Contacts of the strand formed by residues 288 - 294 (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 SER 288 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E GLY 2.9 13.4 + - - +
244E GLN* 3.4 5.7 - - - +
245E LEU* 3.0 18.5 + - - -
279E PHE* 4.4 11.3 - - - -
280E ILE 3.3 10.8 - - - -
281E THR* 4.2 14.4 - - - -
286E GLY 4.2 5.6 + - - -
287E SER* 1.3 77.0 + - - +
289E LYS* 1.3 61.0 - - - +
63F ILE* 4.8 8.7 + - - +
162F VAL* 4.9 4.0 - - - +
163F ASN* 4.9 4.9 - - - -
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Residues in contact with LYS 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E GLN* 5.6 3.6 - - + -
245E LEU* 3.4 31.4 + - + +
247E GLY 5.1 6.5 + - - +
249E HIS* 4.5 20.2 + - - -
279E PHE* 4.4 3.4 - - - -
280E ILE 2.8 34.5 + - - -
288E SER* 1.3 76.8 - - - +
290E CYS* 1.3 69.0 + - - +
291E VAL* 3.6 20.1 + - - -
292E CYS* 3.3 29.7 - - + +
342E TYR* 6.3 0.4 - - - -
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Residues in contact with CYS 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E PHE* 3.2 42.7 - - + +
289E LYS* 1.3 82.6 - - - +
291E VAL* 1.3 80.3 + - + +
12F LYS 3.6 23.6 - - - +
13F GLY* 4.6 0.7 - - - -
14F HIS* 4.0 13.0 - - - -
16F ASP* 6.1 0.4 - - - -
63F ILE* 4.5 6.1 - - - -
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Residues in contact with VAL 291 (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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268E PHE* 3.6 25.0 - - + -
277E ASN* 4.6 18.2 - - - +
278E TYR 3.2 12.0 + - - -
289E LYS* 3.6 13.4 + - - -
290E CYS* 1.3 82.5 - - + +
292E CYS* 1.3 60.7 + - - +
293E SER 4.0 1.2 + - - -
11F ASN 3.4 25.8 - - - +
12F LYS* 4.0 22.0 - - + -
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Residues in contact with CYS 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E LEU* 5.3 5.8 - - - -
247E GLY 5.1 5.2 - - - +
248E LEU* 4.6 11.7 - - + +
249E HIS* 5.7 2.7 - - + +
277E ASN* 4.0 2.0 - - - -
278E TYR 3.1 26.1 + - - -
280E ILE* 3.8 26.2 - - + -
289E LYS* 3.3 55.4 - - + +
291E VAL* 1.3 71.3 - - - +
293E SER* 1.3 63.7 + - - +
294E VAL* 3.1 9.4 + - + +
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Residues in contact with SER 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E LEU 4.4 0.2 - - - +
249E HIS* 3.4 37.2 + - - +
275E VAL* 3.8 18.6 - - - -
276E LYS 3.5 0.4 - - - -
277E ASN* 3.2 20.6 + - - -
291E VAL 4.0 1.6 + - - -
292E CYS* 1.3 68.6 - - - +
294E VAL* 1.3 60.1 + - - +
295E ILE* 4.4 2.3 - - - +
342E TYR* 4.9 0.3 - - - +
343E PRO* 3.2 32.1 - - - +
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Residues in contact with VAL 294 (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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248E LEU 4.3 5.6 - - - +
249E HIS 4.0 2.5 - - - -
251E MET* 4.0 28.9 - - + +
254E LEU* 3.7 34.5 - - + -
274E THR 4.4 0.3 - - - +
275E VAL* 4.1 0.4 - - - -
276E LYS* 2.6 43.0 + - + +
278E TYR* 3.7 26.0 - - + -
280E ILE* 4.0 12.1 - - + -
292E CYS 3.5 12.8 - - - +
293E SER* 1.3 73.7 - - - +
295E ILE* 1.3 63.6 + - - +
296E ASP 5.2 0.4 - - - +
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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