Contacts of the strand formed by residues 355 - 362 (chain B) in PDB entry 2W8B
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 GLN 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B SER 4.0 0.4 - - - -
351B SER* 3.0 6.1 - - - -
352B ASN 2.8 38.8 + - - +
353B GLY 3.2 6.0 - - - +
354B GLY* 1.3 90.4 + - - +
356B GLN* 1.3 63.1 + - - +
357B HIS* 3.8 29.9 + - + +
374B THR 4.7 1.6 - - - +
375B PHE* 3.7 36.9 - - - -
376B LEU* 5.1 2.0 + - - +
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Residues in contact with GLN 356 (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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349B VAL* 4.1 9.1 - - + +
350B SER 3.3 5.4 - - - -
351B SER* 3.5 19.8 + - - +
355B GLN* 1.3 78.6 + - - +
357B HIS* 1.3 72.9 + - - +
376B LEU* 3.8 29.5 + - + +
377B ASP* 2.9 42.9 + - - +
378B GLU* 4.2 1.6 - - - +
112C ARG* 3.9 10.7 - - - +
113C GLY* 2.9 46.9 - - - +
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Residues in contact with HIS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B VAL* 3.4 3.7 - - - -
350B SER* 2.9 35.5 + - - +
355B GLN* 3.8 36.5 + - + +
356B GLN* 1.3 77.0 + - - +
358B ILE* 1.3 65.6 + - - +
359B ALA 3.8 0.2 + - - -
370B VAL* 4.1 14.8 - - + +
372B SER 3.4 24.8 + - - +
373B SER* 3.6 13.3 + - - -
374B THR 2.9 21.5 + - - -
377B ASP* 2.9 24.9 - - - -
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Residues in contact with ILE 358 (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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347B VAL* 4.2 8.3 - - + -
348B MET 3.3 5.8 - - - +
349B VAL* 4.0 20.0 - - + -
357B HIS* 1.3 73.0 - - - +
359B ALA* 1.3 69.2 + - - +
370B VAL* 3.8 3.3 - - - +
371B LEU* 2.8 34.0 + - + -
372B SER* 2.9 27.1 + - - +
377B ASP* 3.8 15.5 - - + -
378B GLU 4.1 2.0 - - - +
380B PRO* 3.9 32.3 - - + -
389B VAL* 4.4 9.0 - - + -
391B TYR* 3.6 31.9 - - + -
404B VAL* 5.1 1.3 - - + -
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Residues in contact with ALA 359 (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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347B VAL* 3.1 6.6 - - - +
348B MET* 2.9 41.3 + - + +
350B SER* 4.3 21.5 - - - -
358B ILE* 1.3 78.0 - - - +
360B LYS* 1.3 59.9 + - - +
368B VAL* 4.1 16.2 - - + -
369B GLN 3.3 13.0 - - - +
370B VAL* 4.1 10.5 - - + -
371B LEU* 4.0 3.4 - - - +
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Residues in contact with LYS 360 (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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345B PHE* 3.7 43.3 - - + -
346B MET 3.3 3.8 - - - +
347B VAL* 4.3 2.0 - - + +
348B MET* 5.3 0.7 - - - -
359B ALA* 1.3 76.2 - - - +
361B GLN* 1.3 64.2 + - - +
362B ASP* 5.0 2.0 - - - +
367B GLY 3.7 0.9 - - - +
368B VAL* 3.3 6.4 - - - +
369B GLN* 2.8 58.3 + - - +
371B LEU* 4.1 13.9 - - + -
406B THR* 3.3 37.6 + - - +
407B ASP* 5.2 0.6 - - - +
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Residues in contact with GLN 361 (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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327B ILE* 2.8 31.6 + - - +
328B THR* 3.5 19.3 - - - +
329B TRP* 4.9 3.2 + - - -
330B GLU* 5.4 0.9 + - - +
345B PHE* 3.1 7.3 - - - -
346B MET* 2.8 60.9 + - + +
348B MET* 3.5 13.5 - - + +
359B ALA 4.3 0.4 + - - -
360B LYS* 1.3 75.9 - - - +
362B ASP* 1.3 72.4 + - - +
363B LEU* 3.3 7.7 + - + +
366B GLY* 4.0 14.5 - - - +
367B GLY 3.3 9.4 - - - +
368B VAL* 3.6 14.4 - - + +
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Residues in contact with ASP 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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344B LYS 3.8 9.3 - - - +
345B PHE* 4.1 4.5 - - - -
360B LYS* 4.2 3.3 + - - +
361B GLN* 1.3 72.5 - - - +
363B LEU* 1.3 58.4 + - - +
364B ALA* 2.9 22.5 + - - +
365B THR* 2.9 32.6 + - - +
366B GLY* 2.8 32.1 + - - -
367B GLY* 3.0 13.7 + - - +
33F SER 5.9 0.2 - - - +
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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