Contacts of the strand formed by residues 21 - 32 (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 HIS 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ALA* 3.3 2.4 - - - -
18C VAL* 3.0 29.8 + - - +
19C ASN* 3.4 18.1 + - + +
20C GLY* 1.3 79.0 - - - +
22C PRO* 1.3 71.4 - - + +
23C PHE* 3.9 4.5 - - - +
51C PRO* 5.2 15.9 - - + +
52C PHE* 5.4 1.4 - - - -
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Residues in contact with PRO 22 (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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117A GLU* 6.1 0.9 - - - +
16C GLY 3.2 12.8 - - - +
17C ALA* 3.9 5.8 - - + -
20C GLY 3.8 6.7 - - - +
21C HIS* 1.3 89.9 - - + +
23C PHE* 1.3 65.5 + - - +
47C GLY* 3.6 15.9 - - - +
119C ARG* 6.1 0.4 - - - +
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Residues in contact with PHE 23 (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* 3.6 26.9 - - + -
15C GLU* 3.8 1.4 - - - +
16C GLY* 2.9 37.0 + - - +
17C ALA* 3.4 31.6 - - - -
18C VAL* 3.8 3.1 - - + -
21C HIS 3.9 4.3 - - - -
22C PRO* 1.3 78.5 - - - +
24C ALA* 1.3 66.2 + - - +
25C ILE* 4.0 22.2 - - + -
46C GLU* 3.3 22.2 - - - +
47C GLY* 4.1 2.2 - - - +
50C LEU* 3.7 20.9 - - + -
52C PHE* 3.7 20.0 - + + -
57C LEU* 3.7 24.0 - - + -
120C PHE* 4.0 9.9 - + - -
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Residues in contact with ALA 24 (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* 3.5 31.4 - - - +
14C MET 3.2 11.0 - - - +
15C GLU* 4.3 4.7 - - + -
23C PHE* 1.3 78.0 - - - +
25C ILE* 1.3 62.5 + - - +
44C VAL 3.7 0.2 - - - -
45C LYS* 2.8 30.2 + - + -
46C GLU* 3.0 31.6 + - + +
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Residues in contact with ILE 25 (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* 3.5 2.3 - - - +
14C MET* 2.7 40.8 + - + +
23C PHE* 4.0 16.4 - - + -
24C ALA* 1.3 79.5 - - - +
26C GLU* 1.3 73.4 + - - +
42C LEU* 4.1 5.6 - - + -
43C LYS 3.3 15.5 - - - +
44C VAL* 3.9 13.5 - - + -
45C LYS 4.3 0.4 - - - +
50C LEU* 4.1 5.6 - - + -
54C TYR* 3.8 24.7 - - + +
57C LEU* 3.7 30.3 - - + -
61C PHE* 3.6 28.3 - - + -
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Residues in contact with GLU 26 (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* 3.5 10.8 - - - +
13C ARG* 2.7 44.4 + - + +
25C ILE* 1.3 82.3 - - - +
27C GLY* 1.3 59.5 + - - +
41C ASP 4.1 0.3 - - - +
42C LEU* 3.4 1.7 - - - -
43C LYS* 2.8 34.6 + - + +
45C LYS* 3.5 32.6 - - + +
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Residues in contact with GLY 27 (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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11C LYS* 3.5 2.3 - - - +
12C LEU* 3.0 42.2 + - - +
26C GLU* 1.3 77.2 - - - +
28C VAL* 1.3 70.4 + - - +
40C MET* 5.7 0.4 - - - -
41C ASP 3.2 10.5 - - - -
42C LEU* 3.9 14.4 - - - -
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Residues in contact with VAL 28 (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* 3.2 11.4 - - - +
11C LYS* 4.7 11.9 - - + -
27C GLY* 1.3 80.1 - - - +
29C GLY* 1.3 58.9 + - - +
40C MET* 3.3 3.8 - - - +
41C ASP* 2.8 43.3 + - + +
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Residues in contact with GLY 29 (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* 3.4 7.1 - - - +
10C ILE* 2.7 42.0 + - - +
28C VAL* 1.3 75.7 - - - +
30C LEU* 1.3 64.8 + - - +
39C SER 3.1 13.9 - - - -
40C MET* 3.7 6.3 - - - -
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Residues in contact with LEU 30 (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* 6.1 0.7 - - - +
8C MET 3.2 14.4 - - - +
9C LYS* 4.2 5.8 - - + +
10C ILE* 4.2 7.0 - - - +
29C GLY* 1.3 77.7 - - - +
31C GLY* 1.3 60.7 + - - +
38C GLN* 3.3 2.4 - - - +
39C SER* 2.8 54.9 + - - +
40C MET* 5.8 0.2 - - - -
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Residues in contact with GLY 31 (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* 3.7 5.5 - - - +
8C MET 2.9 32.0 + - - -
30C LEU* 1.3 78.7 - - - +
32C LYS* 1.3 66.0 + - - +
33C PRO* 3.7 1.0 - - - +
37C LYS 3.2 12.3 - - - -
38C GLN* 3.7 2.0 - - - -
68C PHE* 3.6 15.8 - - - -
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Residues in contact with LYS 32 (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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6C PRO* 3.2 17.7 - - + +
7C ASP* 3.1 31.2 - - - +
31C GLY* 1.3 74.7 - - - +
33C PRO* 1.3 69.5 - - - +
34C PHE 3.2 1.8 - - - -
35C GLU* 3.0 48.1 + - + +
36C GLY 2.9 18.5 + - - -
37C LYS* 2.6 19.0 + - + +
68C PHE* 3.9 0.4 - - - -
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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