Contacts of the strand formed by residues 258 - 265 (chain A) in PDB entry 3V4V
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LEU* 4.1 25.4 - - + +
194A VAL* 3.6 41.5 - - + -
203A LYS* 3.8 12.8 - - + -
204A ALA 2.8 16.6 + - - +
205A PHE* 3.1 41.7 - - + +
206A LEU 4.2 2.3 + - - +
235A VAL* 4.8 4.3 - - + -
251A PHE* 4.3 16.8 - - + -
252A SER 3.4 8.5 - - - +
253A ILE* 4.2 15.5 - - + -
257A GLU* 1.3 85.2 - - - +
259A ASN* 1.3 65.8 + - - +
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Residues in contact with ASN 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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205A PHE* 4.6 2.2 - - - -
206A LEU 5.7 0.3 - - - +
208A LYS* 5.5 3.5 - - - +
251A PHE* 3.1 7.0 - - - -
252A SER* 2.8 41.2 + - - +
254A ASP* 2.5 32.7 + - - +
257A GLU* 3.3 35.1 + - - +
258A LEU* 1.3 82.1 - - - +
260A ILE* 1.3 65.6 + - - +
261A LEU 3.5 0.2 + - - -
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Residues in contact with ILE 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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205A PHE* 3.8 21.0 - - + -
211A GLN* 3.3 34.2 + - + +
212A VAL* 4.6 2.9 - - + -
249A TYR* 3.5 34.8 - - + -
250A ILE 3.6 5.6 - - - +
251A PHE* 3.5 21.1 - - + -
259A ASN* 1.3 73.5 - - - +
261A LEU* 1.3 65.1 + - - +
262A HIS* 3.8 24.5 - - - +
263A GLU* 4.6 3.8 - - + +
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Residues in contact with LEU 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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228A ARG* 3.6 50.5 - - - +
234A GLU* 4.2 4.9 - - + -
250A ILE* 2.6 18.7 + - + +
251A PHE 4.2 9.0 - - - +
252A SER* 3.6 23.8 - - - +
260A ILE* 1.3 77.3 - - - +
262A HIS* 1.3 61.9 + - - +
315A GLY 5.0 7.3 - - - +
316A ALA* 3.8 23.2 - - + +
317A VAL* 6.2 0.2 - - - +
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Residues in contact with HIS 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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248A ALA 4.0 0.3 - - - +
249A TYR* 3.5 4.2 - - - -
250A ILE* 3.0 34.8 + - + -
260A ILE* 3.7 7.0 - - - +
261A LEU* 1.3 83.5 + - - +
263A GLU* 1.3 80.8 + - - +
264A MET* 4.2 12.5 - - + +
309A TYR* 6.2 0.2 - - - -
316A ALA 3.3 28.7 - - - +
317A VAL* 4.9 9.7 - - + +
318A MET* 3.5 41.3 + - + +
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Residues in contact with GLU 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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211A GLN 5.0 4.2 - - - +
242A HIS* 4.8 0.2 + - - -
247A LYS* 2.9 42.9 + - + +
248A ALA 3.7 2.9 - - - -
249A TYR* 3.4 32.5 + - + -
260A ILE* 4.9 4.0 - - + -
262A HIS* 1.3 90.6 + - - +
264A MET* 1.3 72.7 + - - +
265A LYS* 5.2 0.4 - - + +
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Residues in contact with MET 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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236A VAL* 5.3 0.2 - - + -
247A LYS* 3.1 8.1 - - - +
248A ALA* 2.8 73.0 + - + +
249A TYR* 4.1 1.8 - - - +
250A ILE* 4.0 26.0 - - + -
262A HIS* 4.2 20.6 - - + +
263A GLU* 1.3 82.7 - - - +
265A LYS* 1.3 60.4 + - - +
273A PHE* 3.2 15.4 - - + -
290A LEU* 4.1 17.5 - - + -
309A TYR* 4.2 40.8 - - + -
318A MET* 4.6 5.4 - - - -
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Residues in contact with LYS 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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243A GLU* 4.1 11.6 + - - -
245A ILE* 3.6 33.5 - - + +
246A GLY 4.1 2.2 - - - +
247A LYS* 3.7 33.4 - - + +
263A GLU* 5.2 0.9 - - + +
264A MET* 1.3 74.1 - - - +
266A GLY* 1.3 75.9 + - - +
267A LYS* 5.3 6.2 + - - +
273A PHE* 3.9 9.9 - - - -
309A TYR* 4.1 5.9 + - - -
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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