Contacts of the strand formed by residues 8 - 18 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D VAL 4.2 12.3 - - - +
4D ILE* 4.6 0.2 - - - -
5D LYS* 3.4 40.2 - - - +
7D ASP* 1.3 78.2 - - - +
9D LYS* 1.3 64.8 + - - +
30D LEU* 3.2 6.6 - - - +
31D GLY 2.9 35.4 + - - +
33D PRO* 3.7 17.3 - - + -
68D PHE* 4.5 2.7 - - + -
109D LEU* 3.6 24.0 - - + -
111D GLY 4.5 0.2 - - - +
112D ASP* 3.4 24.0 - - - +
114D TYR* 3.5 41.5 - - + +
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D MET* 1.3 75.1 - - - +
10D ILE* 1.3 66.5 + - - +
29D GLY 3.4 10.1 - - - +
30D LEU* 4.9 7.0 - - + -
112D ASP* 2.8 39.1 + - - +
113D CYS* 3.8 17.5 - - + -
114D TYR* 2.8 30.8 + - - -
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 1.3 80.6 - - - +
11D LYS* 1.3 67.0 + - - +
12D LEU* 4.4 3.4 - - + -
27D GLY 5.6 0.2 - - - +
28D VAL* 3.3 6.1 - - - +
29D GLY* 2.6 41.2 + - - +
30D LEU* 4.1 19.7 - - - +
38D GLN* 3.4 29.2 - - - +
39D SER 4.6 0.9 - - - +
40D MET* 4.1 14.4 - - + -
68D PHE* 3.5 28.5 - - + -
113D CYS* 3.8 4.2 - - - -
114D TYR* 3.4 5.6 - - + -
116D TYR* 3.6 35.7 - - + +
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Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 1.3 75.8 - - - +
12D LEU* 1.3 69.2 + - - +
26D GLU* 5.5 6.4 + - - +
27D GLY 3.5 9.0 - - - +
28D VAL* 4.2 19.3 - - + +
113D CYS* 3.8 14.8 - - - -
114D TYR 2.8 8.0 + - - +
115D ILE* 3.1 20.0 - - + +
116D TYR* 2.8 23.0 + - - +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.4 3.8 - - + -
11D LYS* 1.3 80.5 - - - +
13D ARG* 1.3 67.5 + - - +
14D MET 4.4 1.8 - - - +
25D ILE 4.3 1.6 - - - +
26D GLU* 3.4 7.7 - - - +
27D GLY* 3.0 48.0 + - - +
40D MET* 3.7 31.9 - - + -
42D LEU* 4.0 3.1 - - + -
61D PHE* 3.7 36.1 - - + +
115D ILE* 5.7 0.2 - - - -
116D TYR* 3.3 44.6 - - + -
118D ILE* 4.5 3.8 - - + -
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 1.3 76.7 - - - +
14D MET* 1.3 66.8 + - - +
15D GLU* 2.8 32.0 + - + +
24D ALA* 3.6 21.6 - - - +
25D ILE 3.4 8.7 - - - +
26D GLU* 2.8 45.8 + - + +
45D LYS* 4.5 6.9 - - - +
46D GLU* 3.2 27.7 + - - -
116D TYR 3.2 8.6 + - - +
117D GLU* 3.9 2.6 - - - +
118D ILE* 2.9 27.8 + - - +
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Residues in contact with MET 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.4 1.2 - - - +
13D ARG* 1.3 74.0 - - - +
15D GLU* 1.3 73.1 + - - +
23D PHE* 3.6 27.6 - - + -
24D ALA* 3.3 5.9 - - - +
25D ILE* 2.7 37.7 + - + +
57D LEU* 3.9 11.7 - - + +
60D VAL* 3.7 21.8 - - + -
61D PHE* 3.6 40.8 - - + -
118D ILE* 3.3 32.3 - - + -
120D PHE* 3.9 17.7 - - + -
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 2.8 47.0 + - + +
14D MET* 1.3 78.3 - - - +
16D GLY* 1.3 59.4 + - - +
23D PHE 3.8 4.9 - - - +
24D ALA* 4.3 4.7 - - + -
46D GLU* 5.5 0.9 - - - +
118D ILE 3.0 7.8 + - - +
119D ARG* 3.3 28.9 + - - +
120D PHE 3.2 18.2 + - - -
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Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D MET* 4.3 1.0 - - - +
15D GLU* 1.3 76.6 - - - +
17D ALA* 1.3 61.4 + - - +
22D PRO* 3.2 7.4 - - - +
23D PHE* 2.9 42.8 + - - +
119D ARG* 3.6 13.6 + - - +
120D PHE* 2.9 15.0 - - - -
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLY* 1.3 75.4 - - - +
18D VAL* 1.3 66.4 + - - +
20D GLY* 4.3 8.7 - - - +
21D HIS 3.3 24.2 - - - +
22D PRO* 3.9 5.6 - - + -
23D PHE* 3.4 3.6 - - - -
119D ARG* 3.9 5.1 - - - +
120D PHE 2.9 6.0 + - - +
121D ASP* 3.3 16.1 - - - +
122D GLY 2.9 24.9 + - - +
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Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ALA* 1.3 78.8 - - - +
19D ASN* 1.3 68.6 + - + +
20D GLY 3.1 0.4 - - - -
21D HIS* 2.9 28.9 + - - +
23D PHE* 3.8 5.8 - - + -
51D PRO* 5.9 1.0 - - - +
52D PHE* 3.6 52.3 - - + -
56D ILE* 4.0 8.1 - - + -
120D PHE* 3.9 19.7 - - + -
122D GLY* 3.4 4.7 - - - +
125D PHE* 4.3 21.3 - - + -
132D MET* 4.3 12.8 - - + +
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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