLU* 1.3 80.9 - - + +
10A ILE* 1.3 61.9 + - - +
11A GLY* 4.5 0.3 - - - -
34A ALA* 3.5 22.1 + - - +
35A VAL* 3.5 31.1 - - + +
36A PRO* 5.2 2.0 - - - +
59A VAL 3.6 11.3 + - - +
60A VAL* 2.9 51.6 + - + +
61A ARG* 5.1 8.7 - - - +
63A ASN* 4.3 22.4 - - - +
64A ARG 4.6 2.8 + - - -
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Residues in contact with ILE 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 TYR* 3.0 38.3 + - + +
7A LEU* 2.7 42.2 - - + +
9A ARG* 1.3 78.0 - - - +
11A GLY* 1.4 54.4 + - - +
12A TYR* 3.6 14.6 - - + +
27A ILE* 3.2 21.5 - - + +
30A HIS* 2.9 43.1 - - + +
31A GLN* 3.1 34.5 - - - +
34A ALA* 3.6 10.0 - - - +
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Residues in contact with GLY 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 LEU 2.8 3.4 + - - -
8A GLU* 3.0 12.5 + - - -
9A ARG 4.4 0.9 - - - -
10A ILE* 1.4 78.9 - - - +
12A TYR* 1.3 61.9 + - - +
13A LYS* 3.7 5.4 + - - +
30A HIS* 4.5 10.9 + - - -
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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