Contacts of the strand formed by residues 372 - 379 (chain B) in PDB entry 3BEQ
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 SER 372 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B THR* 3.7 2.2 - - - -
366B LYS* 2.9 21.3 + - - +
367B SER* 3.0 23.6 + - - -
370B SER* 2.9 26.9 + - - -
371B ARG* 1.3 71.9 - - - +
373B GLY* 1.3 63.0 + - - +
400B ILE* 3.3 22.7 - - - -
402B ASP 3.4 7.6 - - - -
403B TRP* 3.4 13.3 - - - -
404B SER* 3.8 0.8 + - - -
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Residues in contact with GLY 373 (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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365B THR* 3.3 7.4 - - - -
366B LYS* 3.5 7.0 - - - -
372B SER* 1.3 75.1 - - - +
374B PHE* 1.3 60.7 + - - +
398B VAL* 3.2 7.9 - - - -
399B ALA 3.2 24.8 + - - -
400B ILE* 3.8 3.6 - - - -
402B ASP 2.8 13.9 + - - -
404B SER* 2.7 29.4 + - - -
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Residues in contact with PHE 374 (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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352B PHE* 3.8 2.9 - + - -
363B GLY* 3.7 19.1 - - - -
364B ARG* 3.3 35.2 - - - -
365B THR* 4.0 5.2 - - + +
366B LYS* 3.7 5.8 - - - +
373B GLY* 1.3 77.0 - - - +
375B GLU* 1.3 75.0 + - - +
376B MET* 4.0 2.5 - - - -
397B ILE* 3.0 35.9 + - + -
398B VAL* 2.9 32.5 + - + +
404B SER* 4.4 7.0 - - - -
405B GLY 4.8 4.7 - - - -
407B SER* 3.4 37.2 - - - -
422B PHE* 3.7 21.5 - + - -
424B VAL* 3.8 21.3 - - + -
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Residues in contact with GLU 375 (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 ARG* 4.8 0.5 + - - -
362B ILE 3.7 1.0 - - - +
363B GLY* 3.4 3.5 - - - -
364B ARG* 2.9 78.0 + - + +
365B THR 4.2 2.5 - - - +
366B LYS* 2.9 41.4 + - + +
374B PHE* 1.3 78.3 - - - +
376B MET* 1.3 63.4 + - - +
377B ILE* 3.4 11.4 - - + +
394B ARG* 3.1 28.3 + - + -
395B GLN 3.4 12.6 - - - +
397B ILE* 4.2 2.0 - - - -
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Residues in contact with MET 376 (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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97B TRP* 3.6 54.7 - - + +
352B PHE* 3.7 24.5 - - + -
361B TRP* 3.9 15.8 - - + -
362B ILE 3.4 8.7 - - - +
363B GLY* 3.4 21.3 - - - +
374B PHE* 4.0 2.9 - - - -
375B GLU* 1.3 75.4 - - - +
377B ILE* 1.3 61.0 + - - +
392B VAL 3.9 0.2 - - - +
394B ARG* 3.4 4.7 - - - +
395B GLN* 2.8 41.7 + - + +
397B ILE* 4.1 8.3 - - + -
422B PHE* 3.6 31.6 - - + -
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Residues in contact with ILE 377 (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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321B VAL* 3.8 17.0 - - + -
360B VAL 3.4 2.4 - - - +
361B TRP* 3.3 6.4 - - - -
362B ILE* 2.8 45.9 + - + +
364B ARG* 3.6 25.6 - - + +
375B GLU* 3.4 33.4 - - + +
376B MET* 1.3 78.6 - - - +
378B TRP* 1.3 61.9 + - - +
379B ASP* 4.4 3.6 - - + +
390B PHE* 3.6 46.4 - - + -
392B VAL 3.3 4.3 - - - +
394B ARG* 4.4 7.6 - - + +
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Residues in contact with TRP 378 (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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356B TYR* 3.8 18.8 - - + -
357B ASP* 5.9 0.4 - - - -
359B GLY* 3.8 14.4 - - - -
360B VAL* 3.3 37.2 - - - -
361B TRP* 3.5 47.5 - + + -
377B ILE* 1.3 71.7 - - - +
379B ASP* 1.3 58.7 + - - +
380B PRO* 3.6 29.3 - - + +
390B PHE* 3.6 1.7 - - - +
391B SER* 2.9 49.8 + - - -
392B VAL* 2.9 25.9 + - + -
1002B GOL 3.4 39.5 - - - -
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Residues in contact with ASP 379 (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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3B CA 2.4 30.6 - - - -
319B SER* 2.7 26.8 + - - +
321B VAL* 4.0 2.3 - - + +
360B VAL* 2.9 39.9 + - + +
362B ILE* 4.8 2.7 - - + -
377B ILE* 3.7 5.8 + - + -
378B TRP* 1.3 74.5 - - - +
380B PRO* 1.3 64.0 - - - +
381B ASN* 2.9 13.0 + - - +
382B GLY* 3.0 17.0 + - - -
387B ASP 4.2 0.3 - - - +
389B SER 3.1 12.4 - - - +
390B PHE* 4.0 9.2 - - + -
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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