Contacts of the strand formed by residues 377 - 384 (chain A) in PDB entry 2W27
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 MET 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A HIS* 4.6 18.4 - - + +
368A LEU* 3.6 49.6 - - + +
369A TYR* 3.3 14.4 - - - +
370A SER* 3.7 7.9 - - - -
375A GLY 5.7 0.4 - - - +
376A GLU* 1.3 74.5 - - - +
378A ILE* 1.3 65.3 + - - +
397A TYR* 3.6 44.6 + - + +
400A LEU* 4.2 2.0 - - - +
201B LYS* 3.4 24.9 - - + +
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Residues in contact with ILE 378 (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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310A PHE* 3.6 23.6 - - + -
368A LEU* 3.5 3.2 - - - +
369A TYR* 2.7 71.3 + - + +
371A ASP* 3.6 31.2 - - + +
376A GLU* 3.9 19.3 - - + +
377A MET* 1.3 79.9 - - - +
379A ARG* 1.3 69.4 + - - +
380A THR* 4.2 2.2 - - - +
394A ASP* 4.2 11.0 - - + -
395A LEU 3.1 20.6 - - - +
400A LEU* 3.8 5.2 - - - -
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Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.9 24.9 - - - +
365A PHE* 4.3 23.2 - - + +
366A SER* 3.1 34.4 + - - +
367A ASP* 4.0 14.2 - - - +
368A LEU* 3.7 22.4 - - + +
369A TYR* 4.6 0.7 - - - -
378A ILE* 1.3 83.4 - - - +
380A THR* 1.3 65.2 + - - +
394A ASP* 3.7 1.7 - - - -
395A LEU* 2.8 33.0 + - + +
400A LEU* 3.7 25.3 - - + +
405A GLY 5.1 0.2 + - - -
406A LEU* 2.9 44.4 + - - +
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Residues in contact with THR 380 (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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313A TYR* 5.4 1.5 + - - +
347A ARG* 5.8 0.2 + - - -
364A PHE 3.8 0.5 - - - +
365A PHE* 3.3 5.4 - - - -
366A SER* 2.9 37.6 + - - -
369A TYR* 2.8 25.5 + - - -
378A ILE* 4.2 0.2 - - - +
379A ARG* 1.3 75.6 - - - +
381A PHE* 1.3 74.3 + - - +
382A SER* 4.1 5.8 + - - +
392A PHE* 4.2 18.8 - - + -
393A ILE 3.4 8.5 - - - +
394A ASP* 2.7 29.9 + - - +
395A LEU* 5.2 0.2 - - - -
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Residues in contact with PHE 381 (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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272A SER* 4.2 16.4 - - - -
275A PHE* 3.8 22.4 - + + -
276A TYR* 3.6 29.2 - + + -
279A VAL* 4.0 18.8 - - + -
363A GLY* 3.7 5.2 - - - -
364A PHE* 3.3 39.3 - - - -
365A PHE* 3.7 24.7 - + + -
380A THR* 1.3 74.8 - - - +
382A SER* 1.3 69.1 + - - +
383A TYR* 3.9 17.9 - + + -
391A LEU 3.8 0.7 - - - +
392A PHE* 3.5 4.9 - - - -
393A ILE* 2.9 42.6 + - + +
395A LEU* 4.8 1.3 - - + +
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Residues in contact with SER 382 (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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353A ASN* 5.0 7.1 + - - +
357A MET* 3.3 31.5 - - - +
363A GLY* 3.0 24.8 - - - -
364A PHE* 2.9 28.6 + - - -
365A PHE 5.9 0.2 - - - -
380A THR* 4.4 6.4 + - - +
381A PHE* 1.3 76.9 - - - +
383A TYR* 1.3 59.9 + - - +
391A LEU 3.5 4.9 - - - -
392A PHE* 4.2 16.8 - - - -
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Residues in contact with TYR 383 (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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276A TYR* 3.5 38.6 - + - -
279A VAL* 3.8 15.0 - - + -
280A HIS* 2.9 43.9 + - - -
283A VAL* 4.0 24.7 - - + +
284A THR* 4.4 4.0 - - - +
357A MET* 3.6 3.5 - - - -
363A GLY* 4.4 0.2 - - - -
381A PHE* 3.9 13.2 - + + +
382A SER* 1.3 74.7 - - - +
384A PRO* 1.3 81.3 - - + +
385A MET* 3.9 19.1 - - + -
390A TYR 3.7 0.3 - - - -
391A LEU* 2.7 57.4 + - + +
393A ILE* 5.6 0.9 - - + -
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Residues in contact with PRO 384 (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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276A TYR* 5.0 1.1 - - + -
357A MET* 3.9 29.6 - - + +
358A ARG* 5.7 0.7 - - - -
361A ARG* 4.4 14.1 - - + +
362A LYS* 3.6 32.3 - - - +
363A GLY* 4.1 1.1 - - - +
383A TYR* 1.3 109.9 - - + +
385A MET* 1.3 62.5 + - - +
389A MET 3.9 4.3 - - - +
390A TYR* 4.2 13.7 - - + -
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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
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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