Contacts of the strand formed by residues 37 - 46 (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 LYS 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B GLY* 3.2 0.9 - - - -
32B LYS* 2.8 39.1 + - + +
35B GLU* 3.3 31.1 + - + +
36B GLY* 1.3 84.5 - - - +
38B GLN* 1.3 60.9 + - - +
68B PHE* 3.8 3.9 - - - -
211B GLU 3.4 5.8 - - - +
212B HIS* 3.8 36.8 + - + +
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Residues in contact with GLN 38 (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* 3.4 24.1 - - + +
30B LEU 3.4 12.1 - - - +
31B GLY* 3.8 5.2 - - - -
37B LYS* 1.3 77.8 - - - +
39B SER* 1.3 62.1 + - - +
40B MET* 3.7 5.7 - - - +
63B KZ4 3.7 28.6 - - - +
65B ASN* 4.2 5.2 + - - +
68B PHE* 3.6 32.3 - - + +
116B TYR* 4.3 4.8 + - - -
210B HIS* 3.3 7.2 + - - +
211B GLU* 2.9 63.8 + - + +
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.6 1.7 - - - +
29B GLY* 3.2 1.9 - - - -
30B LEU* 2.9 50.9 + - - +
38B GLN* 1.3 77.6 - - - +
40B MET* 1.3 65.4 + - - +
63B KZ4 6.1 0.2 - - - -
208B ASN* 5.0 4.4 + - - -
209B LEU 3.0 7.4 - - - -
210B HIS* 3.4 36.0 + - - -
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Residues in contact with MET 40 (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* 3.8 17.7 - - + -
12B LEU* 3.8 22.2 - - + -
27B GLY* 5.6 0.2 - - - -
28B VAL 3.3 15.3 - - - +
29B GLY* 3.8 3.6 - - - -
30B LEU* 5.9 0.2 - - - -
38B GLN* 3.7 22.4 - - - +
39B SER* 1.3 77.6 - - - +
41B ASP* 1.3 66.1 + - - +
42B LEU* 3.8 12.3 - - + -
61B PHE* 3.7 42.6 - - - +
63B KZ4 3.9 5.8 - - - -
116B TYR* 4.6 0.2 - - + -
207B VAL 3.5 1.0 - - - +
208B ASN* 3.3 5.9 + - - +
209B LEU* 2.8 48.6 + - + +
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Residues in contact with ASP 41 (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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27B GLY* 3.2 3.1 - - - -
28B VAL* 2.9 45.3 + - + +
40B MET* 1.3 72.5 - - - +
42B LEU* 1.3 61.8 + - - +
43B LYS* 4.3 5.2 + - + +
207B VAL 3.2 4.6 - - - +
208B ASN* 3.1 32.2 + - - +
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Residues in contact with LEU 42 (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* 4.1 2.2 - - + -
25B ILE* 4.0 4.9 - - + -
26B GLU 3.4 4.0 - - - -
27B GLY* 4.0 14.6 - - - -
40B MET* 3.8 16.6 - - + -
41B ASP* 1.3 76.3 - - - +
43B LYS* 1.3 63.2 + - - +
54B TYR* 3.3 25.7 + - + +
61B PHE* 3.5 49.6 - - + -
204B TYR 5.2 0.2 - - - +
205B SER 3.4 1.0 - - - +
206B ASN* 3.4 6.2 - - - -
207B VAL* 2.8 43.8 + - + +
209B LEU* 3.8 29.8 - - + -
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Residues in contact with LYS 43 (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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25B ILE* 3.6 5.1 - - - +
26B GLU 2.9 31.5 + - - +
41B ASP* 5.5 4.9 - - + +
42B LEU* 1.3 76.7 - - - +
44B VAL* 1.3 65.7 + - - +
45B LYS* 3.3 32.1 + - - +
54B TYR* 5.8 0.2 - - - -
205B SER 3.1 3.1 - - - +
206B ASN* 3.0 34.9 + - + +
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Residues in contact with VAL 44 (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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24B ALA 4.2 3.8 - - - +
25B ILE* 4.3 8.1 - - + -
43B LYS* 1.3 70.4 - - - +
45B LYS* 1.3 68.5 + - - +
46B GLU 4.0 8.5 - - - +
47B GLY 4.7 0.2 - - - -
48B GLY* 3.8 34.5 - - - +
49B PRO* 6.2 0.2 - - + -
50B LEU* 4.3 25.4 - - + +
54B TYR* 4.8 2.2 - - + +
203B ASP 5.2 0.9 - - - +
204B TYR 3.5 10.8 - - - +
205B SER* 2.8 43.7 + - - +
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Residues in contact with LYS 45 (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* 4.6 9.0 - - - +
24B ALA 2.9 14.0 + - - +
26B GLU* 3.8 39.7 - - + +
43B LYS* 3.3 38.2 + - - +
44B VAL* 1.3 79.3 - - - +
46B GLU* 1.3 74.6 + - + +
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Residues in contact with GLU 46 (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* 3.0 21.8 + - - -
15B GLU* 5.7 0.5 - - - +
23B PHE* 3.3 11.1 - - - +
24B ALA* 2.9 48.0 + - + +
44B VAL* 4.0 5.5 - - - +
45B LYS* 1.3 88.7 - - + +
47B GLY* 1.3 62.8 + - - +
48B GLY 3.3 3.9 + - - +
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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