Contacts of the strand formed by residues 172 - 176 (chain B) in PDB entry 1NVB
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 LYS 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU 3.9 11.9 + - - -
14B SER* 3.5 13.5 - - - +
16B ILE* 3.4 25.6 - - + +
25B TYR* 4.9 0.2 + - - -
29B ASP* 3.0 20.9 + - - +
33B ASP* 3.6 28.0 + - - -
34B CYS* 4.1 10.8 - - - -
135B VAL* 3.2 25.3 - - + +
136B GLN 2.8 24.1 + - - -
170B PRO* 3.3 2.3 - - - +
171B THR* 1.3 88.3 - - + +
173B ILE* 1.3 67.2 + - - +
174B TYR* 3.4 23.3 - - + +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.1 5.8 - - + -
14B SER* 2.9 17.9 + - - +
15B ILE* 3.7 24.5 - - + -
16B ILE* 3.0 27.5 + - - +
136B GLN* 3.4 7.0 - - + +
138B PRO* 4.5 1.1 - - + -
148B SER* 3.5 39.7 - - - +
149B ILE* 4.0 15.0 - - + -
150B GLY 5.2 1.1 - - - +
170B PRO* 3.7 21.8 - - + -
172B LYS* 1.3 80.9 - - - +
174B TYR* 1.3 63.5 + - - +
175B ILE* 3.4 24.2 + - + -
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.5 7.2 - - + -
21B LEU* 4.3 13.0 - - + -
22B TRP 6.0 0.2 - - - +
25B TYR* 3.5 35.9 - + - -
26B VAL* 3.6 39.0 - - + -
29B ASP* 2.5 32.0 + - + +
30B LEU* 4.1 10.9 + - + +
135B VAL* 4.1 13.2 - - + -
136B GLN 2.8 20.3 + - - +
137B VAL* 4.0 20.5 - - + +
138B PRO* 3.4 18.2 - - - +
172B LYS* 3.4 30.5 - - + +
173B ILE* 1.3 76.5 - - - +
175B ILE* 1.3 60.9 + - - +
176B ASP* 3.1 8.8 + - + +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.8 22.9 - - + -
16B ILE 2.9 8.8 + - - +
17B ALA* 3.3 21.5 - - + -
18B ASP 3.0 23.9 + - - +
21B LEU* 4.0 1.5 - - - +
138B PRO* 4.1 8.3 - - + -
144B MET* 3.9 40.4 - - + +
148B SER* 4.8 0.2 - - - +
149B ILE* 4.8 3.6 - - + -
173B ILE* 3.4 31.6 - - + +
174B TYR* 1.3 67.0 - - - +
176B ASP* 1.3 57.0 + - - +
177B LEU* 3.4 23.5 + - + -
243B ILE* 4.7 8.1 - - + -
244B LEU* 5.7 0.7 - - + -
247B ALA* 5.9 2.5 - - + -
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP 3.2 4.7 - - - -
20B GLY* 2.7 25.4 + - - -
21B LEU* 2.7 35.6 + - + +
22B TRP* 2.8 19.1 + - - +
144B MET* 3.0 16.7 - - - +
174B TYR* 3.1 8.4 + - + +
175B ILE* 1.3 70.4 - - - +
177B LEU* 1.3 64.9 + - - +
178B GLU* 2.9 17.8 + - - +
179B PHE* 2.9 34.3 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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