Contacts of the helix formed by residues 4 - 13 (chain E) in PDB entry 4GDK
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 4 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E ASP* 1.3 84.1 - - - +
5E LYS* 1.3 61.3 + - - +
7E VAL* 3.4 10.5 + - - +
8E LEU* 3.3 23.6 + - - +
253E TRP* 3.0 16.6 + - - -
257E HIS* 3.3 29.2 + - - +
14F LYS* 3.0 34.5 + - - +
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Residues in contact with LYS 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP* 3.3 17.3 + - - +
4E ASP* 1.3 75.5 - - - +
6E ASP* 1.3 67.3 + - - +
7E VAL 3.1 2.0 - - - -
8E LEU* 3.1 14.7 + - + +
9E ARG* 3.0 40.3 + - + +
162E PHE* 4.1 24.7 - - + -
163E ASP* 4.5 9.6 + - - -
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Residues in contact with ASP 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP* 3.0 32.3 + - - +
4E ASP 3.4 0.4 - - - -
5E LYS* 1.3 79.9 - - - +
7E VAL* 1.3 57.8 + - + +
9E ARG* 3.5 15.3 + - - +
10E ASP* 3.1 37.0 + - - +
22F ARG* 6.2 2.5 - - - +
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Residues in contact with VAL 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP 3.5 16.6 - - - +
4E ASP* 3.4 11.2 + - - +
5E LYS 3.1 0.6 - - - -
6E ASP* 1.3 75.7 - - + +
8E LEU* 1.3 63.1 + - - +
10E ASP* 3.4 2.5 + - - +
11E VAL* 3.0 24.3 + - - +
253E TRP* 4.1 23.1 - - + -
257E HIS* 4.5 6.3 - - + -
258E LEU* 3.6 29.4 - - + -
14F LYS* 5.6 2.9 - - + -
17F ILE* 4.4 2.7 - - + -
18F SER* 3.7 24.5 - - - +
21F LEU* 3.8 17.5 - - + -
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Residues in contact with LEU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ASP* 3.3 13.7 + - + +
5E LYS* 3.1 19.2 + - + +
7E VAL* 1.3 78.9 - - - +
9E ARG* 1.3 57.6 + - - +
11E VAL* 3.5 2.6 + - - +
12E TRP* 3.0 30.0 + - - +
162E PHE* 3.5 18.3 - - + -
166E TRP* 3.6 47.3 + - + -
256E GLU 4.0 1.6 - - - +
257E HIS* 3.5 45.5 - - + +
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Residues in contact with ARG 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 3.0 31.5 + - - +
6E ASP* 3.9 15.7 - - - +
8E LEU* 1.3 77.3 - - - +
10E ASP* 1.3 60.5 + - - +
12E TRP 3.3 0.2 + - - -
13E PHE* 2.9 62.8 + - + +
162E PHE* 3.6 41.6 - - + +
163E ASP* 4.2 11.9 + - - -
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Residues in contact with ASP 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ASP* 3.1 25.2 + - - +
7E VAL* 3.9 3.7 - - - +
8E LEU 3.4 0.2 - - - -
9E ARG* 1.3 75.6 - - - +
11E VAL* 1.3 64.2 + - - +
13E PHE* 3.7 2.9 + - - -
14E GLY 3.4 9.5 + - - -
18F SER* 4.9 1.9 - - - +
21F LEU* 4.1 24.0 - - + +
22F ARG* 3.9 23.8 + - - +
24F ARG* 2.8 21.7 + - - -
25F ASP* 4.1 18.7 - - - +
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Residues in contact with VAL 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL 3.0 21.4 + - - +
8E LEU* 3.9 3.8 - - - +
10E ASP* 1.3 76.2 - - - +
12E TRP* 1.3 64.0 + - - +
14E GLY* 3.4 10.7 + - - -
41E ARG* 4.9 1.2 - - - +
42E VAL* 3.4 14.0 - - + +
241E HIS* 3.3 40.4 - - + +
257E HIS 4.1 7.6 - - - +
258E LEU* 3.8 31.4 - - + -
259E SER 4.2 9.9 - - - +
21F LEU* 4.0 15.7 - - + -
24F ARG* 4.3 6.5 + - - +
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Residues in contact with TRP 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU 3.0 18.7 + - - +
9E ARG 3.6 2.5 - - - +
11E VAL* 1.3 79.6 - - - +
13E PHE* 1.3 86.9 + + - +
14E GLY 3.4 3.8 + - - +
15E ARG* 3.9 7.1 + - - -
42E VAL* 3.7 30.3 - - + +
156E GLY 3.3 26.7 - - - -
157E LEU* 3.8 15.3 - - + -
160E ASP* 2.9 22.8 + - - +
161E ARG 3.8 7.9 - - - -
162E PHE* 3.5 31.8 - + + +
165E PHE* 3.4 40.8 - + + -
166E TRP* 4.4 10.1 - - - +
261E PRO* 3.9 25.4 - - + -
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Residues in contact with PHE 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ARG* 2.9 59.6 + - + +
10E ASP* 4.0 3.6 - - - +
12E TRP* 1.3 100.7 - + - +
14E GLY* 1.3 64.6 + - - +
15E ARG* 3.4 18.8 + - - +
160E ASP* 3.9 20.2 - - - -
162E PHE* 4.0 20.6 - + + -
25F ASP* 5.4 1.5 - - - +
29F ARG* 2.8 41.9 + - - +
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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