Contacts of the strand formed by residues 370 - 377 (chain B) in PDB entry 2XAR
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 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B GLU* 3.7 22.6 + - - -
167B ILE 3.2 12.1 - - - -
168B LYS* 3.5 23.4 - - - +
368B ASP 4.3 1.2 + - - -
369B CYS* 1.3 77.6 - - - +
371B ILE* 1.3 61.4 + - - +
405B PHE* 3.5 4.9 - - - +
406B ILE* 2.8 46.5 + - - +
407B ASP* 3.7 11.9 + - - +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL 3.6 0.9 - - - +
166B GLU* 3.2 4.9 - - - +
167B ILE* 2.7 51.0 + - + +
169B PRO* 3.7 27.8 - - + -
217B LEU* 5.6 0.9 - - + -
295B VAL* 6.3 0.4 - - + -
300B VAL* 4.4 7.0 - - + -
301B LEU* 3.3 33.4 - - + -
304B LEU* 4.8 3.1 - - + -
370B SER* 1.3 76.1 - - - +
372B MET* 1.3 65.3 + - - +
373B ILE* 4.0 11.0 - - + -
403B VAL* 3.9 27.4 - - + -
404B HIS 3.4 11.0 - - - +
405B PHE* 4.2 19.3 - - + +
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Residues in contact with MET 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B HIS* 4.3 33.0 - - + +
150B SER* 4.6 3.6 - - - -
164B SER* 3.7 27.6 - - - +
165B VAL 3.3 31.2 - - - +
166B GLU* 3.7 19.1 - - + +
243B PHE* 4.2 10.5 - - + -
371B ILE* 1.3 71.6 - - - +
373B ILE* 1.3 61.6 + - - +
374B SER* 3.9 1.1 + - - -
402B LYS 3.7 0.9 - - - +
403B VAL* 3.4 2.9 - - - -
404B HIS* 2.7 44.9 + - + +
406B ILE* 3.7 32.3 - - + -
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Residues in contact with ILE 373 (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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164B SER* 3.3 3.8 - - - -
165B VAL* 2.9 37.1 + - + +
167B ILE* 4.3 13.0 - - + -
291B VAL* 4.9 7.0 - - + +
294B ALA* 4.3 2.5 - - + -
295B VAL* 3.5 38.6 - - + +
300B VAL* 6.1 0.9 - - + -
371B ILE* 4.0 10.1 - - + -
372B MET* 1.3 72.9 - - - +
374B SER* 1.3 58.4 + - - +
375B PHE* 3.5 31.0 - - + -
401B TYR* 4.2 20.4 - - + -
402B LYS 3.2 12.3 - - - +
403B VAL* 3.4 22.7 - - + -
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Residues in contact with SER 374 (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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149B HIS* 3.0 33.3 + - - +
151B LEU 4.8 0.7 + - - -
152B PHE* 3.7 15.9 + - - -
162B CYS* 4.2 15.7 - - - -
163B ILE 3.8 3.8 - - - -
164B SER* 3.9 3.1 - - - -
372B MET 3.9 0.7 + - - -
373B ILE* 1.3 70.5 - - - +
375B PHE* 1.3 60.7 + - - +
401B TYR* 3.2 6.2 - - - +
402B LYS* 2.9 44.3 + - - +
404B HIS* 4.6 3.6 - - - -
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Residues in contact with PHE 375 (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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152B PHE* 4.1 0.4 - - - -
162B CYS* 3.2 23.4 - - - -
163B ILE* 2.7 31.5 + - + +
165B VAL* 4.0 21.8 - - + -
275B PHE* 3.7 18.2 - - + -
287B PHE* 5.3 0.7 - + - -
290B LEU* 3.7 33.9 - - + -
291B VAL* 3.9 21.8 - - + -
294B ALA* 3.6 33.9 - - + -
373B ILE* 3.5 28.5 - - + -
374B SER* 1.3 73.9 - - - +
376B GLN* 1.3 60.6 + - - +
390B VAL* 5.1 0.4 - - + -
399B PHE* 4.4 7.9 - - + -
400B ASP 3.6 2.0 - - - -
401B TYR* 3.8 16.8 - + + -
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Residues in contact with GLN 376 (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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152B PHE* 2.9 58.0 - - + +
153B SER* 4.6 5.0 + - - -
159B GLY 4.0 23.5 + - - +
160B GLY 5.2 7.2 - - - +
161B ASP 4.5 9.9 - - - +
162B CYS* 5.3 1.4 - - - +
275B PHE* 4.7 0.7 - - - -
375B PHE* 1.3 77.4 - - - +
377B SER* 1.3 72.6 + - - +
384B GLU* 3.1 33.5 + - - +
399B PHE* 3.2 4.8 - - - -
400B ASP* 2.9 34.9 + - + +
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Residues in contact with SER 377 (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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161B ASP 4.5 4.6 + - - -
275B PHE* 4.3 16.3 + - - -
277B GLN* 5.5 0.9 + - - -
376B GLN* 1.3 85.5 - - - +
378B ARG* 1.3 69.3 + - - +
379B ASN* 4.0 7.8 + - - -
384B GLU* 4.5 5.6 + - - +
397B GLN* 4.0 13.2 + - - +
398B THR 3.7 2.1 + - - -
399B PHE* 3.6 33.0 - - - -
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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