Contacts of the strand formed by residues 34 - 40 (chain B) in PDB entry 5NS3
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 LEU 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B TYR* 5.4 0.2 - - - -
33B ARG* 1.3 81.6 - - - +
35B GLU* 1.3 59.4 + - - +
36B LYS 5.7 0.4 - - - +
37B VAL* 5.2 0.4 - - + -
99B MET* 3.7 26.9 - - + +
100B TRP* 3.7 33.2 - - + -
103B LEU* 3.3 32.5 - - + -
159B VAL* 3.9 11.2 - - + -
160B VAL 3.9 3.4 - - - +
161B THR* 3.9 15.3 - - + +
172B LEU* 4.1 7.4 - - + +
173B LEU* 3.8 28.7 - - + -
176B LEU* 4.1 13.2 - - + -
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Residues in contact with GLU 35 (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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33B ARG 3.3 4.8 + - - +
34B LEU* 1.3 74.2 - - - +
36B LYS* 1.3 79.7 + - + +
95B ARG* 4.3 22.4 + - - +
96B ARG 4.9 0.9 + - - -
99B MET* 3.8 9.6 - - - +
160B VAL* 2.9 34.7 + - + +
161B THR* 4.6 3.9 - - - +
162B THR* 4.3 18.4 - - + +
30D C 5.0 0.9 + - - -
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Residues in contact with LYS 36 (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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34B LEU* 5.7 0.2 - - - +
35B GLU* 1.3 95.4 + - - +
37B VAL* 1.3 67.7 + - - +
38B VAL* 4.0 12.4 - - + +
93B THR* 3.8 16.9 - - + +
94B LEU 3.2 13.7 - - - +
95B ARG* 3.7 33.9 - - + +
99B MET* 3.6 5.5 - - - -
158B ALA 3.8 0.3 - - - +
159B VAL* 4.8 0.3 - - - +
160B VAL* 2.9 49.5 + - + +
29D A 3.8 6.3 + - - -
30D C 2.6 31.1 + - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 5.2 0.9 - - + -
36B LYS* 1.3 79.4 - - - +
38B VAL* 1.3 62.6 + - - +
39B ILE* 4.0 4.7 + - + -
92B VAL 3.8 1.6 - - - +
94B LEU* 2.9 37.5 + - + +
99B MET* 3.7 23.6 - - + -
102B PHE* 4.2 23.1 - - + -
103B LEU* 4.0 24.2 - - + -
157B ILE* 3.7 27.1 - - + -
158B ALA 3.2 3.4 - - - +
159B VAL* 4.2 15.5 - - + -
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Residues in contact with VAL 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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36B LYS* 4.0 25.4 - - + +
37B VAL* 1.3 75.9 - - - +
39B ILE* 1.3 62.7 + - - +
91B ARG* 4.0 19.7 - - + -
92B VAL 3.4 10.1 - - - +
93B THR* 4.1 17.3 - - + +
156B ASP 3.7 0.9 - - - +
157B ILE* 3.4 4.9 - - - +
158B ALA* 2.8 41.4 + - + +
160B VAL* 5.1 0.7 - - + -
28D C 3.7 22.1 + - - +
29D A 3.7 27.4 - - - +
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Residues in contact with ILE 39 (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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37B VAL* 4.3 7.9 - - + -
38B VAL* 1.3 76.5 - - - +
40B ASN* 1.3 65.1 + - - +
60B LEU* 3.9 18.9 - - + +
64B THR* 3.9 18.6 - - + -
90B LEU 3.9 0.5 - - - +
91B ARG* 3.2 4.9 - - - +
92B VAL* 2.8 41.9 + - + +
94B LEU* 4.0 8.7 - - + -
102B PHE* 3.2 46.0 - - + -
155B MET* 3.7 31.0 - - + -
156B ASP 3.5 3.1 - - - +
157B ILE* 4.4 5.6 - - + -
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Residues in contact with ASN 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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38B VAL 4.1 0.4 - - - -
39B ILE* 1.3 79.5 - - - +
60B LEU* 5.9 1.8 - - - -
71B THR* 4.4 3.3 + - - -
89B GLY* 5.1 4.1 - - - -
90B LEU 3.3 27.0 + - - +
91B ARG* 3.6 10.4 - - + +
154B GLY 3.8 7.3 - - - +
155B MET* 3.7 8.7 - - - -
156B ASP* 2.9 54.6 + - + +
27D G 3.5 17.3 + - - +
28D C 3.2 52.6 + - - +
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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