Contacts of the strand formed by residues 362 - 366 (chain B) in PDB entry 3GSB
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 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ILE* 4.2 11.0 - - + +
215B VAL 4.1 1.6 - - - +
216B GLY* 3.6 34.5 - - - +
220B PHE* 3.9 20.1 - - + -
248B MET* 4.1 20.2 - - + +
249B THR* 4.9 4.7 - - + -
252B ARG* 4.4 9.0 - - - -
253B ILE* 4.1 23.6 - - + -
336B THR* 3.9 0.6 - - - +
358B GLN* 3.1 4.8 - - - +
359B VAL 3.1 33.0 + - - +
360B SER 3.0 3.0 + - - -
361B GLY* 1.3 79.0 - - - +
363B PHE* 1.3 64.2 + - - +
407B ALA* 4.0 8.7 - - + -
408B GLY 3.6 11.4 - - - +
409B PHE* 4.1 15.0 - - + -
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Residues in contact with PHE 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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63B TYR* 4.4 17.3 - + + -
220B PHE* 3.5 9.0 - - - -
336B THR* 4.1 12.3 - - + -
339B LEU* 4.0 28.3 - - + -
340B SER* 4.8 8.1 - - - -
343B LEU* 4.3 15.9 - - + -
357B GLY 3.1 14.4 - - - +
358B GLN* 3.6 11.0 - - + +
362B MET* 1.3 78.7 - - - +
364B GLY* 1.3 71.9 + - - +
365B PHE* 5.0 4.3 - - + -
400B LEU* 4.8 10.5 - - + -
407B ALA* 3.3 10.6 - - - +
408B GLY* 3.0 57.7 + - - -
409B PHE* 3.6 12.3 - - - -
410B THR* 5.2 2.5 - - - -
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Residues in contact with GLY 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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220B PHE* 3.5 21.9 - - - +
340B SER* 5.6 1.7 + - - -
356B GLY* 3.2 22.7 - - - -
357B GLY 2.9 10.9 + - - +
363B PHE* 1.3 84.7 - - - +
365B PHE* 1.3 63.9 + - - +
366B PHE* 4.3 4.0 - - - -
406B GLU 5.7 1.1 - - - -
407B ALA* 5.1 2.5 - - - -
408B GLY 5.1 0.4 - - - -
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Residues in contact with PHE 365 (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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340B SER 5.1 0.7 - - - -
343B LEU* 3.7 41.7 - - + -
344B LEU* 3.2 36.1 - - + -
347B ALA* 4.4 2.7 - - + -
354B ALA* 3.9 16.8 - - + -
355B CYS 3.6 2.9 - - - -
363B PHE* 5.0 5.8 - - + -
364B GLY* 1.3 76.4 - - - +
366B PHE* 1.3 58.0 + - - +
367B PHE* 4.2 26.9 - + - -
386B PHE* 4.6 7.6 - + - -
389B PHE* 4.9 16.6 - + - -
404B GLN* 2.8 24.8 + - - -
430B MET* 3.9 26.0 - - + -
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Residues in contact with PHE 366 (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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218B SER 3.7 8.5 - - - -
219B GLY* 3.5 29.8 - - - -
220B PHE* 3.4 29.2 - + - -
354B ALA* 3.3 5.3 - - - +
355B CYS* 2.8 42.4 + - - +
356B GLY* 4.7 3.8 - - - -
364B GLY* 4.8 2.7 - - - -
365B PHE* 1.3 83.3 - - - +
367B PHE* 1.3 60.2 + - - +
368B THR* 2.8 21.0 + - + -
372B VAL* 3.9 36.3 - - + -
378B ALA* 4.3 11.4 - - + -
381B SER* 3.6 16.2 - - - +
404B GLN* 3.4 22.2 - - + +
405B PHE* 4.8 1.3 - + - -
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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