Contacts of the strand formed by residues 268 - 272 (chain O) 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 CYS 268 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259O ARG* 3.6 33.9 - - - -
260O VAL 3.3 12.3 - - - +
261O TRP* 3.9 21.8 - - + -
267O GLU* 1.3 79.8 - - - +
269O LYS* 1.3 65.4 + - - +
270O ALA* 3.3 24.4 - - - -
271O GLU* 4.7 2.2 - - - -
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Residues in contact with LYS 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248O LEU* 5.0 5.8 - - + -
260O VAL* 3.1 10.3 + - + +
262O VAL* 3.9 22.6 - - + +
267O GLU* 3.7 20.2 - - - +
268O CYS* 1.3 74.0 - - - +
270O ALA* 1.3 61.4 + - + +
325O VAL* 5.0 13.4 - - + +
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Residues in contact with ALA 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O VAL 4.4 0.2 - - - -
259O ARG* 3.5 1.4 - - - -
260O VAL* 3.1 31.2 + - + -
268O CYS* 3.2 16.3 - - - -
269O LYS* 1.3 81.3 - - - +
271O GLU* 1.3 60.0 + - - +
272O LEU* 4.1 18.6 - - + -
325O VAL* 4.0 28.9 - - + +
328O GLY* 5.1 5.6 - - - -
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Residues in contact with GLU 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257O THR* 4.0 17.0 + - + +
258O VAL 3.6 2.5 - - - -
259O ARG* 3.7 49.8 + - + +
268O CYS* 5.2 2.4 - - - -
270O ALA* 1.3 72.2 - - - +
272O LEU* 1.3 65.9 + - - +
273O ARG* 3.6 31.4 + - + +
328O GLY 5.4 1.2 - - - +
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Residues in contact with LEU 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256O GLN 4.2 1.0 - - - +
257O THR* 3.6 6.9 - - - -
258O VAL* 2.7 54.4 + - + +
260O VAL* 4.9 5.4 - - + -
270O ALA* 4.3 14.8 - - + -
271O GLU* 1.3 75.1 - - - +
273O ARG* 1.3 59.9 + - - +
274O GLU 3.8 1.1 - - - -
275O HIS* 5.3 2.4 + - - -
311O LEU* 3.6 31.4 - - + -
323O TRP* 3.5 46.7 - - + -
324O ASP 5.5 0.2 - - - +
325O VAL* 5.7 3.8 - - + -
328O GLY* 3.5 30.3 - - - +
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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
------------------------------------------------------------
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