Contacts of the strand formed by residues 377 - 385 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LYS* 3.6 21.1 - - - +
190B HIS* 4.0 25.4 - - + +
368B LEU* 3.6 55.4 - - + +
369B TYR* 3.4 11.7 - - - -
370B SER* 3.6 6.5 - - - +
375B GLY 4.0 0.4 + - - +
376B GLU* 1.3 78.8 - - - +
378B ILE* 1.3 62.8 + - - +
397B TYR* 3.8 38.5 + - + +
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Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 3.5 33.0 - - + -
368B LEU* 3.6 4.5 - - - -
369B TYR* 2.7 74.9 + - + +
371B ASP* 3.6 29.2 - - + +
376B GLU* 3.8 18.2 - - + +
377B MET* 1.3 81.0 - - - +
379B ARG* 1.3 71.2 + - - +
380B THR* 4.2 7.4 - - - +
394B ASP* 4.5 5.6 - - + -
395B LEU 3.5 12.1 - - - +
396B PRO* 4.3 1.6 - - + -
397B TYR 5.0 1.3 - - - +
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 4.0 30.1 - - - +
365B PHE* 4.3 25.4 - - + +
366B SER* 3.1 33.1 + - - +
367B ASP* 3.9 14.6 - - - +
368B LEU* 3.6 38.2 - - + +
369B TYR* 4.6 0.4 - - - -
378B ILE* 1.3 84.1 - - - +
380B THR* 1.3 65.3 - - - +
394B ASP* 3.6 1.6 - - - -
395B LEU* 2.8 40.6 + - + +
397B TYR* 5.3 10.3 - - - +
399B TYR 5.9 0.6 + - - -
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Residues in contact with THR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 5.3 3.2 + - - +
347B ARG* 5.7 0.2 + - - -
364B PHE 3.9 0.5 - - - +
365B PHE* 3.4 5.0 - - - -
366B SER* 3.0 37.8 + - - -
369B TYR* 2.7 28.4 + - - -
378B ILE* 4.2 0.5 - - - +
379B ARG* 1.3 74.2 - - - +
381B PHE* 1.3 72.8 + - - +
382B SER* 4.1 5.4 + - - +
392B PHE* 4.2 18.8 - - + -
393B ILE 3.2 13.7 - - - +
394B ASP* 2.7 21.9 + - - +
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B SER* 4.2 16.4 - - - -
275B PHE* 3.8 21.8 - + + -
276B TYR* 3.6 25.4 - + + -
279B VAL* 4.0 19.5 - - + -
363B GLY* 3.7 9.4 - - - -
364B PHE* 3.3 40.8 - - - -
365B PHE* 3.6 25.8 - + + -
379B ARG 4.2 0.4 + - - -
380B THR* 1.3 73.0 - - - +
382B SER* 1.3 69.0 + - - +
383B TYR* 3.9 18.2 - + + -
391B LEU 3.8 0.9 - - - +
392B PHE* 3.6 2.9 - - - -
393B ILE* 2.6 44.3 + - + +
395B LEU* 5.8 2.2 - - + +
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Residues in contact with SER 382 (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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353B ASN* 5.0 6.3 + - - +
357B MET* 3.3 31.8 - - - +
363B GLY* 3.0 25.1 - - - -
364B PHE* 2.9 28.9 + - - -
365B PHE 5.8 0.2 - - - -
366B SER 5.8 0.2 + - - -
380B THR* 4.4 6.1 + - - +
381B PHE* 1.3 76.8 - - - +
383B TYR* 1.3 58.4 + - - +
391B LEU 3.5 4.9 - - - -
392B PHE* 4.0 16.7 - - - -
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Residues in contact with TYR 383 (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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276B TYR* 3.5 39.7 - + - -
279B VAL* 3.8 15.3 - - + -
280B HIS* 2.9 44.2 + - - -
283B VAL* 4.0 23.5 - - + +
284B THR* 4.5 3.3 - - - +
357B MET* 3.6 2.9 - - - -
381B PHE* 3.9 12.8 - + + +
382B SER* 1.3 74.7 - - - +
384B PRO* 1.3 87.8 + - + +
385B MET* 3.7 18.4 - - + -
390B TYR* 3.6 0.7 - - - -
391B LEU* 2.7 56.6 + - + +
393B ILE* 5.6 0.7 - - + -
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Residues in contact with PRO 384 (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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276B TYR* 5.0 1.1 - - + +
357B MET* 3.9 29.6 - - + +
358B ARG* 5.7 0.4 - - - -
361B ARG* 4.4 15.5 - - - +
362B LYS 3.4 33.9 - - - +
363B GLY* 4.0 1.3 - - - +
383B TYR* 1.3 110.8 - - + +
385B MET* 1.3 61.9 + - - +
389B MET 4.1 4.3 - - - +
390B TYR* 4.2 13.2 - - + -
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Residues in contact with MET 385 (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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283B VAL* 5.1 6.3 - - + -
287B ARG* 5.3 6.7 - - - -
297B PHE* 4.7 7.9 - - - -
314B MET* 3.2 39.9 - - + +
383B TYR* 3.7 20.0 - - + +
384B PRO* 1.3 81.0 - - - +
386B ASP* 1.3 75.2 + - - +
387B ASP 3.8 0.3 + - - -
388B GLN* 3.8 7.4 + - - -
389B MET* 3.0 16.2 + - + +
390B TYR* 3.4 16.2 - - - +
391B LEU* 3.4 42.2 - - + +
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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