Contacts of the strand formed by residues 88 - 97 (chain B) in PDB entry 3NPS
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 ALA 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 3.9 11.9 - - - -
39B GLN 3.5 16.8 - - - +
41B ALA* 3.6 14.6 - - + +
86B ASP 3.1 5.5 + - - +
87B THR* 1.3 78.4 - - - +
89B VAL* 1.3 64.7 + - - +
90B TYR* 3.4 21.5 - - + -
108B LEU* 3.6 5.6 - - - +
109B VAL 2.9 29.7 + - - +
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Residues in contact with VAL 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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38B ARG* 3.3 4.0 - - - +
39B GLN* 2.8 39.9 + - + +
88B ALA* 1.3 75.0 - - - +
90B TYR* 1.3 61.5 + - - +
91B TYR* 3.5 37.2 - - + +
105B GLN 5.0 1.3 - - - +
106B GLY* 3.7 19.1 - - - -
107B THR 3.5 6.7 - - - +
108B LEU* 4.1 21.5 - - + +
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Residues in contact with TYR 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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6B GLN* 2.8 13.8 + - - -
20B VAL* 4.8 5.2 - - + -
36B TRP* 4.8 7.6 - + + -
37B VAL 3.8 2.0 - - - -
38B ARG* 3.0 40.6 + - + -
48B MET* 3.5 33.9 - - + -
80B MET* 3.6 20.0 - - + -
82B LEU* 3.3 17.3 - - + +
86B ASP 2.7 29.9 + - - -
88B ALA* 3.4 20.2 - - + -
89B VAL* 1.3 71.9 - - - +
91B TYR* 1.3 54.9 + - - +
106B GLY* 3.3 0.3 - - - -
107B THR* 2.7 48.8 + - - +
109B VAL* 3.7 20.6 - - + -
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Residues in contact with TYR 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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6B GLN* 3.4 2.0 - - - -
36B TRP* 3.3 10.3 - - - -
37B VAL* 2.7 46.8 + - + +
38B ARG 5.0 0.4 - - - -
39B GLN* 4.2 13.5 - - + +
45B LEU* 5.2 1.3 - - + -
89B VAL* 3.5 31.5 - - + +
90B TYR* 1.3 74.8 - - - +
92B CYS* 1.3 61.4 + - - +
103B TRP* 3.7 30.1 - + + -
104B GLY 3.6 13.2 - - - -
105B GLN 4.0 4.7 + - - -
106B GLY* 3.6 24.2 - - - -
38C GLN* 3.4 23.7 + - - -
41C GLY 5.9 0.2 - - - -
42C THR 3.8 7.8 + - - -
43C ALA* 3.7 23.2 - - + -
44C PRO* 4.1 10.5 - - + -
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Residues in contact with CYS 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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4B LEU* 3.8 9.4 - - - -
6B GLN* 3.0 26.5 + - - +
22B CYS* 2.0 53.4 - - + -
34B ILE* 4.3 3.4 - - + -
35B SER 3.3 6.7 - - - +
36B TRP* 3.7 19.7 - - + -
91B TYR* 1.3 80.5 - - - +
93B ALA* 1.3 61.0 + - - +
103B TRP* 3.6 1.0 - - - -
104B GLY* 2.8 26.2 + - - -
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Residues in contact with ALA 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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4B LEU* 3.7 5.4 - - - -
34B ILE* 3.4 4.7 - - - -
35B SER* 2.9 33.1 + - - +
37B VAL* 5.9 0.2 - - + -
92B CYS* 1.3 77.7 - - - +
94B ARG* 1.3 60.4 + - - +
95B THR 3.9 0.3 + - - -
100B MET* 3.8 29.4 - - - +
102B HIS 3.1 11.4 - - - +
103B TRP* 3.7 26.2 - - + +
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Residues in contact with ARG 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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60A ARG* 6.2 0.6 - - - +
2B VAL* 3.2 42.3 - - - +
4B LEU* 3.4 20.0 - - + +
28B THR 5.0 6.4 + - - -
29B PHE* 4.6 11.6 + - + +
30B SER* 4.8 3.6 - - - -
32B TYR* 3.5 60.1 + - + -
33B ALA 3.3 8.3 - - - +
34B ILE* 4.0 9.4 - - + -
93B ALA* 1.3 72.9 - - - +
95B THR* 1.3 65.0 + - - +
100B MET* 3.8 0.8 - - - +
101B ASP* 3.0 29.3 + - - +
102B HIS* 2.7 40.2 + - + +
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Residues in contact with THR 95 (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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32B TYR* 3.2 17.3 - - - +
33B ALA* 2.9 47.0 + - + +
35B SER* 4.3 12.3 - - - -
94B ARG* 1.3 80.4 + - - +
96B PHE* 1.3 76.4 + - - +
100B LYS* 3.1 58.7 - - + +
101B ASP* 3.9 5.9 - - - +
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Residues in contact with PHE 96 (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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32B TYR* 3.5 5.7 - - - -
95B THR* 1.3 95.4 + - - +
97B HIS* 1.3 68.2 + - - +
98B ILE* 3.3 2.6 + - - +
100B LYS* 2.9 81.4 - - + +
101B ASP* 3.2 38.6 - - + -
46C LEU* 3.8 15.7 - - + -
49C TYR* 3.5 43.5 - + - -
55C PRO* 4.5 10.5 - - + -
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Residues in contact with HIS 97 (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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96A ASP* 2.8 52.4 + - - -
97A PHE 4.6 0.9 - - - -
99A PHE* 3.5 20.1 - + - -
31B SER* 3.3 22.5 - - - -
32B TYR* 3.4 23.6 - - + +
96B PHE* 1.3 74.9 - - - +
98B ILE* 1.3 66.7 + - + +
99B ARG* 3.0 30.8 + - + -
100B TYR* 3.4 46.5 + - + +
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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