Contacts of the strand formed by residues 8 - 18 (chain E) in PDB entry 6NQN
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 MET 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E VAL 4.3 13.5 - - - +
4E ILE* 4.4 1.3 - - - -
5E LYS* 3.4 27.1 - - - +
7E ASP* 1.3 82.4 - - - +
9E LYS* 1.3 66.8 + - - +
30E LEU* 3.3 5.2 - - - +
31E GLY 2.9 33.0 + - - +
33E PRO* 3.6 26.2 - - + -
68E PHE* 4.6 3.1 - - + -
109E LEU* 3.7 22.7 - - + -
111E GLY 4.7 0.4 - - - +
112E ASP* 3.6 21.8 - - - +
114E TYR* 3.5 40.8 - - + +
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Residues in contact with LYS 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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8E MET* 1.3 78.3 - - - +
10E ILE* 1.3 64.3 + - - +
29E GLY 3.4 9.2 - - - +
30E LEU* 4.8 7.0 - - + -
112E ASP* 2.9 41.5 + - - +
113E CYS* 3.8 14.8 - - - -
114E TYR* 2.7 33.4 + - - -
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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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9E LYS* 1.3 81.1 - - - +
11E LYS* 1.3 66.3 + - - +
12E LEU* 4.4 3.4 - - + -
28E VAL* 3.3 8.0 - - - +
29E GLY* 2.6 41.0 + - - +
30E LEU* 4.1 18.8 - - - +
38E GLN* 3.3 30.1 - - + +
39E SER 4.5 0.9 - - - +
40E MET* 4.1 15.3 - - + -
68E PHE* 3.6 26.7 - - + -
113E CYS* 3.8 3.5 - - - -
114E TYR* 3.6 5.2 - - + -
116E TYR* 3.6 35.2 - - + +
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Residues in contact with LYS 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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10E ILE* 1.3 76.2 - - - +
12E LEU* 1.3 67.8 + - - +
26E GLU* 5.4 8.7 + - - +
27E GLY 3.5 8.5 - - - +
28E VAL* 4.6 12.5 - - + +
113E CYS* 3.8 16.4 - - - -
114E TYR 2.9 7.0 + - - +
115E ILE* 3.2 21.3 - - + +
116E TYR* 2.9 23.6 + - - +
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Residues in contact with LEU 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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10E ILE* 4.4 4.5 - - + -
11E LYS* 1.3 81.3 + - - +
13E ARG* 1.3 69.4 + - - +
14E MET 4.3 1.6 - - - +
25E ILE 4.3 1.6 - - - +
26E GLU* 3.4 9.4 - - - +
27E GLY* 3.0 48.6 + - - +
40E MET* 3.7 35.2 - - + -
42E LEU* 4.0 2.9 - - + -
61E PHE* 3.7 34.5 - - + +
115E ILE* 5.7 0.4 - - - -
116E TYR* 3.5 40.4 - - + -
118E ILE* 4.7 3.6 - - + -
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Residues in contact with ARG 13 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LEU* 1.3 79.7 - - - +
14E MET* 1.3 65.8 + - - +
15E GLU* 2.9 39.6 + - + +
24E ALA* 3.7 15.3 - - - +
25E ILE 3.4 8.5 - - - +
26E GLU* 2.9 37.4 + - + +
45E LYS* 4.6 7.3 - - - +
46E GLU* 3.1 27.3 + - - -
116E TYR 3.2 8.6 + - - +
117E GLU* 4.0 3.2 - - + +
118E ILE* 3.1 26.8 + - - +
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Residues in contact with MET 14 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LEU* 4.3 1.0 - - + +
13E ARG* 1.3 72.8 - - - +
15E GLU* 1.3 72.4 + - - +
23E PHE* 3.5 32.5 - - + -
24E ALA* 3.2 6.2 - - - +
25E ILE* 2.7 42.3 + - + +
57E LEU* 4.1 9.2 - - + +
60E VAL* 3.6 34.3 - - + -
61E PHE* 3.6 39.9 - - + -
118E ILE* 3.5 19.1 - - + -
120E PHE* 3.9 16.2 - - + -
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Residues in contact with GLU 15 (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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13E ARG* 2.9 44.6 + - + +
14E MET* 1.3 79.4 - - - +
16E GLY* 1.3 59.7 + - - +
23E PHE 3.8 5.5 - - - +
24E ALA* 4.4 3.3 - - + +
46E GLU* 5.0 3.3 - - - +
118E ILE 3.1 9.5 + - - +
119E ARG* 3.3 26.8 + - - +
120E PHE 3.1 19.6 + - - -
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Residues in contact with GLY 16 (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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14E MET* 4.6 1.0 - - - +
15E GLU* 1.3 75.9 - - - +
17E ALA* 1.3 59.7 - - - +
22E PRO* 3.4 4.7 - - - +
23E PHE* 2.8 50.5 + - - +
119E ARG* 3.7 12.4 + - - +
120E PHE 2.9 15.3 - - - -
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Residues in contact with ALA 17 (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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104B THR* 6.1 1.1 - - + +
119B ARG* 5.6 3.8 - - + -
16E GLY* 1.3 76.7 - - - +
18E VAL* 1.3 67.6 + - - +
19E ASN 4.3 0.4 - - - -
20E GLY* 4.4 9.0 - - - +
21E HIS 3.3 24.7 - - - +
22E PRO* 4.1 4.0 - - + -
23E PHE* 3.4 4.0 - - - -
119E ARG* 4.0 4.5 - - - +
120E PHE 2.9 6.0 + - - +
121E ASP* 3.3 16.3 - - - +
122E GLY 2.9 23.7 + - - +
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Residues in contact with VAL 18 (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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17E ALA* 1.3 80.7 - - - +
19E ASN* 1.3 77.1 + - - +
20E GLY 3.2 0.9 + - - -
21E HIS* 3.3 23.2 + - - +
23E PHE* 4.0 2.4 - - + -
51E PRO* 5.9 1.0 - - - +
52E PHE* 3.7 51.2 - - + -
56E ILE* 4.0 7.9 - - + -
120E PHE* 3.9 23.3 - - + -
122E GLY* 3.4 6.1 - - - +
125E PHE* 4.1 23.1 - - + -
132E MET* 4.4 7.5 - - + +
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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