Contacts of the strand formed by residues 276 - 282 (chain E) 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 LYS 276 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LYS* 6.0 2.5 - - - +
267E ASP* 2.9 36.9 + - - -
269E ILE* 3.0 31.5 + - - +
271E MET 3.4 17.0 + - - +
272E ASP* 4.7 5.6 - - - +
273E SER* 3.3 37.8 + - - +
274E THR 4.0 0.4 - - - -
275E VAL* 1.3 72.7 - - - +
277E ASN* 1.3 64.8 + - - +
278E TYR* 3.5 28.5 - - + +
292E CYS 3.6 0.7 - - - +
293E SER* 3.5 0.6 - - - -
294E VAL* 2.6 48.2 + - - +
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Residues in contact with ASN 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E GLU 4.2 1.2 - - - +
267E ASP* 4.2 11.3 - - - +
268E PHE* 4.0 26.5 + - + -
269E ILE* 4.8 7.7 - - + +
275E VAL* 4.2 5.5 + - - +
276E LYS* 1.3 80.2 + - - +
278E TYR* 1.3 70.2 + - - +
291E VAL* 4.6 20.1 - - - +
292E CYS 3.7 2.0 - - - +
293E SER* 3.2 30.5 + - - -
10F VAL 5.8 1.2 + - - -
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Residues in contact with TYR 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LYS* 5.8 2.1 + - - -
251E MET* 5.6 5.4 - - + +
265E LEU* 3.8 36.8 - - + -
266E GLU 3.5 4.3 - - - +
267E ASP* 3.9 34.2 + - + -
268E PHE* 3.7 6.1 - - - -
276E LYS* 3.5 37.8 - - + +
277E ASN* 1.3 78.7 - - - +
279E PHE* 1.3 60.5 + - - +
280E ILE* 3.4 24.2 + - + -
291E VAL 3.2 4.0 + - - -
292E CYS* 3.1 29.2 + - - -
294E VAL* 3.7 35.4 - - + -
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Residues in contact with PHE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E LYS* 3.7 3.5 - - - +
266E GLU* 3.1 57.6 + - + +
268E PHE* 3.5 12.0 - - + -
278E TYR* 1.3 69.2 - - - +
280E ILE* 1.3 66.2 + - - +
281E THR* 3.7 12.1 + - - -
288E SER* 4.4 9.4 - - - -
289E LYS 3.5 5.8 - - - -
290E CYS* 3.2 36.3 - - + +
13F GLY 4.5 14.4 - - - +
14F HIS* 4.2 7.6 - + + -
61F ARG* 5.1 1.6 - - - -
63F ILE* 3.8 30.5 - - + -
163F ASN* 3.3 36.8 - - - -
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Residues in contact with ILE 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E LEU* 3.8 19.4 - - + +
248E LEU* 4.1 19.5 - - + -
254E LEU* 4.3 8.1 - - + -
263E LEU* 4.0 19.3 - - + -
264E LYS 3.4 8.1 - - - +
265E LEU* 4.0 13.0 - - + -
278E TYR* 3.4 19.3 + - + -
279E PHE* 1.3 72.7 - - - +
281E THR* 1.3 66.5 + - - +
288E SER* 3.3 4.2 - - - -
289E LYS 2.8 35.1 + - - -
292E CYS* 3.8 26.9 - - + -
294E VAL* 4.0 25.6 - - + -
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Residues in contact with THR 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E LEU* 3.6 1.2 - - - -
264E LYS* 2.8 50.0 + - - +
266E GLU* 5.2 0.2 + - - -
279E PHE* 3.7 20.3 + - - -
280E ILE* 1.3 80.2 + - - +
282E ASP* 1.3 69.7 + - - +
283E ALA* 3.5 1.9 + - - +
286E GLY* 5.0 1.1 - - - +
287E SER 3.5 8.5 - - - +
288E SER* 4.2 2.7 - - - +
162F VAL* 3.9 38.1 - - + +
163F ASN* 3.9 10.5 + - - +
165F VAL* 4.6 8.0 - - + +
167F LEU* 5.5 1.3 - - + -
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Residues in contact with ASP 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E PHE* 3.3 23.4 - - + -
245E LEU* 4.1 3.7 - - + +
257E ARG* 2.7 38.0 + - - -
261E SER* 3.5 13.5 + - - -
262E PRO 3.8 0.9 - - - +
263E LEU* 3.6 10.6 - - - +
281E THR* 1.3 73.3 - - - +
283E ALA* 1.3 61.1 + - - +
284E GLN 3.7 3.0 + - - -
285E THR* 2.6 28.2 + - - +
286E GLY* 3.1 27.2 + - - -
287E SER* 2.8 16.6 + - - +
167F LEU* 4.4 0.7 - - - +
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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