Contacts of the strand formed by residues 8 - 18 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 4.4 9.2 - - + -
5C LYS* 3.4 38.8 - - - +
7C ASP* 1.3 78.4 - - - +
9C LYS* 1.3 64.3 + - - +
30C LEU* 3.2 6.4 - - - +
31C GLY 2.9 33.2 + - - +
33C PRO* 3.5 20.0 - - + -
68C PHE* 4.5 3.4 - - + -
109C LEU* 3.6 25.1 - - + -
111C GLY 4.7 1.1 - - - +
112C ASP* 3.5 20.2 - - - +
114C TYR* 3.4 42.6 - - + +
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Residues in contact with LYS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASP 5.8 0.4 - - - +
8C MET* 1.3 75.9 - - - +
10C ILE* 1.3 69.7 + - - +
29C GLY 3.4 9.9 - - - +
30C LEU* 5.1 4.3 - - + -
112C ASP* 2.9 39.5 + - - +
113C CYS* 3.8 16.6 - - + -
114C TYR* 2.9 27.4 + - - -
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Residues in contact with ILE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LYS* 1.3 81.2 - - - +
11C LYS* 1.3 66.6 + - - +
12C LEU* 4.3 11.2 - - + -
28C VAL* 3.2 7.8 - - - +
29C GLY* 2.7 41.1 + - - +
30C LEU* 4.2 17.5 - - - +
38C GLN* 3.3 26.9 - - + +
39C SER 4.6 0.4 - - - +
40C MET* 4.1 11.7 - - + -
68C PHE* 3.5 28.5 - - + -
113C CYS* 3.9 3.4 - - - -
114C TYR* 3.6 4.5 - - + -
116C TYR* 3.7 34.3 - - + +
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Residues in contact with LYS 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 1.3 75.4 - - - +
12C LEU* 1.3 66.0 + - - +
27C GLY 3.5 9.2 - - - +
28C VAL* 4.7 10.5 - - + -
110C ASP* 5.3 5.5 + - - +
113C CYS* 3.8 16.8 - - - +
114C TYR 2.9 6.2 + - - +
115C ILE* 3.2 30.5 - - + +
116C TYR* 2.9 23.6 + - - +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.3 5.2 - - + -
11C LYS* 1.3 77.8 - - - +
13C ARG* 1.3 68.4 + - - +
14C MET 4.3 2.2 - - - +
25C ILE 4.3 2.2 - - - +
26C GLU* 3.5 7.6 - - - +
27C GLY* 3.0 48.1 + - - +
40C MET* 3.9 30.1 - - + -
42C LEU* 4.0 4.0 - - + -
61C PHE* 3.7 33.7 - - + +
115C ILE* 5.8 0.2 - - - -
116C TYR* 3.4 45.1 - - + -
118C ILE* 4.5 2.9 - - + -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 1.3 77.8 - - - +
14C MET* 1.3 66.1 + - - +
15C GLU* 2.9 31.9 + - + +
24C ALA* 3.5 21.0 - - - +
25C ILE 3.5 9.2 - - - +
26C GLU* 2.7 45.6 + - + +
45C LYS* 4.6 6.7 - - - +
46C GLU* 3.1 27.1 + - - -
116C TYR 3.2 9.5 + - - +
117C GLU* 3.9 3.4 - - - +
118C ILE* 2.9 26.4 + - - +
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Residues in contact with MET 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.3 1.0 - - - +
13C ARG* 1.3 74.3 - - - +
15C GLU* 1.3 74.1 + - - +
23C PHE* 3.6 26.7 - - + -
24C ALA* 3.2 7.1 - - - +
25C ILE* 2.7 40.5 + - + +
57C LEU* 4.1 8.3 - - + +
60C VAL* 3.8 21.3 - - + -
61C PHE* 3.5 40.4 - - + -
118C ILE* 3.4 33.4 - - + -
120C PHE* 3.9 20.2 - - + -
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 2.9 45.3 + - + +
14C MET* 1.3 77.6 - - - +
16C GLY* 1.3 59.7 + - - +
23C PHE 3.8 4.5 - - - +
24C ALA* 4.3 4.0 - - + -
46C GLU* 5.9 0.7 - - - +
118C ILE 3.0 8.2 + - - +
119C ARG* 3.3 28.7 + - - +
120C PHE 3.1 19.4 + - - -
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C MET* 4.3 1.0 - - - +
15C GLU* 1.3 77.8 - - - +
17C ALA* 1.3 62.0 + - - +
22C PRO* 3.2 7.4 - - - +
23C PHE* 2.9 43.4 + - - +
119C ARG* 3.6 14.1 + - - +
120C PHE* 2.9 14.6 - - - -
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 6.1 1.1 - - + +
119A ARG* 5.6 4.3 - - + -
16C GLY* 1.3 75.5 - - - +
18C VAL* 1.3 65.4 + - - +
19C ASN 4.3 0.2 - - - -
20C GLY* 4.3 9.0 - - - +
21C HIS 3.3 20.4 - - - +
22C PRO* 3.9 9.0 - - + -
23C PHE* 3.4 4.2 - - - -
119C ARG* 3.9 4.7 - - - +
120C PHE 2.9 5.8 + - - +
121C ASP* 3.3 16.1 - - - +
122C GLY 2.9 24.0 + - - +
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ALA* 1.3 79.1 - - - +
19C ASN* 1.3 84.7 + - - +
20C GLY 3.1 0.2 - - - -
21C HIS* 3.0 24.6 + - - +
23C PHE* 3.8 4.9 - - + -
51C PRO* 5.9 1.0 - - - +
52C PHE* 3.7 54.2 - - + -
56C ILE* 4.0 7.6 - - + -
120C PHE* 3.9 19.3 - - + -
122C GLY* 3.4 5.4 - - - +
125C PHE* 4.2 17.0 - - + -
132C MET* 4.3 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