Contacts of the strand formed by residues 358 - 362 (chain B) in PDB entry 2XYN
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 TYR 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ARG* 3.8 35.4 + - + +
288B ILE* 5.1 7.0 - - + -
290B MET* 3.2 42.0 - - + +
316B VAL* 3.4 19.7 - - + -
317B LYS 3.3 2.7 - - - -
318B THR* 4.0 11.4 - - + -
329B PHE* 4.1 1.3 - - - -
350B VAL* 3.4 8.3 - - - +
351B CYS* 2.7 59.0 + - + +
352B THR* 3.9 4.2 - - - +
356B PRO* 4.0 20.4 - - + +
357B PHE* 1.3 95.4 - - - +
359B ILE* 1.3 67.2 + - - +
360B VAL* 4.1 11.0 - - + -
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA 3.2 5.2 - - - +
316B VAL* 3.4 1.4 - - - -
317B LYS* 2.9 47.3 + - + +
329B PHE* 3.8 41.5 - - + +
332B GLU* 4.2 11.2 - - + -
333B ALA* 4.1 23.3 - - + +
336B MET* 4.2 10.1 - - - -
347B LEU* 3.2 29.2 - - + -
349B GLY 3.9 2.7 - - - -
350B VAL* 4.8 0.4 - - + +
352B THR* 5.7 0.2 - - + -
358B TYR* 1.3 77.3 - - - +
360B VAL* 1.3 60.9 + - - +
361B THR* 4.0 14.9 + - + +
547B VX6 4.7 4.9 - - + -
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 3.7 26.5 - - + -
288B ILE* 4.1 16.2 - - + -
307B TRP* 4.9 2.5 - - + -
314B VAL* 3.5 42.6 - - + -
315B ALA 3.3 3.8 - - - +
316B VAL* 4.6 6.3 - - + -
347B LEU* 3.6 3.6 - - - +
348B LEU* 2.7 35.3 + - + -
349B GLY 3.0 21.8 + - - +
350B VAL 4.6 0.4 - - - +
358B TYR* 4.4 16.2 - - + -
359B ILE* 1.3 73.9 - - - +
361B THR* 1.3 55.7 + - - +
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Residues in contact with THR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B VAL* 3.4 8.7 - - - +
315B ALA* 3.0 43.5 + - - +
336B MET* 3.5 32.5 - - + -
345B VAL* 4.2 8.7 - - + -
346B GLN 3.3 11.9 - - - +
347B LEU* 4.2 1.1 - - - -
348B LEU* 3.9 5.8 - - - +
359B ILE* 4.2 7.3 + - + +
360B VAL* 1.3 77.9 - - - +
362B GLU* 1.3 70.6 + - - +
547B VX6 3.6 23.7 + - + +
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Residues in contact with GLU 362 (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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312B LEU* 6.2 0.4 - - - -
313B THR 5.2 0.7 - - - -
314B VAL* 5.1 0.4 - - - +
344B LEU 3.8 0.7 - - - +
345B VAL* 3.6 7.5 - - + +
346B GLN* 3.0 50.5 + - + +
348B LEU* 3.7 17.4 - - + +
361B THR* 1.3 74.8 + - - +
363B TYR* 1.3 59.9 + - - +
364B MET* 3.8 10.1 + - - +
424B LYS* 2.8 46.0 + - - +
547B VX6 2.9 20.3 + - - -
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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