Contacts of the strand formed by residues 133 - 139 (chain B) in PDB entry 3NBV
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 PHE 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B GLY* 4.1 7.0 - - - -
5B GLN* 3.3 41.5 - - + +
7B LEU* 3.7 39.3 - - + -
58B ALA* 4.0 8.7 - - + -
85B GLN* 4.2 18.4 - - + -
128B VAL* 3.9 13.5 - - + -
129B ASP 3.7 17.7 - - - -
130B LEU* 2.8 22.0 + - + +
131B THR 4.2 1.6 - - - +
132B GLN* 1.3 96.0 - - + +
134B LYS* 1.3 60.2 + - - +
135B TRP 4.2 1.6 - - - +
136B ILE* 4.0 24.7 - - + -
166B ILE* 3.5 20.0 - - + +
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Residues in contact with LYS 134 (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 GLY* 3.4 26.8 - - - +
4B SER* 4.2 11.2 + - - +
5B GLN 2.8 21.4 + - - +
6B ILE* 4.3 15.3 - - + -
132B GLN 4.1 0.8 + - - -
133B PHE* 1.3 74.1 - - - +
135B TRP* 1.3 62.3 + - + +
165B LYS 4.3 3.8 - - - +
166B ILE* 3.8 7.6 - - - +
167B ARG* 3.1 23.2 + - - +
269B SER* 4.3 30.9 + - - +
270B GLN* 4.6 10.1 + - - -
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Residues in contact with TRP 135 (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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5B GLN 3.6 1.1 + - - +
6B ILE* 3.4 23.8 - - + -
7B LEU 2.9 24.8 + - - -
133B PHE* 3.5 0.9 - - - +
134B LYS* 1.3 85.3 - - + +
136B ILE* 1.3 91.2 + - - +
137B HIS* 3.9 2.5 - - + -
167B ARG* 3.2 42.0 - - + -
168B VAL 4.7 2.2 - - - -
169B SER* 2.9 39.3 + - - +
187B ASP* 5.9 0.4 - - + -
188B VAL* 4.3 14.6 - - + -
190B PHE* 6.1 0.2 - + - -
265B ILE* 3.8 31.7 - - + +
268B LEU* 3.8 38.8 - - + -
269B SER* 3.9 23.6 - - - -
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Residues in contact with ILE 136 (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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7B LEU* 3.5 27.4 - - + +
9B VAL* 4.4 3.8 - - + -
125B PHE* 4.4 3.6 - - + -
130B LEU* 4.0 25.6 - - + -
133B PHE* 4.0 18.8 - - + -
135B TRP* 1.3 81.9 - - - +
137B HIS* 1.3 61.2 + - - +
138B ILE* 4.2 15.5 - - + -
153B ILE* 4.0 32.5 - - + -
166B ILE* 3.7 21.3 - - + -
167B ARG 2.8 12.1 + - - +
168B VAL* 3.3 7.4 - - + +
169B SER 2.9 23.9 + - - +
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Residues in contact with HIS 137 (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 ILE* 5.4 0.7 - - + -
7B LEU 2.7 14.9 + - - +
8B CYS* 3.4 20.7 - - + -
9B VAL* 2.9 27.5 + - - +
43B ALA* 5.6 3.1 - - - -
46B SER* 5.2 9.0 + - - -
135B TRP* 3.9 4.0 - - + +
136B ILE* 1.3 71.4 - - - +
138B ILE* 1.3 70.3 + - - +
139B GLU* 4.5 5.2 + - + +
169B SER* 2.5 32.1 + - - +
170B VAL 4.0 7.0 - - - -
171B GLU* 3.9 27.3 + - + +
190B PHE* 3.8 27.4 - + - -
261B ASN* 4.9 8.4 + - + +
265B ILE* 3.5 19.1 - - + +
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Residues in contact with ILE 138 (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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9B VAL* 3.8 20.6 - - + +
125B PHE* 5.7 1.6 - - + -
136B ILE* 4.2 7.2 - - + +
137B HIS* 1.3 82.8 - - - +
139B GLU* 1.3 64.4 + - - +
140B GLY* 3.4 2.3 + - - +
146B GLN* 3.7 37.0 - - + +
149B MET* 4.6 17.5 - - + -
150B LEU* 3.7 32.5 - - + -
153B ILE* 4.4 15.9 - - + -
168B VAL* 5.2 0.7 - - + -
169B SER 2.8 15.2 + - - +
170B VAL* 3.3 11.3 - - + +
171B GLU 2.9 25.3 + - - -
182B LEU* 5.9 1.3 - - + -
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Residues in contact with GLU 139 (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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9B VAL 2.9 18.7 + - - +
10B GLY* 3.5 0.9 - - - -
11B LEU* 3.1 29.0 + - - +
42B ASN* 3.5 22.6 + - + +
43B ALA* 3.1 23.9 + - + +
137B HIS* 4.1 5.3 + - - +
138B ILE* 1.3 70.9 - - - +
140B GLY* 1.3 66.5 + - - +
141B ARG* 3.0 37.7 + - + +
146B GLN* 2.9 21.9 + - - -
171B GLU* 3.9 24.7 - - - +
173B GLU* 5.9 2.7 - - + -
300B SO4 5.0 0.3 + - - -
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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