Contacts of the strand formed by residues 87 - 94 (chain B) in PDB entry 5NC5
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 THR 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 6.1 1.3 - - - -
47B ALA 3.5 10.8 - - - +
48B SER* 4.8 6.4 + - - +
57B VAL* 4.2 4.1 - - - +
81B ASN 3.9 0.9 - - - +
82B SER* 3.5 1.7 - - - -
83B ASP* 2.9 44.9 + - - +
85B THR* 3.2 14.3 + - - -
86B GLY* 1.3 79.7 + - - +
88B VAL* 1.3 74.3 + - - +
89B GLN* 4.6 10.1 - - + +
620B ARG* 3.4 20.0 + - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE 4.3 0.7 - - - +
46B SER* 3.4 4.7 - - - -
47B ALA* 3.1 53.0 + - + +
57B VAL* 3.7 10.3 - - + -
61B VAL* 3.9 16.6 - - + -
62B THR* 3.1 29.8 - - + +
65B ILE* 5.6 1.6 - - + -
80B SER* 5.0 0.2 - - - -
81B ASN 3.4 9.4 - - - +
87B THR* 1.3 81.7 - - - +
89B GLN* 1.3 64.4 + - - +
90B ILE* 3.8 27.4 - - + +
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Residues in contact with GLN 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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44B THR* 3.8 27.7 - - + +
45B ILE 3.3 3.6 - - - +
46B SER* 4.4 9.5 - - - -
80B SER* 3.2 4.7 - - - -
81B ASN* 3.0 48.1 + - - +
87B THR* 4.6 8.9 - - + +
88B VAL* 1.3 76.6 - - - +
90B ILE* 1.3 62.4 + - - +
91B THR* 4.1 5.0 + - - +
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Residues in contact with ILE 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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43B VAL 3.9 0.3 - - - +
44B THR* 3.2 3.6 - - - +
45B ILE* 2.6 52.7 + - + +
62B THR* 3.8 19.7 - - + -
65B ILE* 3.8 36.6 - - + -
66B GLU* 3.9 10.5 - - + -
69B MET* 5.4 0.7 - - + -
78B MET* 4.1 15.3 - - + -
79B SER 3.4 9.0 - - - +
80B SER* 3.8 11.0 - - - -
88B VAL* 3.8 15.9 - - + -
89B GLN* 1.3 75.0 - - - +
91B THR* 1.3 62.7 + - - +
92B LEU* 3.5 23.6 - - + -
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Residues in contact with THR 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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42B ALA* 4.2 11.7 - - + -
43B VAL 3.4 7.9 - - - +
44B THR* 3.2 20.3 + - - +
77B TYR* 4.1 0.5 - - - +
78B MET* 3.3 2.9 - - - -
79B SER* 2.9 50.9 + - - +
89B GLN* 4.1 5.6 + - - +
90B ILE* 1.3 72.2 - - - +
92B LEU* 1.3 65.9 + - - +
93B THR* 4.0 16.7 + - - +
132B SER* 4.4 2.2 + - - +
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Residues in contact with LEU 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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42B ALA* 3.2 3.3 - - - +
43B VAL 2.7 39.7 + - - +
45B ILE* 4.2 21.8 - - + -
69B MET* 3.9 31.2 - - + -
72B ILE* 4.5 4.5 - - + -
75B LEU* 3.7 26.0 - - + -
77B TYR 3.6 4.0 - - - -
78B MET* 4.0 12.8 - - + -
90B ILE* 3.5 28.0 - - + -
91B THR* 1.3 73.2 - - - +
93B THR* 1.3 60.9 + - - +
94B PHE* 3.5 13.9 - - + -
107B VAL* 4.1 15.9 - - + -
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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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40B PRO* 4.4 13.9 - - + +
41B PRO 3.7 8.1 - - - +
42B ALA* 4.1 8.1 - - + +
75B LEU* 3.6 3.1 - - - +
76B MET* 2.9 42.1 + - + +
77B TYR* 2.9 49.6 + - - +
91B THR* 4.0 14.6 + - - +
92B LEU* 1.3 74.2 + - - +
94B PHE* 1.3 63.8 + - - +
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Residues in contact with PHE 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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40B PRO* 3.6 3.1 - - - +
41B PRO* 2.8 32.4 + - + +
43B VAL* 3.6 22.2 - - + -
72B ILE* 3.6 24.5 - - + -
73B ASP 3.6 17.9 - - - -
74B ASN 3.4 13.0 - - - +
75B LEU* 4.0 10.3 - - + -
76B MET* 3.4 15.6 - - - +
92B LEU* 3.5 33.4 - - + -
93B THR* 1.3 73.9 - - - +
95B GLU* 1.4 64.9 + - - +
98B THR* 4.1 16.6 - - + -
103B ALA* 3.9 22.2 - - + -
107B VAL* 3.6 24.9 - - + -
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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