Contacts of the strand formed by residues 4 - 12 (chain E) in PDB entry 4XH9
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 ILE 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 ALA* 1.3 75.0 - - - +
5E ARG* 1.3 57.5 + - - +
6E LYS* 4.1 14.1 - - - -
51E LYS* 4.1 40.2 - - + +
52E GLN 3.5 22.9 + - - +
53E VAL* 3.4 9.5 - - + +
54E GLU* 2.7 34.2 + - - +
179E LEU* 4.0 22.7 - - + -
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Residues in contact with ARG 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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291D GLN* 2.8 35.1 + - - +
294D LEU* 3.6 49.5 + - - +
295D GLU* 4.1 20.4 + - - +
301D LYS 5.3 1.6 - - - -
3E ALA* 3.7 31.1 + - + +
4E ILE* 1.3 77.3 - - - +
6E LYS* 1.3 74.3 + - - +
54E GLU* 3.2 33.0 + - + +
78E ASP* 4.1 3.1 - - - +
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Residues in contact with LYS 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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4E ILE* 4.1 17.5 - - + -
5E ARG* 1.3 82.5 + - - +
7E LYS* 1.3 61.4 + - - +
53E VAL* 3.8 18.2 - - + -
54E GLU 3.0 7.7 + - - +
55E LEU* 3.4 18.2 - - + +
56E ALA* 2.8 28.6 + - - +
78E ASP* 3.3 25.1 + - + +
178E ALA* 3.7 36.8 + - + +
179E LEU* 4.2 13.7 - - + +
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Residues in contact with LYS 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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303D ASP* 6.0 1.3 - - - +
305D TRP* 4.4 9.1 - - - +
6E LYS* 1.3 72.5 - - - +
8E LEU* 1.3 62.5 + - - +
9E VAL* 3.6 13.7 - - + -
56E ALA* 3.7 6.7 - - + -
58E TRP* 3.6 49.5 - - + +
73E SER 3.0 27.8 + - - -
75E PRO 2.8 21.8 + - - +
76E ASP* 3.6 28.9 - - + +
77E THR* 3.7 4.8 - - - +
78E ASP* 2.7 35.5 + - - +
79E VAL* 3.2 10.0 + - - +
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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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6E LYS 3.9 0.4 + - - -
7E LYS* 1.3 75.8 - - - +
9E VAL* 1.3 70.4 + - - +
10E ILE* 4.0 6.5 - - + +
22E LEU* 4.6 4.9 - - + -
55E LEU* 3.9 22.4 - - + -
56E ALA 2.7 16.0 + - - +
57E LEU* 4.0 14.1 - - + -
58E TRP* 2.8 36.5 + - - +
79E VAL* 3.4 17.0 - - + +
81E LEU* 4.0 32.1 - - + -
171E PHE* 4.0 7.6 - - + -
174E ALA* 3.6 31.6 - - + -
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Residues in contact with VAL 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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7E LYS* 3.6 11.7 - - - -
8E LEU* 1.3 79.8 - - - +
10E ILE* 1.3 62.0 + - - +
11E VAL* 3.9 13.6 + - + -
58E TRP* 3.6 10.3 - - + +
60E THR* 3.7 25.8 - - + -
73E SER* 3.4 18.8 - - - +
74E TYR* 4.1 13.0 - - + -
77E THR* 3.3 24.0 - - + +
79E VAL 3.2 6.3 + - - -
80E ILE* 3.4 17.6 - - + +
81E LEU 2.8 24.6 + - - -
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Residues in contact with ILE 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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8E LEU* 4.0 6.6 - - + +
9E VAL* 1.3 72.5 - - - +
11E VAL* 1.3 56.6 + - - +
18E LYS* 3.5 33.9 - - + +
21E LEU* 4.2 6.5 - - + -
22E LEU* 3.7 15.7 - - + -
58E TRP 3.1 16.4 + - - +
59E ASP* 3.6 24.9 - - - +
60E THR* 2.6 33.3 + - - +
81E LEU* 3.3 32.1 - - + +
83E CYS* 3.4 27.4 - - - -
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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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9E VAL* 3.9 8.7 - - + -
10E ILE* 1.3 80.2 - - - +
12E GLY* 1.3 55.2 + - - +
18E LYS* 4.0 4.7 - - - -
60E THR* 3.9 8.1 - - + +
74E TYR* 3.9 35.9 - - + +
80E ILE* 3.7 26.0 - - + -
81E LEU 2.8 9.3 + - - +
82E MET* 3.6 27.1 - - - -
83E CYS* 2.7 35.2 + - - +
99E TRP* 4.6 10.8 - - + -
103E VAL* 4.1 7.2 - - + -
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Residues in contact with GLY 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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11E VAL* 1.3 77.8 - - - +
13E ASP* 1.3 63.2 + - - -
14E GLY 3.7 0.3 + - - -
18E LYS* 2.9 26.2 + - - +
64E GLU* 3.9 0.9 - - - +
83E CYS 3.6 13.9 - - - -
95E ILE* 5.0 0.7 - - - -
99E TRP* 3.4 35.6 - - - -
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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