Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 2R5A
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 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ASN* 3.0 16.2 + - - -
230A VAL* 3.5 1.2 - - - -
231A LEU 2.9 31.0 + - - +
232A GLY 3.1 0.4 - - - -
233A SER* 1.3 83.9 - - - +
235A LEU* 1.3 60.8 + - - +
249A TRP* 3.2 41.5 + - + +
250A ARG 3.5 7.2 - - - +
251A LEU* 3.8 26.9 - - + +
323A VAL* 3.6 18.1 - - - +
328A PRO* 2.6 29.9 + - - +
329A GLN* 3.3 14.5 + - - +
331A ILE* 3.7 19.7 - - + +
365A ASP* 5.2 2.6 + - - -
367A PHE* 4.8 4.5 - - + -
371A TRP* 6.1 1.1 - - + -
377A HIS* 3.3 32.6 + - + -
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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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203A ASN* 3.6 17.7 - - - +
205A PHE* 3.4 54.3 - - + -
211A LEU* 5.3 0.9 - - + -
227A VAL* 4.2 15.5 - - + -
229A GLY 3.6 3.8 - - - +
230A VAL* 4.3 3.4 - - + -
234A ARG* 1.3 73.6 - - - +
236A ARG* 1.3 59.8 + - - +
237A LEU* 3.8 22.4 + - + +
248A PHE 3.6 0.5 - - - +
249A TRP* 3.2 10.1 - - - -
250A ARG 2.8 35.8 + - - +
252A VAL* 3.9 6.7 - - + -
257A ILE* 3.8 29.2 - - + -
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Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 3.6 6.1 - - - -
228A VAL* 2.9 39.8 + - + +
229A GLY* 2.9 23.0 + - - +
235A LEU* 1.3 71.2 - - - +
237A LEU* 1.3 60.4 + - - +
238A ARG* 4.5 5.6 - - - +
244A SER 4.7 5.7 + - - -
247A ASP* 2.8 41.5 + - + +
248A PHE 3.5 3.8 - - - +
249A TRP* 3.6 41.9 - - + +
329A GLN* 3.6 24.2 - - - +
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Residues in contact with LEU 237 (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 LEU* 3.7 35.0 - - + -
213A ALA* 4.6 1.6 - - + -
225A ALA* 4.3 4.5 - - + -
226A THR 3.5 13.0 - - - +
227A VAL* 4.0 8.7 - - + -
228A VAL* 4.3 1.8 - - - -
235A LEU* 4.1 15.9 - - + +
236A ARG* 1.3 80.7 - - - +
238A ARG* 1.3 61.4 + - - +
247A ASP* 3.2 9.9 - - - +
248A PHE* 2.7 69.3 + - + +
250A ARG* 3.9 22.0 - - + -
257A ILE* 3.9 17.9 - - + -
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Residues in contact with ARG 238 (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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225A ALA* 3.3 3.0 - - - -
226A THR* 2.9 31.3 + - - -
228A VAL* 3.9 36.7 - - + +
236A ARG* 4.5 5.1 - - - +
237A LEU* 1.3 75.0 - - - +
239A LEU* 1.3 71.9 + - - +
240A ASP* 3.5 1.6 + - - +
243A ASP 3.6 22.0 - - - +
244A SER* 3.7 26.8 + - - +
246A ASN 5.8 0.4 - - - -
247A ASP* 2.8 40.8 + - - +
248A PHE* 4.8 0.9 - - - -
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Residues in contact with LEU 239 (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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213A ALA* 4.7 5.6 - - + +
215A ASP* 3.4 39.7 - - + +
216A PRO* 4.5 3.1 - - + -
217A ARG* 6.2 2.9 - - - +
223A CYS* 3.9 15.3 - - + -
224A ILE 3.5 15.3 - - - +
225A ALA* 3.9 16.6 - - + -
238A ARG* 1.3 78.0 - - - +
240A ASP* 1.3 65.9 + - - +
241A GLY 3.4 0.2 + - - -
242A SER* 2.7 34.0 + - - +
248A PHE* 3.9 22.1 - - + -
273A PRO* 3.7 23.8 - - + -
274A LEU 5.2 0.2 - - - +
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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