Contacts of the strand formed by residues 77 - 83 (chain R) in PDB entry 1NVU
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 GLY 77 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5R LYS 3.5 4.1 + - - +
6R LEU* 3.5 3.7 - - - -
7R VAL* 3.1 23.9 + - - +
76R GLU* 1.3 82.9 + - - +
78R PHE* 1.3 67.7 + - - -
110R PRO* 3.3 10.5 - - - -
159R LEU* 3.7 11.7 - - - -
163R ILE* 3.9 16.9 - - - +
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Residues in contact with PHE 78 (chain R).
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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7R VAL* 3.4 34.1 - - + +
9R VAL* 4.8 3.8 - - + -
72R MET* 3.1 41.3 - - + -
75R GLY 3.7 21.5 - - - -
76R GLU 4.3 0.2 - - - -
77R GLY* 1.3 78.4 - - - -
79R LEU* 1.3 60.9 + - - +
80R CYS* 3.9 2.5 - - - -
100R ILE* 3.7 36.8 - - + -
104R LYS* 3.9 11.9 - - + -
109R VAL* 3.6 33.0 - - + -
110R PRO 2.9 10.2 + - - -
111R MET* 3.1 12.9 - - + +
112R VAL 3.0 25.3 + - - -
159R LEU* 3.6 8.7 - - - +
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Residues in contact with LEU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R VAL 3.0 10.5 + - - +
8R VAL* 3.6 15.4 - - + -
9R VAL* 2.9 30.8 + - - +
19R LEU* 5.2 6.5 - - + -
78R PHE* 1.3 72.0 - - - +
80R CYS* 1.3 60.2 + - - +
81R VAL* 3.7 3.5 + - + +
112R VAL* 3.6 14.8 - - + -
114R VAL* 3.8 17.5 - - + -
155R ALA* 3.7 26.7 - - + +
156R PHE* 3.4 47.6 - - + -
159R LEU* 3.6 27.3 - - + +
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Residues in contact with CYS 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R VAL* 3.7 12.6 - - + -
10R GLY* 5.7 0.2 - - - -
78R PHE* 4.7 2.9 - - - -
79R LEU* 1.3 70.6 - - - +
81R VAL* 1.3 56.3 + - - +
93R ILE* 4.1 21.8 - - + -
96R TYR* 4.8 9.0 - - + -
97R ARG* 5.0 3.6 - - - -
100R ILE* 3.7 29.6 - - - -
111R MET* 4.0 20.6 - - - -
112R VAL 2.9 14.8 + - - +
113R LEU* 3.6 12.8 - - + +
114R VAL 2.8 30.7 + - - +
139R ILE* 6.0 1.3 - - + -
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Residues in contact with VAL 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R VAL* 3.7 29.6 - - + -
9R VAL 2.9 12.5 + - - +
10R GLY* 3.5 20.1 - - - -
11R ALA 4.1 2.1 + - - -
14R VAL* 3.8 18.1 - - + +
16R LYS* 4.0 9.6 - - + +
19R LEU* 4.1 26.0 - - + -
79R LEU* 4.0 7.6 - - + +
80R CYS* 1.3 77.0 - - - +
82R PHE* 1.3 71.5 + - - +
89R SER 4.8 0.7 - - - +
93R ILE* 3.9 5.7 - - - +
114R VAL* 3.3 17.3 - - + +
116R ASN* 4.2 10.8 - - + -
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Residues in contact with PHE 82 (chain R).
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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14R VAL* 3.9 8.7 - - - -
81R VAL* 1.3 77.5 - - - +
83R ALA* 1.3 69.9 + - - +
84R ILE* 4.1 9.6 - - + -
89R SER* 3.5 30.3 - - - +
90R PHE* 3.7 37.0 - + + -
93R ILE* 4.0 3.4 - - + -
113R LEU* 3.9 22.2 - - + -
114R VAL 3.0 20.5 + - - +
115R GLY* 3.6 17.0 - - - -
116R ASN* 2.9 24.4 + - - +
125R VAL* 3.8 19.3 - - + -
130R ALA* 3.9 9.9 - - + -
141R TYR* 3.6 31.6 - + - -
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Residues in contact with ALA 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R GLY 4.9 1.8 - - - +
14R VAL* 3.6 19.6 - - + +
82R PHE* 1.3 79.8 - - - +
84R ILE* 1.3 60.6 + - - +
85R ASN* 3.1 17.5 - - - +
86R ASN* 2.9 36.1 + - + +
89R SER* 2.9 6.7 + - - -
116R ASN 3.4 5.6 - - - -
118R CYS* 3.9 20.9 - - - -
125R VAL* 4.5 0.5 - - - +
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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