Contacts of the strand formed by residues 368 - 372 (chain B) in PDB entry 2XGZ
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 GLY 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B ASP 2.8 12.4 + - - -
341B ALA* 3.3 9.2 - - - -
342B LEU* 3.0 20.1 + - - +
363B PHE* 4.5 3.6 - - - -
367B TRP* 1.3 76.7 - - - +
369B VAL* 1.3 68.6 + - - +
392B THR 5.7 0.2 - - - -
394B GLN* 4.1 5.6 - - - -
431B HIS* 3.3 28.8 - - - -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.4 8.1 - - + +
344B LEU* 3.8 36.6 - - + -
359B ALA* 3.9 12.3 - - + +
362B SER* 3.7 22.7 - - - +
363B PHE* 3.4 33.8 - - + -
368B GLY* 1.3 78.6 - - - +
370B MET* 1.3 61.9 + - - +
371B VAL* 4.5 2.9 - - + +
390B LEU* 5.1 0.4 - - + -
392B THR* 2.8 38.7 + - + -
394B GLN* 3.3 12.6 - - - +
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Residues in contact with MET 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 3.8 31.4 - - + -
170B MET* 5.3 2.9 - - + +
293B SER* 4.0 7.6 - - - +
295B GLU* 5.1 2.5 - - - +
316B GLN* 3.7 13.7 - - - +
318B VAL* 4.4 11.0 - - + -
341B ALA* 5.3 1.7 - - + +
342B LEU 2.8 11.7 + - - +
343B LEU* 3.4 17.9 - - + +
344B LEU 2.9 23.9 + - - -
368B GLY 4.3 0.4 - - - -
369B VAL* 1.3 70.6 - - - +
371B VAL* 1.3 63.7 + - - +
372B SER 3.5 0.7 + - - -
394B GLN* 3.4 39.2 - - - +
395B ILE 4.2 0.2 - - - -
396B LYS* 3.5 45.3 - - + +
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.9 11.0 - - + +
346B VAL* 6.0 0.2 - - + -
369B VAL* 3.8 4.0 + - + -
370B MET* 1.3 71.1 - - - +
372B SER* 1.3 61.8 + - - +
383B ILE* 3.8 41.5 - - + +
386B LEU* 4.4 11.0 - - + -
387B VAL* 3.7 37.0 - - + +
390B LEU* 4.4 13.0 - - + -
392B THR* 4.0 14.8 - - + -
394B GLN 3.3 6.0 + - - +
395B ILE* 3.4 7.0 - - + +
396B LYS* 2.8 27.5 + - - +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.5 29.8 - - - +
344B LEU 3.0 19.2 + - - +
345B LYS* 3.8 13.2 - - - +
346B VAL 5.2 0.7 + - - -
371B VAL* 1.3 76.8 - - - +
373B HIS* 1.3 74.8 + - - +
374B ARG* 5.2 0.7 - - - +
377B GLU* 4.9 0.3 - - - +
383B ILE* 4.0 17.7 - - - +
396B LYS* 3.4 4.5 + - - -
1440B PEP 3.2 22.7 - - - +
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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