Contacts of the strand formed by residues 288 - 294 (chain B) in PDB entry 2RHB
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 SER 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLY 3.2 12.3 + - - +
244B GLN* 3.1 16.3 - - - +
245B LEU* 3.3 10.2 + - - -
279B PHE* 4.6 3.8 - - - -
280B ILE 3.2 12.8 - - - -
281B THR* 3.9 16.2 - - - -
286B GLY 3.4 8.3 + - - -
287B SER* 1.3 75.5 + - - +
289B LYS* 1.3 60.5 + - - +
290B CYS 4.4 0.2 - - - -
63C ILE* 4.8 4.3 + - - +
162C VAL* 4.5 5.6 - - - +
163C ASN* 4.0 14.0 + - - -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLN* 3.5 31.0 - - - +
245B LEU* 3.3 42.7 - - + +
246B GLY* 5.3 2.2 - - - -
247B GLY 6.0 0.7 - - - +
249B HIS* 6.2 4.7 - - - -
278B TYR 3.7 3.1 - - - +
279B PHE* 3.5 4.1 - - - -
280B ILE* 2.8 33.4 + - + -
288B SER* 1.3 75.5 - - - +
290B CYS* 1.3 68.9 + - - +
291B VAL* 3.6 15.8 + - - +
292B CYS* 4.0 23.1 - - + +
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Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLN* 5.1 1.0 + - - -
279B PHE* 3.5 41.7 - - + -
289B LYS* 1.3 80.8 + - - +
291B VAL* 1.3 81.6 + - + +
12C LYS 3.5 15.7 - - - +
14C HIS* 3.7 22.9 - - - -
63C ILE* 4.3 9.2 - - - -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B PHE* 4.1 23.2 - - + -
277B ASN* 3.9 24.0 - - + +
278B TYR 3.6 6.8 + - - -
289B LYS* 3.6 15.2 + - - +
290B CYS* 1.3 90.3 - - + +
292B CYS* 1.3 58.2 + - - +
293B SER* 4.0 3.4 + - - +
11C ASN 4.3 17.5 - - - +
12C LYS* 4.2 23.7 + - - +
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Residues in contact with CYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.4 16.6 - - - -
247B GLY 4.8 2.5 - - - -
248B LEU* 3.5 26.5 - - - -
249B HIS* 5.6 4.0 - - - -
277B ASN* 4.3 0.7 - - - -
278B TYR* 2.8 36.1 + - - +
280B ILE* 3.7 23.6 - - + -
289B LYS* 4.0 25.6 - - + +
291B VAL* 1.3 72.2 - - - +
293B SER* 1.3 63.4 + - - +
294B VAL* 3.4 7.5 - - - +
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU 3.9 1.2 - - - +
249B HIS* 3.3 44.3 + - - +
275B VAL* 4.0 15.7 - - - -
276B LYS 3.5 2.0 - - - -
277B ASN* 3.2 24.7 + - - -
291B VAL* 3.8 4.1 + - - +
292B CYS* 1.3 72.6 - - - +
294B VAL* 1.3 63.7 + - - +
295B ILE* 5.6 1.3 - - - -
343B PRO* 4.0 20.3 + - - +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU 3.9 14.8 - - - +
249B HIS 3.1 4.9 - - - +
251B MET* 3.9 42.4 - - + +
254B LEU* 4.0 14.6 - - + -
274B THR 4.3 0.2 - - - +
275B VAL* 4.0 1.2 - - - +
276B LYS* 2.7 39.5 + - - +
278B TYR* 4.1 21.1 - - + -
280B ILE* 4.2 4.5 - - + -
292B CYS* 3.4 17.9 - - - +
293B SER* 1.3 80.7 - - - +
295B ILE* 1.3 65.6 + - - +
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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