Contacts of the strand formed by residues 315 - 322 (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 315 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313F VAL* 3.3 11.3 - - - +
314F ILE* 1.3 84.7 - - - +
316F LYS* 1.3 64.2 + - - +
330F MET* 4.7 6.1 - - - -
331F LEU 3.3 7.9 - - - -
332F TRP* 3.5 41.3 - - - -
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Residues in contact with LYS 316 (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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309F GLN* 5.7 3.4 - - - +
310F ASP* 5.5 13.7 + - + +
313F VAL* 4.1 28.0 - - + -
315F SER* 1.3 76.7 - - - +
317F VAL* 1.3 82.2 + - - +
318F VAL* 3.8 11.7 + - + -
330F MET* 4.0 8.6 - - - +
331F LEU* 3.3 47.9 + - + +
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Residues in contact with VAL 317 (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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316F LYS* 1.3 86.1 - - - +
318F VAL* 1.3 65.3 + - - +
319F LYS* 4.0 12.8 + - + +
328F SER* 4.0 26.2 - - - +
329F PHE 3.4 12.1 - - - +
330F MET* 3.8 19.3 - - + -
344F LYS 5.8 0.9 - - - +
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Residues in contact with VAL 318 (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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309F GLN* 3.4 45.3 - - + +
316F LYS* 3.8 14.1 + - + +
317F VAL* 1.3 76.5 - - - +
319F LYS* 1.3 62.3 + - - +
320F VAL* 4.0 17.7 - - + -
327F ILE 3.6 0.7 - - - +
329F PHE* 2.7 42.0 + - + +
331F LEU* 3.9 26.2 - - + -
341F PHE* 4.0 18.6 - - + -
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Residues in contact with LYS 319 (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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317F VAL* 4.0 12.9 + - + +
318F VAL* 1.3 75.2 - - - +
320F VAL* 1.3 65.4 + - - +
326F GLU* 3.2 42.5 + - + +
327F ILE 3.7 4.3 - - - -
328F SER* 4.4 16.4 - - - +
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Residues in contact with VAL 320 (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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193F TYR* 4.3 9.6 - - + -
305F ILE* 3.7 47.6 - - + -
318F VAL* 4.0 11.9 - - + -
319F LYS* 1.3 80.3 - - - +
321F THR* 1.3 65.6 + - - +
322F ILE* 3.5 16.0 + - + +
325F ALA 3.5 1.4 - - - +
326F GLU* 4.7 2.0 - - - -
327F ILE* 3.0 33.7 + - - +
329F PHE* 3.7 28.9 - - + -
341F PHE* 5.0 0.2 - - + -
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Residues in contact with THR 321 (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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190F PRO* 4.2 20.2 - - + +
191F GLU 3.4 24.0 + - - +
192F THR* 3.5 18.9 - - + +
193F TYR* 2.9 29.2 + - - -
320F VAL* 1.3 73.5 - - - +
322F ILE* 1.3 63.6 + - - +
324F TYR* 4.2 3.6 - - - -
325F ALA 3.3 19.0 + - - +
326F GLU* 4.7 9.7 + - - +
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Residues in contact with ILE 322 (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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193F TYR* 3.4 15.7 - - + +
195F THR* 3.8 11.4 - - - +
274F THR* 3.9 13.8 - - + +
295F ILE* 3.5 25.1 - - + -
297F LEU* 3.9 25.6 - - + -
305F ILE* 5.8 0.4 - - + -
320F VAL* 3.5 19.4 + - + +
321F THR* 1.3 79.2 - - - +
323F ASP* 1.3 87.9 + - - +
324F TYR 3.2 0.7 - - - -
325F ALA* 3.0 24.7 + - - +
327F ILE* 4.6 6.5 - - + +
329F PHE* 4.0 24.7 - - + -
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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
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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