Contacts of the strand formed by residues 87 - 94 (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 PRO 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.4 42.0 - - + -
70B VAL* 3.9 7.9 - - + -
71B THR 3.6 7.2 - - - +
72B ARG* 3.4 18.1 - - - +
86B MET* 1.4 88.0 - - + +
88B ILE* 1.3 61.7 + - - +
89B GLY 3.7 0.7 - - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B THR* 2.9 31.4 + - + +
72B ARG 4.2 3.1 - - - +
73B ALA* 4.3 17.7 - - + +
86B MET* 3.6 35.2 - - + +
87B PRO* 1.3 78.0 - - - +
89B GLY* 1.3 58.6 + - - +
26D C 4.3 7.6 - - - +
27D G 3.6 43.8 + - - +
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Residues in contact with GLY 89 (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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40B ASN* 5.3 4.9 - - - -
53B LEU* 4.9 3.1 - - - +
70B VAL* 3.5 7.8 - - - +
71B THR* 2.8 39.8 + - - +
87B PRO* 3.7 1.2 - - - +
88B ILE* 1.3 81.0 - - - +
90B LEU* 1.3 64.3 + - - +
27D G 5.7 2.7 - - - -
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Residues in contact with LEU 90 (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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39B ILE 3.9 0.5 - - - +
40B ASN* 3.3 29.8 + - - +
53B LEU* 3.6 26.9 - - + -
56B ALA* 3.6 21.3 - - + +
57B ALA* 3.5 39.0 - - + +
60B LEU* 4.0 19.8 - - + +
68B PRO* 4.3 10.1 - - + +
69B ALA 3.2 10.8 - - - +
70B VAL* 4.1 13.5 - - + -
71B THR* 4.4 0.4 + - - -
89B GLY* 1.3 80.3 - - - +
91B ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 91 (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* 4.0 18.2 - - + -
39B ILE 3.2 5.2 - - - +
40B ASN* 3.6 11.9 - - - +
60B LEU* 5.0 1.1 - - - -
68B PRO* 3.4 4.7 - - - +
69B ALA* 2.8 44.2 + - + +
71B THR* 4.4 10.5 + - - +
90B LEU* 1.3 76.9 - - - +
92B VAL* 1.3 66.2 + - - +
93B THR* 4.5 5.6 - - - +
42C C 3.5 40.6 - - - +
28D C 3.6 27.6 + - - -
29D A 2.7 33.4 + - - -
48D U 5.3 8.1 + - - -
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Residues in contact with VAL 92 (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 3.8 1.0 - - - +
38B VAL* 3.4 3.5 - - - +
39B ILE* 2.8 57.7 + - + +
60B LEU* 4.4 11.2 - - + -
64B THR* 3.9 23.8 - - + +
66B GLN* 3.2 39.5 - - + +
67B LYS 4.8 0.2 - - - +
68B PRO* 4.6 7.6 - - + -
91B ARG* 1.3 75.7 - - - +
93B THR* 1.3 61.2 + - - +
94B LEU* 3.5 19.3 - - + -
42C C 3.5 5.2 - - - +
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Residues in contact with THR 93 (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* 3.8 23.8 - - + +
37B VAL 3.8 2.9 - - - -
38B VAL* 4.1 16.8 - - + +
66B GLN* 2.9 20.4 + - - +
91B ARG* 4.5 2.6 + - - +
92B VAL* 1.3 73.3 + - - +
94B LEU* 1.3 59.9 + - - +
95B ARG* 3.8 18.3 + - - +
42C C 2.6 43.1 + - - +
43C C 3.6 26.5 + - + +
29D A 5.4 0.7 + - - -
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Residues in contact with LEU 94 (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* 3.2 7.8 - - - +
37B VAL* 2.9 42.3 + - + +
39B ILE* 4.0 13.5 - - + -
64B THR* 4.0 20.2 - - + +
66B GLN* 3.3 23.3 - - + +
92B VAL* 3.5 24.2 - - + -
93B THR* 1.3 73.6 - - - +
95B ARG* 1.3 61.2 + - - +
98B ARG* 4.0 8.1 - - + +
99B MET* 3.6 18.1 - - + +
102B PHE* 3.7 43.1 - - + -
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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