Contacts of the strand formed by residues 2 - 10 (chain B) in PDB entry 4NWO
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 VAL 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 86.7 - - - +
3B ARG* 1.3 82.4 + - - +
4B GLY 4.3 0.4 - - - +
43B ALA* 5.2 5.4 - - + -
93B LEU* 4.0 24.2 - - + -
94B TRP 3.4 22.9 - - - +
95B ASN* 3.5 20.4 - - - +
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Residues in contact with ARG 3 (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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1B MET* 3.8 23.7 - - - +
2B VAL* 1.3 84.0 + - - +
4B GLY* 1.3 63.6 + - - +
5B ILE* 4.3 0.2 - - - +
94B TRP* 2.8 41.2 + - + +
96B THR* 3.7 23.6 - - + +
98B THR 3.0 24.3 + - - +
99B PRO* 4.3 3.4 - - - +
100B GLN* 3.7 52.8 - - - +
103B VAL* 4.0 18.2 - - + -
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Residues in contact with GLY 4 (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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2B VAL* 4.3 0.4 - - - +
3B ARG* 1.3 76.1 - - - +
5B ILE* 1.3 63.7 + - - +
6B ARG* 4.2 0.4 - - - -
91B LEU* 4.0 14.6 - - - -
92B ALA 3.2 7.4 - - - -
93B LEU* 4.2 10.7 - - - +
103B VAL* 3.7 6.6 - - - +
105B HIS* 3.5 15.2 - - - -
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Residues in contact with ILE 5 (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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3B ARG 4.3 2.5 - - - +
4B GLY* 1.3 79.0 - - - +
6B ARG* 1.3 64.8 + - - +
30B MET* 3.5 28.7 - - + +
31B LEU* 6.2 0.2 - - + -
34B ASN* 3.6 15.3 - - - +
36B ILE* 4.1 13.9 - - + -
90B VAL 3.4 1.0 - - - +
91B LEU* 3.3 6.4 - - - +
92B ALA* 2.7 46.9 + - + +
94B TRP* 3.6 38.6 - - + -
103B VAL* 4.0 10.3 - - + -
104B ARG 3.6 24.0 - - - +
105B HIS* 3.9 3.8 - - - +
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Residues in contact with ARG 6 (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 GLY 6.0 0.2 - - - -
5B ILE* 1.3 75.9 - - - +
7B GLY* 1.3 75.0 + - - +
8B ALA* 4.1 5.5 - - - +
30B MET* 3.8 5.0 - - - +
89B ARG* 3.5 34.4 - - - +
90B VAL 3.1 21.2 + - - +
91B LEU* 4.0 21.5 - - + -
105B HIS* 3.0 26.7 + - + +
106B VAL 3.1 21.5 + - - -
107B TYR* 3.7 31.0 + - - +
114B LEU* 5.7 0.2 - - - +
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Residues in contact with GLY 7 (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 ARG* 1.3 85.2 + - - +
8B ALA* 1.3 63.7 + - - +
26B LEU* 3.7 6.7 - - - -
30B MET* 3.8 20.0 - - - +
89B ARG* 3.4 0.3 - - - -
90B VAL 2.9 28.9 + - - -
106B VAL 3.1 11.9 - - - -
107B TYR* 5.0 2.0 - - - -
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Residues in contact with ALA 8 (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 ARG* 4.1 7.0 - - - +
7B GLY* 1.3 76.2 - - - +
9B ILE* 1.3 64.3 + - - +
26B LEU* 3.5 7.7 - - - +
87B VAL* 4.2 5.6 - - + -
88B ILE 3.2 10.8 - - - +
89B ARG* 4.2 0.9 - - + -
106B VAL 3.0 7.9 + - - +
107B TYR* 3.6 26.5 - - + -
108B LEU 2.9 24.9 + - - -
111B ALA* 3.8 9.9 - - + -
114B LEU* 4.1 10.1 - - + -
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Residues in contact with ILE 9 (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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8B ALA* 1.3 77.1 - - - +
10B THR* 1.3 76.2 + - - +
22B ALA* 3.4 50.7 - - + +
23B THR* 4.6 0.4 - - - +
25B LEU* 4.6 9.2 - - + -
26B LEU* 3.9 14.8 - - + -
87B VAL* 3.5 2.4 - - - -
88B ILE* 2.9 43.1 + - + +
108B LEU* 3.7 33.0 - - + +
109B SER* 4.4 6.3 - - - -
111B ALA* 3.7 6.5 - - - -
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Residues in contact with THR 10 (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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137A ALA* 5.7 3.1 - - - +
9B ILE* 1.3 90.2 - - - +
11B VAL* 1.3 74.3 + - - +
12B ASN* 5.7 0.7 + - - -
22B ALA* 4.4 1.4 - - - +
84B LEU* 3.9 21.3 - - + -
85B PRO 4.0 8.7 - - - +
86B ARG 3.3 12.6 - - - +
87B VAL* 4.1 3.6 - - + -
108B LEU 3.9 2.4 + - - -
109B SER* 3.0 26.5 + - - -
110B GLU* 3.1 17.3 + - + +
111B ALA* 3.6 19.3 - - + +
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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