Contacts of the strand formed by residues 288 - 294 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ILE 4.9 3.6 + - - -
162D VAL* 4.2 5.6 - - - +
163D ASN* 4.0 23.6 + - - -
243F GLY 3.4 9.4 + - - +
244F GLN* 3.4 11.8 - - - +
245F LEU* 3.3 15.6 + - - -
279F PHE* 4.6 3.7 - - - -
280F ILE 3.1 13.7 - - - -
281F THR* 4.1 5.6 - - - -
286F GLY 3.3 8.8 + - - -
287F SER* 1.3 76.8 + - - +
289F LYS* 1.3 60.9 + - - +
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Residues in contact with LYS 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F GLN* 3.6 24.9 - - + +
245F LEU* 3.3 34.6 + - + +
246F GLY* 5.3 0.6 - - - -
247F GLY 5.2 3.6 + - - +
249F HIS* 3.6 32.3 + - - -
279F PHE* 3.6 3.8 - - - -
280F ILE 2.9 29.3 + - - -
288F SER* 1.3 76.2 - - - +
290F CYS* 1.3 69.9 + - - +
291F VAL 3.5 17.7 + - - -
292F CYS* 3.5 23.0 - - + +
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Residues in contact with CYS 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS 3.7 14.8 - - - +
13D GLY* 4.7 0.9 - - - -
14D HIS* 3.7 22.2 - - - -
63D ILE* 4.2 6.7 - - - -
279F PHE* 3.5 49.0 - - + -
289F LYS* 1.3 79.0 - - - +
291F VAL* 1.3 76.5 + - - +
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Residues in contact with VAL 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN 3.4 26.7 - - - +
12D LYS* 3.5 24.9 - - - +
13D GLY 4.0 2.0 - - - +
268F PHE* 4.2 11.0 - - + -
277F ASN* 3.8 29.4 - - + +
278F TYR 3.1 11.3 + - - -
289F LYS* 3.5 12.5 + - - -
290F CYS* 1.3 78.2 - - - +
292F CYS* 1.3 60.5 + - - +
293F SER 4.0 1.1 + - - -
344F LYS* 6.4 2.0 - - + -
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Residues in contact with CYS 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F LEU* 4.3 14.8 - - + -
247F GLY 4.9 1.6 - - - +
248F LEU* 5.9 2.5 - - - +
249F HIS* 4.2 7.4 - - + +
277F ASN* 3.9 1.8 - - - -
278F TYR* 3.1 22.3 + - - -
280F ILE* 3.5 35.0 - - - -
289F LYS* 3.5 48.5 - - + +
291F VAL* 1.3 74.4 - - - +
293F SER* 1.3 64.4 + - - +
294F VAL* 3.8 7.2 + - + +
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Residues in contact with SER 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F LEU 4.3 0.2 - - - +
249F HIS* 2.8 38.5 + - - +
275F VAL* 3.8 23.1 - - - -
276F LYS 3.1 6.3 - - - -
277F ASN* 3.1 18.3 + - - -
291F VAL 4.0 1.0 + - - -
292F CYS* 1.3 72.7 - - - +
294F VAL* 1.3 63.4 + - - +
295F ILE* 4.2 1.3 - - - +
342F TYR* 5.8 0.3 - - - -
343F PRO* 3.4 29.6 + - - +
344F LYS* 5.9 1.2 - - - +
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Residues in contact with VAL 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F LEU 4.0 6.1 - - - +
249F HIS 3.9 2.5 - - - -
251F MET* 3.8 44.6 - - + +
254F LEU* 3.8 23.8 - - + -
274F THR 4.3 0.9 - - - +
276F LYS* 2.5 37.1 + - - +
278F TYR* 3.9 24.0 - - + -
280F ILE* 4.3 9.6 - - + -
292F CYS* 3.9 11.0 - - - +
293F SER* 1.3 79.7 - - - +
295F ILE* 1.3 61.8 - - - +
296F ASP* 6.0 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