Contacts of the strand formed by residues 251 - 263 (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 LEU 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.3 0.9 - - - +
173A ASN* 2.8 57.8 + - + +
175A GLY* 4.3 13.5 - - - -
249A LYS* 4.0 33.9 - - + -
250A PHE* 1.3 75.5 - - - +
252A ASP* 1.3 79.7 + - - +
253A PHE 3.3 3.3 + - - -
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Residues in contact with ASP 252 (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* 3.9 6.1 + - - +
172A VAL* 4.2 2.3 - - - -
173A ASN* 4.8 9.9 + - + +
250A PHE 4.0 1.4 + - - -
251A LEU* 1.3 85.5 - - - +
253A PHE* 1.3 68.0 + - - +
254A LYS* 3.4 7.5 + - - +
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Residues in contact with PHE 253 (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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170A SER* 3.4 34.8 - - - -
171A THR 3.4 14.1 - - - -
172A VAL* 3.9 8.7 - - + -
227A GLU 4.7 0.9 - - - -
230A SER* 3.9 4.9 - - - -
231A ARG* 3.2 76.3 + - + +
234A ALA* 4.1 5.4 - - + -
250A PHE* 3.8 31.1 + + + -
251A LEU 3.3 2.8 + - - -
252A ASP* 1.3 78.7 - - - +
254A LYS* 1.3 61.6 + - - +
255A ILE* 3.2 29.6 - - + -
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Residues in contact with LYS 254 (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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170A SER* 3.2 3.1 - - - -
171A THR* 2.9 32.9 + - - +
252A ASP 3.9 6.3 - - - +
253A PHE* 1.3 83.9 - - - +
255A ILE* 1.3 79.9 + - - +
256A GLN* 3.5 24.3 + - - +
316A LYS* 3.9 24.5 - - - +
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Residues in contact with ILE 255 (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* 3.9 22.9 - - + -
169A VAL 3.8 3.4 - - - -
170A SER* 4.1 1.3 - - - -
227A GLU* 4.9 20.6 - - + +
230A SER* 4.9 2.5 - - - +
253A PHE* 3.2 35.4 - - + -
254A LYS* 1.3 87.6 - - - +
256A GLN* 1.3 60.5 + - - +
257A ASN 4.1 2.5 - - - +
258A MET* 3.7 33.0 - - + -
316A LYS* 3.6 29.7 - - - +
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Residues in contact with GLN 256 (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* 2.7 19.2 + - + +
170A SER* 4.5 0.4 - - - -
171A THR* 2.9 30.7 + - + -
254A LYS* 3.8 31.3 + - - +
255A ILE* 1.3 77.1 - - - +
257A ASN* 1.3 61.0 + - + +
314A GLY 5.1 0.9 - - - +
315A ALA 4.0 4.1 - - - +
316A LYS* 3.3 40.2 + - - +
13E A 3.4 14.1 - - + +
14E A 3.4 47.0 + - - +
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Residues in contact with ASN 257 (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* 5.5 0.2 - - - +
168A ILE* 3.3 5.2 - - - +
169A VAL* 2.9 34.2 + - + +
255A ILE* 3.8 1.2 - - - +
256A GLN* 1.3 80.9 - - - +
258A MET* 1.3 70.9 + - - +
259A VAL* 4.1 5.1 - - - +
313A THR* 3.5 2.4 + - - -
314A GLY* 3.0 34.1 + - - -
315A ALA 3.2 5.6 + - - -
12E A 3.2 33.2 + - - -
13E A 3.2 40.8 + - - +
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Residues in contact with MET 258 (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* 3.7 31.9 - - + -
167A ASN 3.4 6.7 - - - +
168A ILE* 4.3 11.2 - - + -
227A GLU* 3.8 22.7 - - + +
255A ILE* 3.7 15.5 - - + -
257A ASN* 1.3 81.3 + - - +
259A VAL* 1.3 64.3 - - - +
313A THR* 3.6 3.6 - - - -
314A GLY 3.5 19.4 + - - -
315A ALA* 2.9 22.3 + - + +
316A LYS 3.8 3.8 - - - +
317A VAL* 3.3 37.5 - - - +
318A ARG* 3.4 15.0 - - - +
321A ILE* 3.7 9.9 - - + +
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Residues in contact with VAL 259 (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* 3.4 9.4 - - - +
166A GLN* 2.7 38.9 + - + -
167A ASN* 2.8 29.9 + - + +
257A ASN* 4.1 5.2 - - - +
258A MET* 1.3 75.5 - - - +
260A GLY* 1.3 64.2 + - - +
311A VAL* 4.1 2.9 - - + -
312A LEU 3.2 10.1 - - - +
313A THR* 3.4 21.8 - - - +
321A ILE* 4.7 0.4 - - - -
12E A 3.8 7.9 - - + +
6F T 3.6 17.7 - - - +
7F A 3.7 29.4 - - + +
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Residues in contact with GLY 260 (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 3.2 13.7 - - - -
165A LEU* 4.2 6.1 - - - -
166A GLN* 4.4 2.2 - - - -
259A VAL* 1.3 76.0 - - - +
261A SER* 1.3 63.1 + - - -
311A VAL* 3.4 6.4 - - - +
312A LEU* 2.8 37.8 + - - +
321A ILE* 4.3 14.7 - - - +
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Residues in contact with SER 261 (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* 3.5 1.0 - - - +
164A GLN* 2.9 31.7 + - - +
166A GLN* 2.9 36.2 + - - +
260A GLY* 1.3 75.3 - - - -
262A CYS* 1.3 65.7 + - - +
310A VAL 3.1 13.5 - - - -
311A VAL* 4.6 0.7 - - - -
312A LEU* 4.3 2.1 - - - +
7F A 3.9 27.8 + - - -
8F T 5.4 2.0 - - - -
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Residues in contact with CYS 262 (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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161A ILE* 4.1 11.7 - - + -
162A VAL 4.2 4.0 - - - +
163A PRO* 4.0 18.8 - - + -
164A GLN* 6.1 0.2 - - - -
261A SER* 1.3 79.8 - - - +
263A ASP* 1.3 59.4 + - - +
309A LYS* 3.5 7.3 - - - +
310A VAL* 2.8 40.2 + - - +
312A LEU* 4.5 3.6 - - - -
325A PHE* 3.3 48.2 - - - -
8F T 5.9 0.3 - - - +
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Residues in contact with ASP 263 (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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161A ILE* 3.6 21.5 - - - +
262A CYS* 1.3 77.0 - - - +
264A VAL* 1.3 62.8 + - - +
265A LYS* 2.6 61.0 + - - +
307A SER 4.5 2.8 - - - +
308A GLY* 3.8 11.1 - - - +
309A LYS* 3.0 35.5 - - + -
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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