Contacts of the strand formed by residues 342 - 348 (chain A) in PDB entry 1M2V
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 THR 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ALA 2.9 17.3 + - - +
283A ARG* 3.9 19.4 - - - +
284A ILE* 2.7 35.0 + - - +
341A HIS* 1.3 74.3 - - - +
343A VAL* 1.3 64.1 + - - +
344A ASP* 4.1 1.6 - - - +
365A THR* 3.9 4.9 - - - +
366A GLY 3.9 1.6 - - - +
367A GLY* 3.6 28.5 - - - +
400A PHE* 4.9 1.2 - - - -
448A ALA* 3.4 13.3 + - - +
449A SER* 2.9 33.8 + - - +
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Residues in contact with VAL 343 (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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266A LEU* 4.5 15.7 - - + -
284A ILE* 3.2 15.0 - - + +
332A ILE* 5.7 1.1 - - + -
336A VAL* 3.8 36.8 - - + -
342A THR* 1.3 82.8 - - - +
344A ASP* 1.3 68.6 + - - +
345A ILE* 4.3 8.5 - - + -
361A LEU* 4.0 41.1 - - + +
362A THR* 3.5 18.7 - - - +
365A THR* 3.5 4.2 + - - -
367A GLY* 3.5 10.8 - - - -
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Residues in contact with ASP 344 (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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283A ARG* 2.7 63.2 + - - +
284A ILE 2.6 12.0 + - - +
285A ILE* 3.3 17.4 - - + +
286A LEU* 2.8 30.0 + - - +
342A THR* 4.6 0.2 - - - -
343A VAL* 1.3 75.4 - - - +
345A ILE* 1.3 62.0 + - - +
346A PHE* 4.1 17.7 - - + -
367A GLY* 3.5 3.1 - - - -
368A VAL* 2.9 24.8 + - + +
387A LEU* 4.6 3.8 - - - +
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Residues in contact with ILE 345 (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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286A LEU* 3.8 19.7 - - + -
343A VAL* 4.3 6.1 - - + -
344A ASP* 1.3 80.1 - - - +
346A PHE* 1.3 66.0 + - - +
353A ILE* 3.7 29.8 - - + -
355A MET* 4.0 9.0 - - + -
358A MET* 3.8 40.8 - - + +
361A LEU* 4.2 12.3 - - + -
362A THR* 4.1 18.4 - - + -
368A VAL 3.0 8.7 + - - +
369A LEU* 3.5 14.5 + - + -
370A LEU 2.9 26.2 + - - +
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Residues in contact with PHE 346 (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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285A ILE* 3.9 29.4 - - + -
286A LEU 3.0 12.4 + - - +
287A PHE* 3.6 11.4 - + + -
288A ALA* 3.2 25.3 + - - +
344A ASP* 4.1 14.6 - - + -
345A ILE* 1.3 77.9 - - - +
347A ALA* 1.3 61.0 + - - +
368A VAL* 3.6 22.4 - - + -
370A LEU* 3.7 28.0 - - + -
375A PHE* 3.9 3.2 - - + -
380A PHE* 3.3 34.5 - + + -
383A SER* 4.9 1.8 - - - -
384A TYR* 3.8 33.4 - + - -
387A LEU* 4.0 13.9 - - + -
706A PHE* 5.4 0.9 - + - -
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Residues in contact with ALA 347 (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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288A ALA 3.6 4.5 - - - -
346A PHE* 1.3 71.7 - - - +
348A GLY* 1.3 53.0 + - - +
349A CYS* 5.1 1.1 - - - +
353A ILE* 3.5 28.9 - - + -
355A MET* 3.5 24.6 - - + +
370A LEU 2.8 11.4 + - - +
371A LEU* 4.1 14.4 - - + -
372A THR* 2.5 40.9 + - - +
375A PHE* 4.2 1.8 - - - -
380A PHE* 5.6 0.2 - - - -
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Residues in contact with GLY 348 (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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136A ASN* 3.5 22.5 + - - +
288A ALA 2.9 12.3 + - - -
289A SER* 3.7 6.9 - - - -
347A ALA* 1.3 74.2 - - - +
349A CYS* 1.3 62.4 + - - +
372A THR* 3.6 8.7 - - - -
373A ASP 3.4 5.9 - - - +
374A ALA* 3.9 8.7 - - - -
375A PHE* 3.6 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