Contacts of the strand formed by residues 359 - 364 (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 GLY 359 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ARG* 3.6 7.4 - - - +
356B TYR 2.7 32.9 + - - -
357B ASP* 4.4 0.2 - - - +
358B ASN* 1.3 82.4 - - - +
360B VAL* 1.3 62.4 + - - +
378B TRP* 3.8 10.1 - - - -
379B ASP 3.3 7.4 - - - -
380B PRO 3.2 20.5 + - - -
383B TRP* 3.9 1.1 - - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 4.5 4.9 - - + -
353B SER* 3.7 18.2 - - - -
354B PHE 3.4 12.3 - - - +
359B GLY* 1.3 75.4 - - - +
361B TRP* 1.3 72.6 + - - +
362B ILE* 3.8 23.1 - - + -
377B ILE 3.4 2.4 - - - +
378B TRP* 3.3 8.9 - - - -
379B ASP* 2.9 36.6 + - + +
382B GLY* 3.6 30.1 - - - +
383B TRP* 3.8 23.1 - - + +
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Residues in contact with TRP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.6 11.6 - - + +
95B SER 3.8 27.6 - - - -
96B GLY* 4.5 1.6 - - - -
97B TRP* 3.3 43.1 - + + -
353B SER* 3.1 7.8 - - - -
354B PHE* 2.9 42.7 + - + +
356B TYR* 3.7 26.0 - + - -
360B VAL* 1.3 71.9 - - - +
362B ILE* 1.3 60.2 + - - +
363B GLY 4.1 0.2 + - - -
376B MET* 3.9 21.1 - - + +
377B ILE 3.3 25.6 - - - -
378B TRP* 3.5 45.4 - + + -
392B VAL* 4.2 15.3 - - + -
395B GLN* 5.2 2.9 - - + -
1002B GOL 2.8 27.1 + - - -
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Residues in contact with ILE 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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317B ILE* 4.9 7.9 - - + -
319B SER* 4.4 8.3 - - - +
321B VAL* 3.6 37.5 - - + +
323B GLY* 4.3 14.1 - - - -
353B SER* 3.7 12.3 - - - +
360B VAL* 3.8 33.4 - - + -
361B TRP* 1.3 72.7 - - - +
363B GLY* 1.3 72.4 + - - +
364B ARG* 4.2 19.1 - - + -
375B GLU 3.7 1.0 - - - +
376B MET* 3.4 4.5 - - - -
377B ILE* 2.8 44.0 + - + +
379B ASP* 4.8 5.2 - - + -
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Residues in contact with GLY 363 (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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300B ARG* 5.0 3.8 + - - -
323B GLY 4.3 5.0 - - - +
351B GLY* 5.4 0.5 - - - -
352B PHE* 3.7 26.6 + - - +
361B TRP 4.1 1.4 + - - -
362B ILE* 1.3 76.1 - - - +
364B ARG* 1.3 64.7 + - - +
374B PHE* 3.7 14.3 - - - -
375B GLU 3.4 7.4 - - - -
376B MET* 3.4 19.8 - - - +
407B SER* 4.9 1.2 + - - -
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Residues in contact with ARG 364 (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* 3.4 10.1 - - - +
322B PHE 2.9 30.4 + - - +
323B GLY 3.8 16.6 - - - +
327B ARG* 3.6 25.3 - - - +
330B ASP* 2.8 41.6 + - - -
362B ILE* 4.2 14.4 - - + +
363B GLY* 1.3 76.2 - - - +
365B THR* 1.3 68.1 - - - +
374B PHE* 3.3 13.7 - - - -
375B GLU* 2.9 62.0 + - + +
377B ILE* 3.6 16.3 - - + +
390B PHE* 5.2 0.8 - - - -
394B ARG* 5.0 7.1 - - - +
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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