Contacts of the strand formed by residues 2 - 10 (chain Q) 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 THR 2 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1Q MET* 1.3 73.5 - - - +
3Q GLU* 1.3 70.2 + - - +
4Q TYR* 3.5 39.1 + - + +
49Q GLU* 5.4 6.9 + - - +
50Q THR 3.8 5.7 + - - -
51Q CYS* 3.5 5.0 - - - -
52Q LEU* 2.9 23.9 + - - -
164Q ARG* 5.7 0.9 - - - -
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Residues in contact with GLU 3 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET 3.8 2.7 + - - +
2Q THR* 1.3 82.6 - - - +
4Q TYR* 1.3 65.1 + - - +
5Q LYS* 3.1 21.8 + - + +
41Q ARG* 3.3 26.2 + - - -
52Q LEU* 3.2 21.7 - - + +
54Q ASP* 2.3 33.4 - - - +
76Q GLU* 3.8 10.9 - - - +
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Residues in contact with TYR 4 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q THR* 3.5 31.8 + - + +
3Q GLU* 1.3 78.3 - - - +
5Q LYS* 1.3 62.8 + - - +
6Q LEU* 3.6 17.5 + - + +
51Q CYS* 3.6 37.9 - - + -
52Q LEU 2.9 8.0 + - - +
53Q LEU* 3.7 9.8 - - + -
54Q ASP* 2.8 30.3 + - - +
76Q GLU* 3.3 4.9 - - - +
160Q VAL* 3.8 17.0 - - + -
163Q ILE* 3.6 31.4 - - + -
164Q ARG* 2.9 47.9 + - + +
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Residues in contact with LYS 5 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q GLU* 3.1 27.0 + - + +
4Q TYR* 1.3 72.9 - - - +
6Q LEU* 1.3 63.8 + - - +
7Q VAL* 5.8 0.7 - - + -
54Q ASP* 3.5 17.3 + - + +
74Q THR* 3.8 26.0 - - - +
75Q GLY* 3.8 4.8 - - - -
76Q GLU* 2.8 58.5 + - - +
77Q GLY 3.3 5.7 + - - -
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Residues in contact with LEU 6 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR* 4.0 16.2 - - + +
5Q LYS* 1.3 76.9 - - - +
7Q VAL* 1.3 64.3 + - - +
8Q VAL* 5.7 0.9 - - + -
53Q LEU* 4.1 23.1 - - + -
54Q ASP 2.8 14.8 + - - +
55Q ILE* 4.4 12.6 - - + -
56Q LEU* 2.8 26.6 + - - +
77Q GLY 3.5 3.4 - - - -
156Q PHE* 3.9 28.7 - - + +
159Q LEU* 4.1 20.4 - - + -
160Q VAL* 4.2 14.1 - - + -
163Q ILE* 3.3 32.5 - - + -
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Residues in contact with VAL 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q LYS* 5.0 0.7 - - + -
6Q LEU* 1.3 81.0 - - - +
8Q VAL* 1.3 64.1 + - - +
9Q VAL* 3.7 21.7 + - + -
56Q LEU* 3.5 15.5 - - + +
58Q THR* 3.8 17.9 - - + -
71Q TYR* 3.9 20.6 - - + +
74Q THR* 4.9 1.3 - - - +
75Q GLY* 3.7 28.0 - - - +
77Q GLY 2.9 7.0 + - - +
78Q PHE* 3.2 23.6 - - + +
79Q LEU* 2.8 25.5 + - - +
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Residues in contact with VAL 8 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q LEU* 5.7 0.7 - - + -
7Q VAL* 1.3 75.1 - - - +
9Q VAL* 1.3 64.9 + - - +
16Q LYS* 3.6 39.4 - - + +
19Q LEU* 5.5 1.6 - - + -
20Q THR* 3.9 10.8 - - - +
55Q ILE* 3.9 26.5 - - + -
56Q LEU 2.9 9.4 + - - +
57Q ASP* 4.6 3.8 - - - -
58Q THR* 2.9 26.7 + - - +
79Q LEU* 3.6 13.7 - - + +
81Q VAL* 3.9 16.8 - - + -
156Q PHE* 4.1 15.5 - - + -
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Residues in contact with VAL 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q VAL* 3.7 20.6 - - + -
8Q VAL* 1.3 80.1 - - - +
10Q GLY* 1.3 59.8 + - - +
16Q LYS* 3.3 11.9 - - - +
58Q THR* 3.8 11.4 - - + +
68Q ARG* 6.2 0.7 - - - -
71Q TYR* 6.0 0.4 - - + -
72Q MET* 4.5 15.7 - - + -
78Q PHE* 4.4 10.5 - - + -
79Q LEU 2.9 14.8 + - - +
80Q CYS* 4.0 21.3 - - - -
81Q VAL* 2.9 27.4 + - - +
96Q TYR* 4.0 24.5 - - + -
100Q ILE* 4.5 7.6 - - + -
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Residues in contact with GLY 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q VAL* 1.3 79.3 - - - +
11Q ALA* 1.3 68.0 + - - -
14Q VAL* 4.5 0.4 - - - -
16Q LYS* 3.0 14.9 + - - +
58Q THR* 5.0 0.6 + - - -
60Q GLY* 3.1 14.4 - - - -
81Q VAL 3.5 15.0 - - - -
93Q ILE* 5.4 1.1 - - - -
96Q TYR* 3.3 26.0 + - - -
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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