Contacts of the strand formed by residues 258 - 262 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H SER 3.4 14.6 - - - +
252H CYS* 5.0 0.2 - - - -
257H THR* 1.3 77.5 - - - +
259H ARG* 1.3 71.4 + - - +
260H VAL* 4.7 0.4 - - + -
270H ALA 3.9 0.2 - - - +
271H GLU* 3.5 1.6 - - - -
272H LEU* 2.7 68.5 + - + +
275H HIS* 5.2 3.1 - - + -
279H VAL* 4.1 13.5 - - + -
282H ILE* 4.5 10.1 - - + -
311H LEU* 4.0 19.3 - - + -
313H SER* 4.0 26.7 - - - +
323H TRP* 5.4 1.3 - - + -
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Residues in contact with ARG 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H THR 4.8 0.8 + - - -
232H GLY* 3.1 38.8 + - - -
233H HIS* 3.5 26.8 - - + +
249H ILE 3.5 0.9 - - - +
250H ALA* 3.3 2.9 - - - -
251H SER* 2.7 39.4 + - - +
255H ASP* 5.4 1.2 + - - -
257H THR* 3.9 5.6 - - + +
258H VAL* 1.3 78.3 - - - +
260H VAL* 1.3 62.7 + - - +
261H TRP* 3.4 36.6 - - + +
268H CYS* 3.9 24.3 - - - -
270H ALA 3.5 4.7 - - - +
271H GLU* 3.6 35.1 + - + +
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Residues in contact with VAL 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H LEU* 4.3 23.8 - - + -
249H ILE 3.1 5.4 - - - +
250H ALA* 4.1 3.4 - - + -
258H VAL* 4.1 2.4 + - + -
259H ARG* 1.3 73.9 - - - +
261H TRP* 1.3 63.7 + - - +
268H CYS* 3.2 4.7 - - - +
269H LYS* 3.0 34.1 + - + -
270H ALA* 3.1 13.2 + - + +
272H LEU* 5.3 2.0 - - + -
284H TRP* 4.0 12.1 - - + -
311H LEU* 3.6 31.4 - - + -
325H VAL* 3.7 31.9 - - + -
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Residues in contact with TRP 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H ILE* 3.7 11.5 - - + +
230H PHE* 3.4 38.1 - + + -
231H THR 3.3 29.6 - - - -
232H GLY* 3.7 9.4 - - - -
233H HIS* 3.9 14.8 - + - -
248H LEU* 3.3 9.2 - - - +
249H ILE* 2.6 67.3 + - + -
251H SER* 3.1 23.5 + - - -
259H ARG* 3.4 36.3 - - + +
260H VAL* 1.3 73.5 - - - +
262H VAL* 1.3 62.5 + - - +
266H LYS 3.9 18.4 - - - -
267H GLU 3.6 4.3 - - - +
268H CYS* 3.8 16.8 - - + -
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Residues in contact with VAL 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H PHE* 4.1 1.6 - - - -
247H THR* 4.7 2.0 - - + +
248H LEU* 3.2 22.9 - - + -
260H VAL 4.3 0.4 + - - -
261H TRP* 1.3 72.3 - - - +
263H VAL* 1.3 64.0 + - - +
264H ALA* 3.7 4.9 - - + +
265H THR* 3.3 37.5 - - - +
266H LYS* 3.0 20.6 + - - -
267H GLU* 2.8 22.6 + - + +
268H CYS* 4.5 0.6 - - - +
269H LYS* 4.0 26.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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