Contacts of the strand formed by residues 164 - 173 (chain A) in PDB entry 1NVP
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 GLN 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A VAL* 2.8 39.2 + - - +
163A PRO* 1.3 78.4 + - - +
165A LEU* 1.3 65.1 + - - +
166A GLN* 3.5 20.3 + - - +
260A GLY* 3.2 2.0 - - - -
261A SER 2.9 31.8 + - - +
262A CYS* 6.0 0.4 - - + -
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Residues in contact with LEU 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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163A PRO 3.9 3.3 + - - +
164A GLN* 1.3 75.3 - - - +
166A GLN* 1.3 62.0 + - - +
167A ASN 5.1 0.9 - - - +
168A ILE* 4.6 7.2 - - + -
225A LYS* 3.4 40.5 - - - +
227A GLU* 4.5 1.1 - - - +
258A MET* 3.7 30.7 - - + -
259A VAL 3.4 14.1 - - - +
260A GLY* 4.5 2.0 - - - -
318A ARG* 3.5 46.2 - - + +
321A ILE* 4.2 28.7 - - + -
322A TYR* 5.4 2.2 - - + +
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Residues in contact with GLN 166 (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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164A GLN* 3.5 26.5 + - - +
165A LEU* 1.3 77.6 - - - +
167A ASN* 1.3 62.8 + - + +
223A GLY 4.2 1.0 - - - +
225A LYS* 3.0 46.6 + - - +
259A VAL* 2.7 18.7 + - + +
260A GLY 4.4 0.4 - - - -
261A SER* 2.9 33.1 + - - +
6F T 3.2 15.6 - - - +
7F A 3.6 33.8 + - - +
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Residues in contact with ASN 167 (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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165A LEU 3.9 0.4 - - - -
166A GLN* 1.3 82.7 - - - +
168A ILE* 1.3 73.3 + - - +
169A VAL* 4.4 5.7 - - - +
222A THR* 4.6 0.2 - - - -
223A GLY* 3.0 31.5 + - - -
224A ALA 3.4 6.8 + - - -
225A LYS* 4.8 0.2 - - - +
257A ASN 5.4 0.2 - - - -
258A MET* 3.4 0.7 - - - -
259A VAL* 2.8 39.0 + - + +
12E A 4.9 1.8 - - - -
13E A 4.9 0.6 - - - -
5F T 2.9 30.2 + - - +
6F T 3.0 41.4 + - - +
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Residues in contact with ILE 168 (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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165A LEU* 4.6 5.2 - - + -
167A ASN* 1.3 82.5 + - - +
169A VAL* 1.3 67.4 + - - +
221A CYS 3.5 5.4 - - - +
222A THR* 3.5 0.5 - - - -
223A GLY 3.4 19.9 + - - -
224A ALA 3.0 12.9 + - - +
225A LYS 3.7 4.0 - - - +
226A SER* 3.2 50.5 - - - +
227A GLU* 3.6 4.7 - - - +
230A SER* 3.7 24.3 + - - +
255A ILE* 3.9 22.9 - - + -
257A ASN 3.3 10.8 - - - +
258A MET* 4.3 23.3 - - + -
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Residues in contact with VAL 169 (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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167A ASN* 4.4 4.9 - - - +
168A ILE* 1.3 78.4 - - - +
170A SER* 1.3 59.2 + - - +
220A VAL* 3.7 15.3 - - + -
221A CYS 3.2 3.4 - - - +
222A THR* 4.2 9.4 - - + -
255A ILE* 3.7 1.9 - - - -
256A GLN* 2.7 39.4 + - + -
257A ASN* 2.9 18.1 + - + +
13E A 3.6 33.7 - - + +
14E A 3.6 29.4 - - + +
5F T 3.6 12.6 - - - +
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Residues in contact with SER 170 (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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168A ILE 4.2 0.2 - - - -
169A VAL* 1.3 74.9 - - - +
171A THR* 1.3 71.2 + - - +
220A VAL* 3.3 2.6 - - - +
221A CYS* 2.8 45.6 + - - +
230A SER* 2.8 26.0 + - - -
253A PHE* 3.4 25.6 - - - -
254A LYS 3.2 14.4 - - - -
255A ILE* 4.1 3.8 - - - -
256A GLN 4.2 0.4 - - - +
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Residues in contact with THR 171 (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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169A VAL* 5.3 0.4 - - + -
170A SER* 1.3 80.4 - - - +
172A VAL* 1.3 67.1 + - - +
218A LYS* 6.5 0.2 - - - -
219A MET 3.2 12.8 - - - +
220A VAL* 4.1 6.7 - - + -
221A CYS* 4.9 0.4 - - - +
234A ALA* 6.3 0.2 - - - -
252A ASP 3.9 2.4 + - - +
253A PHE* 3.4 3.8 - - - -
254A LYS* 2.9 34.0 + - - +
256A GLN* 2.9 35.1 + - + -
14E A 3.8 32.8 + - + +
15E A 4.9 6.1 - - - -
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Residues in contact with VAL 172 (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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171A THR* 1.3 79.9 - - - +
173A ASN* 1.3 64.2 + - - +
174A LEU* 3.9 3.9 + - + -
218A LYS* 3.6 3.5 - - - +
219A MET* 3.0 64.4 + - + +
221A CYS* 6.4 0.2 - - + -
234A ALA* 4.4 6.5 - - + -
250A PHE* 3.8 38.1 - - + -
251A LEU 3.3 18.2 - - - +
252A ASP 4.2 3.1 - - - -
253A PHE* 3.9 17.0 - - + -
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Residues in contact with ASN 173 (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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172A VAL* 1.3 73.6 - - - +
174A LEU* 1.3 64.2 + - - +
175A GLY* 2.8 29.1 + - - +
216A SER 4.9 2.1 - - - +
217A GLY* 3.8 8.1 - - - +
218A LYS* 3.9 33.7 - - + +
251A LEU* 2.8 58.8 + - + +
252A ASP* 4.8 9.1 + - + +
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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