Contacts of the strand formed by residues 21 - 32 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ALA* 3.4 2.0 - - - -
18B VAL* 3.2 29.4 + - - +
19B ASN* 3.7 17.2 + - + -
20B GLY* 1.3 80.6 + - - +
22B PRO* 1.3 71.6 - - + +
23B PHE* 3.9 4.5 - - - +
51B PRO* 5.4 14.6 - - + -
52B PHE* 5.4 1.9 - - - -
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Residues in contact with PRO 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY 3.2 12.6 - - - +
17B ALA* 3.9 5.8 - - + -
20B GLY 3.8 8.0 - - - +
21B HIS* 1.3 91.4 - - + +
23B PHE* 1.3 63.4 + - - +
46B GLU* 5.9 0.2 - - - -
47B GLY* 3.6 14.7 + - - +
119B ARG* 6.0 1.1 - - - +
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MET* 3.6 28.7 - - + -
15B GLU* 3.8 1.4 - - - +
16B GLY* 2.8 38.2 + - - +
17B ALA* 3.4 31.6 - - - -
18B VAL* 4.0 2.2 - - + -
21B HIS 3.9 4.7 - - - -
22B PRO* 1.3 78.6 - - - +
24B ALA* 1.3 66.0 + - - +
25B ILE* 4.0 20.6 - - + -
46B GLU* 3.3 22.9 - - - +
47B GLY* 4.1 2.2 - - - +
50B LEU* 3.8 20.4 - - + -
52B PHE* 3.7 20.2 - + - -
57B LEU* 3.6 26.2 - - + -
120B PHE* 4.1 8.1 - + - -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.5 32.3 - - - +
14B MET 3.2 11.0 - - - +
15B GLU* 4.2 4.7 - - + -
23B PHE* 1.3 78.6 - - - +
25B ILE* 1.3 65.9 + - - +
45B LYS* 2.9 10.1 + - + -
46B GLU* 2.9 48.0 + - + +
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.2 0.9 - - - +
13B ARG* 3.4 2.3 - - - +
14B MET* 2.6 41.6 + - + +
23B PHE* 4.0 17.9 - - + -
24B ALA* 1.3 79.1 - - - +
26B GLU* 1.3 74.7 + - - +
42B LEU* 4.0 6.7 - - + -
43B LYS 3.6 12.8 - - - +
44B VAL* 4.3 13.5 - - + -
45B LYS* 4.3 0.9 - - - +
50B LEU* 4.1 11.7 - - + -
54B TYR* 3.9 18.8 - - + +
57B LEU* 3.7 30.1 - - + -
61B PHE* 3.7 26.0 - - + -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 3.4 14.8 - - - +
13B ARG* 2.9 44.2 + - + +
25B ILE* 1.3 81.9 - - - +
27B GLY* 1.3 58.2 + - - +
42B LEU* 3.4 2.1 - - - -
43B LYS* 2.9 33.0 + - - +
45B LYS* 3.8 30.1 - - + +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE 5.3 0.2 - - - -
11B LYS* 3.5 1.3 - - - +
12B LEU* 3.0 49.4 + - - +
26B GLU* 1.3 75.9 - - - +
28B VAL* 1.3 68.8 + - - +
40B MET* 5.6 0.2 - - - -
41B ASP 3.2 11.9 - - - -
42B LEU* 4.0 7.2 - - - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.2 9.4 - - - +
11B LYS* 4.3 16.6 - - + -
27B GLY* 1.3 78.8 - - - +
29B GLY* 1.3 60.1 + - - +
40B MET* 3.3 3.9 - - - -
41B ASP* 2.9 41.3 + - + +
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 3.3 9.7 - - - +
10B ILE* 2.7 40.3 + - - +
28B VAL* 1.3 76.6 - - - +
30B LEU* 1.3 65.2 + - - +
39B SER 3.2 13.9 - - - -
40B MET* 3.8 5.6 - - - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP* 6.5 1.3 - - + -
8B MET 3.2 13.5 - - - +
9B LYS* 4.0 9.6 - - + +
10B ILE* 4.3 6.6 - - - +
29B GLY* 1.3 79.2 - - - +
31B GLY* 1.3 60.6 + - - +
38B GLN* 3.4 1.6 - - - +
39B SER* 2.9 50.6 + - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP* 3.6 4.3 - - - +
8B MET* 2.8 33.5 + - - -
30B LEU* 1.3 78.0 - - - +
32B LYS* 1.3 66.5 + - - +
33B PRO* 3.6 1.2 - - - +
37B LYS 3.2 12.6 - - - -
38B GLN* 3.8 2.7 - - - -
68B PHE* 3.5 16.0 - - - -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PRO* 3.3 13.0 - - - +
7B ASP* 3.4 30.7 + - - +
31B GLY* 1.3 75.1 - - - -
33B PRO* 1.3 68.2 - - - +
34B PHE 3.3 1.8 - - - +
35B GLU* 3.1 42.0 + - + +
36B GLY 3.0 18.0 + - - -
37B LYS* 2.8 20.9 + - + +
68B PHE* 4.0 1.1 - - - -
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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