Contacts of the strand formed by residues 230 - 235 (chain A) in PDB entry 4OIB
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 ARG 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A SER 3.3 22.7 + - - -
228A GLU* 4.0 13.0 + - - +
229A ALA* 1.3 81.4 + - - +
231A VAL* 1.3 61.1 + - - +
246A LEU* 6.0 1.8 - - - +
273A VAL* 3.2 3.3 - - - +
274A THR* 3.2 41.1 + - - +
1F NAG 5.8 0.2 - - - +
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Residues in contact with VAL 231 (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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229A ALA 5.5 1.8 - - - +
230A ARG* 1.3 77.2 - - - +
232A TYR* 1.3 71.5 + - - +
233A LEU* 5.6 1.8 - - + -
242A PRO* 5.7 5.2 - - + +
244A VAL* 4.2 33.2 - - + -
251A PHE* 4.2 22.0 - - + -
253A ALA* 5.1 6.1 - - + -
271A CYS* 4.7 9.2 - - - -
272A ASN 3.5 13.5 - - - +
273A VAL* 3.6 20.6 - - + -
1F NAG 5.8 0.7 - - - -
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Residues in contact with TYR 232 (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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231A VAL* 1.3 77.7 - - - +
233A LEU* 1.3 61.8 + - - +
234A ALA* 3.1 27.2 - - + +
236A GLY 4.5 5.5 + - - -
237A ASP* 4.8 5.2 + - - -
239A ASN* 3.2 36.2 - - + +
242A PRO* 6.0 0.2 - - - -
270A VAL* 3.4 21.5 - - + +
271A CYS* 3.6 1.9 - - - -
272A ASN* 2.9 49.7 + - - +
281A GLU* 6.0 0.2 - - - -
1F NAG 3.6 34.5 - - + -
2F NAG 5.3 10.1 + - - -
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Residues in contact with LEU 233 (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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202A LEU* 4.6 11.0 - - + -
216A VAL* 4.8 18.8 - - + +
218A CYS* 4.5 14.4 - - + -
231A VAL* 5.6 2.0 - - + -
232A TYR* 1.3 78.4 - - - +
234A ALA* 1.3 68.2 + - - +
239A ASN* 3.2 10.1 + - - +
240A LEU* 3.2 40.4 + - + +
241A SER 4.0 1.7 + - - -
242A PRO* 3.5 34.9 - - + +
253A ALA* 4.8 8.7 - - + +
255A ALA* 5.4 1.3 - - + -
269A LEU* 5.0 4.5 - - + -
270A VAL 3.3 24.5 - - - +
271A CYS* 4.1 15.7 - - + -
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Residues in contact with ALA 234 (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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232A TYR* 3.1 34.1 - - + +
233A LEU* 1.3 79.4 - - - +
235A LEU* 1.3 61.1 + - - +
236A GLY 3.9 7.7 + - - +
238A GLN 3.2 14.8 - - - +
239A ASN* 3.7 5.4 - - - -
240A LEU* 3.7 10.5 - - - +
269A LEU* 3.4 13.6 - - - +
270A VAL* 3.5 25.3 + - + +
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Residues in contact with LEU 235 (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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208A LEU* 5.0 9.6 - - + -
234A ALA* 1.3 70.1 - - - +
236A GLY* 1.3 65.7 + - - +
237A ASP 3.3 0.2 + - - -
238A GLN* 2.7 37.9 + - + +
240A LEU* 3.8 16.0 - - + +
257A ALA* 5.4 6.1 - - + -
258A THR 5.3 5.2 - - - +
259A ALA* 5.5 0.9 - - - -
260A SER* 4.0 27.8 - - - +
267A ARG* 4.1 20.6 - - + +
268A GLN 3.7 7.4 - - - +
269A LEU* 3.7 24.7 - - + -
286A VAL* 4.8 7.9 - - + -
288A ILE* 4.1 20.9 - - + -
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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