Contacts of the strand formed by residues 362 - 368 (chain A) in PDB entry 2IN6
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 362 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A VAL* 4.3 9.5 - - + +
350A HIS* 3.5 42.0 - - + +
351A ALA* 4.0 30.7 - - + +
354A GLY* 4.8 8.4 - - - -
360A VAL 3.8 1.2 + - - -
361A ARG* 1.3 78.3 - - - +
363A PHE* 1.3 78.4 + - - +
364A SER* 3.5 26.3 - - - -
365A ALA* 3.5 20.8 + - + +
374A ILE* 3.6 22.0 - - + -
376A ASN* 3.5 7.0 - - - -
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Residues in contact with PHE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 3.5 41.5 - + - -
361A ARG* 4.1 17.9 - - + -
362A TYR* 1.3 88.9 - - - +
364A SER* 1.3 64.6 + - - +
375A GLN* 2.9 28.3 + - - +
376A ASN 3.9 1.1 - - - -
377A GLU* 3.7 31.2 - - + -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 2.7 34.1 + - - -
362A TYR* 3.5 16.7 - - - -
363A PHE* 1.3 80.7 - - - +
365A ALA* 1.3 67.1 + - - +
366A TRP* 4.1 2.7 - - - -
374A ILE* 3.5 0.3 - - - -
375A GLN* 2.8 45.6 + - - +
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Residues in contact with ALA 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 4.4 1.4 + - - -
347A VAL* 4.0 27.4 - - + -
362A TYR* 3.5 22.3 + - + +
364A SER* 1.3 81.3 + - - +
366A TRP* 1.3 69.0 + - - +
372A MET* 6.2 1.1 - - + -
373A LEU 3.1 15.0 - - - +
374A ILE* 4.4 4.0 - - + -
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ARG* 3.3 58.6 - - + +
295A TYR* 4.2 8.5 - + + -
299A PHE* 3.5 31.6 - + - -
327A ILE* 4.7 6.3 - - + -
364A SER* 4.1 4.3 - - - -
365A ALA* 1.3 82.5 - - - +
367A ALA* 1.3 62.7 + - - +
368A GLU* 2.9 41.1 + - + +
372A MET* 3.7 6.1 - - - +
373A LEU* 2.9 62.7 + - + +
375A GLN* 4.0 27.4 - - + -
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LYS* 4.1 23.3 - - + +
366A TRP* 1.3 78.3 - - - +
368A GLU* 1.3 66.8 + - - +
371A HIS 3.4 9.9 - - - +
372A MET* 4.9 7.0 - - + -
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A SER* 2.8 30.2 + - - +
294A ARG* 2.8 22.4 + - - +
295A TYR* 3.0 15.8 + - - +
329A ARG* 4.7 3.3 + - - +
332A LYS* 5.2 1.5 - - - +
366A TRP* 2.9 30.9 + - + +
367A ALA* 1.3 77.1 - - - +
369A ASP* 1.3 75.4 + - - +
371A HIS* 2.9 27.5 + - - +
373A LEU* 3.9 8.9 - - + +
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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