Contacts of the strand formed by residues 258 - 266 (chain A) in PDB entry 3NVQ
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 ASN 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A NAG 1.3 83.4 + - - +
245A ARG* 5.0 11.2 - - + -
246A GLU 3.1 16.0 + - - +
247A ASP* 4.4 3.6 + - - -
248A ASN* 4.0 2.6 - - - +
256A PRO* 4.1 9.4 - - - +
257A LEU* 1.3 84.7 + - - +
259A VAL* 1.3 65.4 + - - +
301A ASN* 3.1 26.3 + - - +
302A ARG* 5.7 4.0 - - + -
297E ASN* 5.6 0.2 - - - +
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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
----------------------------------------------------------
245A ARG* 3.2 7.2 - - - +
246A GLU* 2.8 38.6 + - + +
247A ASP 4.1 12.1 - - - +
248A ASN* 4.3 14.6 - - - +
249A PRO* 4.6 1.1 - - + -
256A PRO* 6.4 0.4 - - + -
258A ASN* 1.3 76.0 - - - +
260A SER* 1.3 69.3 + - - +
261A ARG* 3.8 28.3 - - - +
288A MET* 3.1 46.9 - - + -
289A LEU 5.6 0.2 - - - +
301A ASN* 4.2 9.4 - - + +
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Residues in contact with SER 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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244A PHE 3.6 3.8 - - - -
245A ARG* 4.4 2.2 - - - +
259A VAL* 1.3 75.7 - - - +
261A ARG* 1.3 64.6 + - - +
288A MET* 3.3 9.7 - - - +
289A LEU* 2.9 33.4 + - - -
301A ASN 2.8 25.7 + - - -
302A ARG* 3.9 0.2 - - - -
303A LEU* 2.9 35.8 + - - +
325A PHE* 3.9 14.4 - - - -
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Residues in contact with ARG 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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243A PHE* 3.3 8.8 - - - +
244A PHE* 2.7 58.6 + - + +
246A GLU* 2.8 41.9 + - + +
249A PRO* 3.9 20.6 - - - +
259A VAL* 3.8 10.9 - - - +
260A SER* 1.3 85.1 - - - +
262A VAL* 1.3 62.6 + - - +
286A LYS* 3.9 17.1 - - + +
287A ALA 3.3 11.9 - - - +
288A MET* 3.4 25.6 - - - +
289A LEU* 4.1 7.5 - - - +
303A LEU* 4.5 1.1 - - - +
386A GLU* 2.8 46.7 + - - +
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Residues in contact with VAL 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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241A TYR* 4.5 8.3 - - + -
242A TYR 3.3 7.2 - - - +
243A PHE* 3.5 35.2 - - + -
244A PHE* 4.3 1.8 - - - -
261A ARG* 1.3 74.6 - - - +
263A ALA* 1.3 71.2 + - - +
286A LYS* 3.4 1.7 - - - +
287A ALA* 2.9 44.2 + - + +
289A LEU* 4.1 18.8 - - + -
342A ILE* 4.1 24.0 - - + -
346A PHE* 3.5 14.3 - - + -
391A VAL* 4.3 1.3 - - + -
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Residues in contact with ALA 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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240A ILE 4.3 0.2 - - - -
241A TYR* 3.0 10.0 - - - +
242A TYR* 2.8 45.7 + - + -
244A PHE* 3.8 16.6 - - + -
262A VAL* 1.3 75.4 - - - +
264A GLN* 1.3 61.8 + - - +
284A PHE* 3.7 26.2 - - + -
285A LEU 3.3 11.9 - - - +
286A LYS* 4.4 0.7 - - + -
346A PHE* 4.2 2.5 - - - -
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Residues in contact with GLN 264 (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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239A LYS* 3.6 22.4 - - + +
240A ILE 3.2 4.9 - - - -
241A TYR* 3.5 16.4 + - + -
263A ALA* 1.3 76.0 - - - +
265A LEU* 1.3 67.8 + - - +
283A THR* 2.9 34.9 + - - +
284A PHE* 3.4 4.9 - - - -
285A LEU* 3.0 36.0 + - + +
343A ASP* 5.3 1.0 - - - +
346A PHE* 3.5 43.5 - - + +
364A GLY* 3.0 24.3 + - - +
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Residues in contact with LEU 265 (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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203A PHE* 3.4 38.1 - - + -
214A THR* 4.9 1.1 - - + -
239A LYS* 3.2 9.9 - - - +
240A ILE* 2.7 42.0 + - + +
242A TYR* 4.0 15.3 - - + -
264A GLN* 1.3 74.7 - - - +
266A CYS* 1.3 60.2 + - - +
281A TRP* 3.7 46.4 - - + +
283A THR* 3.9 5.8 - - - -
284A PHE* 3.6 42.6 - - + +
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Residues in contact with CYS 266 (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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238A ASP 3.6 4.5 - - - -
239A LYS* 4.0 4.5 - - - -
265A LEU* 1.3 72.8 - - - +
267A ARG* 1.3 67.1 + - - +
268A GLY 4.3 2.5 - - - +
269A ASP* 3.0 26.0 + - - +
281A TRP* 3.6 6.9 - - - -
283A THR* 3.0 27.9 + - + +
364A GLY 3.6 13.9 - - - -
366A CYS* 2.1 61.9 - - + -
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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