Contacts of the strand formed by residues 159 - 165 (chain A) in PDB entry 2NVU
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A THR* 3.4 5.7 - - - -
156A TYR* 2.9 40.8 + - + +
157A GLY 3.3 0.4 - - - -
158A LEU* 1.3 83.9 - - - +
160A GLY* 1.3 73.4 + - - +
161A TYR* 5.3 0.2 - - + -
425A LEU* 4.4 23.6 - - + +
429A LEU* 4.6 17.7 - - + -
482A PHE* 4.0 23.3 - - + -
485A TYR* 4.5 8.7 - - + +
493A ILE* 3.9 7.4 - - - +
521A ILE* 4.3 13.0 - - + -
522A TYR 3.3 8.1 - - - +
523A SER* 5.4 0.7 - - - -
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Residues in contact with GLY 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG 3.5 5.4 - - - -
159A VAL* 1.3 79.6 - - - +
161A TYR* 1.3 61.0 + - - -
493A ILE* 4.7 1.6 - - - -
497A LEU* 4.2 19.3 - - - -
520A TYR* 4.4 0.9 - - - -
521A ILE* 3.4 7.1 - - - +
522A TYR* 2.9 45.9 + - - +
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 4.1 19.5 - - + +
153A CYS* 3.4 3.6 - - - -
154A ARG* 2.8 57.9 + - + +
159A VAL* 5.3 0.4 - - + -
160A GLY* 1.3 73.2 - - - -
162A MET* 1.3 65.2 + - - +
163A ARG* 3.2 40.5 - - + +
398A LEU* 5.1 3.8 - - - +
401A GLU* 4.1 11.6 + - - -
402A TYR* 5.4 3.8 + - - -
426A TYR* 4.0 20.2 - + + -
429A LEU* 3.9 24.9 - - + -
497A LEU* 3.8 7.2 - - - +
519A THR* 3.4 26.4 - - + +
520A TYR 3.6 3.6 - - - -
521A ILE* 4.9 5.2 - - + -
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Residues in contact with MET 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.0 12.6 - - + -
152A ILE 3.3 3.4 - - - -
153A CYS* 4.2 8.1 - - - -
161A TYR* 1.3 79.3 - - - +
163A ARG* 1.3 61.0 + - - +
497A LEU* 3.8 22.7 - - + -
500A ALA* 4.0 8.7 - - + +
501A ALA* 3.8 23.6 - - - -
504A GLU* 3.9 15.5 - - + -
516A PHE* 3.6 33.3 - - + -
518A ASN 3.5 1.0 - - - +
519A THR* 3.2 7.6 - - - +
520A TYR* 2.9 46.1 + - + +
2330B LEU* 3.9 24.0 - - + -
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU 3.8 1.0 - - - +
151A LEU* 3.3 6.6 - - - +
152A ILE* 2.8 52.6 + - + +
161A TYR* 3.2 31.6 - - + +
162A MET* 1.3 70.8 - - - +
164A ILE* 1.3 69.6 + - - +
165A ILE* 3.3 25.5 - - - +
395A CYS* 4.2 0.6 - - - +
396A ARG 2.8 29.1 + - - -
397A SER 3.9 4.8 + - - -
398A LEU* 4.5 12.2 - - + +
401A GLU* 2.8 34.6 + - - +
518A ASN* 3.3 39.9 + - - +
519A THR* 4.0 5.4 - - - +
534A LEU 3.7 10.5 + - - -
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU 3.7 14.6 - - - +
151A LEU* 3.7 15.7 - - + -
163A ARG* 1.3 86.8 + - - +
165A ILE* 1.3 60.6 + - - +
166A ILE* 4.1 11.0 - - + -
395A CYS* 3.3 16.1 - - - +
504A GLU* 5.7 0.7 - - + -
508A ILE* 3.5 30.5 - - + -
515A ILE* 4.3 19.3 - - + -
516A PHE* 3.2 52.4 - - + +
518A ASN* 3.0 18.6 + - - +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA* 4.4 2.7 - - + +
144A TRP* 3.6 34.8 - - + -
148A ILE 4.2 3.1 - - - +
149A PRO* 4.0 2.1 - - - +
150A LEU* 2.7 55.7 + - + +
152A ILE* 4.0 24.2 - - + -
163A ARG* 3.3 26.7 - - - +
164A ILE* 1.3 74.4 - - - +
166A ILE* 1.3 62.3 + - - +
395A CYS* 4.0 1.6 - - - -
396A ARG 4.2 7.2 - - - +
397A SER* 4.4 3.6 - - - -
398A LEU* 3.8 28.5 - - + +
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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