Contacts of the strand formed by residues 258 - 262 (chain T) in PDB entry 1VYH
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 258 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251T SER 3.4 17.3 - - - +
252T CYS* 4.3 3.4 - - - -
257T THR* 1.3 78.1 - - - +
259T ARG* 1.3 68.3 + - - +
270T ALA 4.0 0.2 - - - +
271T GLU* 3.5 1.9 - - - -
272T LEU* 2.7 68.6 + - + +
275T HIS* 5.6 1.6 - - + -
279T VAL* 4.1 23.3 - - + -
282T ILE* 4.2 13.7 - - + -
311T LEU* 3.7 23.1 - - + -
313T SER* 4.3 7.9 - - - -
323T TRP* 5.4 2.0 - - + +
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Residues in contact with ARG 259 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231T THR 5.5 0.2 + - - -
232T GLY* 3.7 26.5 + - - -
233T HIS* 3.4 33.2 + - + +
249T ILE 3.6 0.9 - - - +
250T ALA* 3.3 3.5 - - - -
251T SER* 2.7 36.1 + - - +
255T ASP* 5.3 2.4 + - - -
257T THR* 3.8 10.8 - - + +
258T VAL* 1.3 75.1 - - - +
260T VAL* 1.3 62.6 + - - +
261T TRP* 3.1 39.6 - - + +
268T CYS* 3.2 26.4 - - - -
270T ALA 3.5 5.2 - - - +
271T GLU* 2.8 38.5 + - + +
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Residues in contact with VAL 260 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248T LEU* 4.0 32.8 - - + -
249T ILE 3.1 6.7 - - - +
250T ALA* 4.3 0.9 - - + -
258T VAL* 4.2 2.0 + - + -
259T ARG* 1.3 76.9 - - - +
261T TRP* 1.3 60.7 + - - +
268T CYS* 3.2 5.2 - - - +
269T LYS* 3.1 33.4 + - + -
270T ALA* 3.1 14.1 + - + +
272T LEU* 5.2 1.1 - - + +
284T TRP* 4.0 20.9 - - + -
311T LEU* 4.0 17.3 - - + -
325T VAL* 3.8 32.1 - - + -
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Residues in contact with TRP 261 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216T ILE* 4.3 8.6 - - + +
230T PHE* 3.6 32.1 - + + -
231T THR 3.0 30.5 - - - -
232T GLY* 3.6 11.7 - - - -
233T HIS* 4.3 6.7 - + - -
248T LEU* 3.0 10.9 - - - +
249T ILE* 2.6 66.8 + - + -
251T SER* 3.6 13.0 - - - -
259T ARG* 3.1 50.9 - - + +
260T VAL* 1.3 74.6 - - - +
262T VAL* 1.3 63.8 + - - +
266T LYS 3.6 24.7 - - - -
267T GLU 3.6 4.9 - - - -
268T CYS* 3.8 17.7 - - + -
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Residues in contact with VAL 262 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230T PHE* 4.2 2.6 - - - -
247T THR* 4.8 2.9 - - + +
248T LEU* 3.7 15.3 - - + -
260T VAL 4.3 0.2 + - - -
261T TRP* 1.3 71.4 - - - +
263T VAL* 1.3 65.9 + - - +
264T ALA* 3.7 6.5 - - + +
265T THR* 3.4 30.1 - - - +
266T LYS* 3.0 21.5 + - - -
267T GLU* 2.9 38.9 + - + +
269T LYS* 4.3 19.5 - - + +
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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