Contacts of the strand formed by residues 370 - 376 (chain B) in PDB entry 2G5T
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 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B PHE* 3.4 8.5 - - - +
365B THR* 2.9 49.8 + - - +
367B ASP* 4.6 0.5 + - - -
368B GLY 3.3 0.2 - - - -
369B ASN* 1.3 79.0 - - - +
371B PHE* 1.3 70.0 + - - +
386B TYR* 3.2 23.9 + - - -
387B PHE 3.1 15.9 - - - -
388B GLN* 3.7 10.8 - - - -
389B ILE* 4.2 2.5 - - - -
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Residues in contact with PHE 371 (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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325B MET* 3.6 33.7 - - + -
327B ILE* 3.9 11.7 - - + -
345B HIS* 4.0 13.0 - + + -
362B PRO* 3.9 13.5 - - + -
363B HIS 3.3 15.7 - - - +
364B PHE* 3.6 32.3 - + + +
365B THR 4.5 0.2 - - - +
370B SER* 1.3 80.0 - - - +
372B TYR* 1.3 72.8 + - - +
373B LYS* 4.0 12.3 - - + -
385B CYS 3.8 0.2 - - - +
386B TYR* 3.6 3.2 - - - -
387B PHE* 2.8 79.0 + + + -
389B ILE* 3.9 8.5 - - + -
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Residues in contact with TYR 372 (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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362B PRO* 3.5 1.0 - - - +
363B HIS* 2.8 45.5 + - + +
365B THR* 3.8 10.9 - - + +
371B PHE* 1.3 77.0 - - - +
373B LYS* 1.3 63.4 + - - +
384B ILE* 3.8 15.0 - - + -
385B CYS 3.3 4.3 - - - -
386B TYR* 3.2 50.7 + + + -
397B ILE* 3.9 29.4 - - + -
407B ILE* 3.8 10.5 - - + +
410B LEU* 3.8 27.1 - - + -
415B LEU* 4.2 9.2 - - + -
436B LEU* 3.5 30.7 + - + +
439B TYR* 5.0 5.2 + + - -
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Residues in contact with LYS 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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314B GLN* 2.9 31.4 - - - +
325B MET* 4.9 6.1 - - - +
347B GLU* 2.9 22.9 + - - +
360B SER* 3.1 21.3 + - - +
361B GLU 3.7 13.0 - - - +
362B PRO* 4.0 12.8 - - + -
371B PHE* 4.0 10.5 - - + -
372B TYR* 1.3 78.4 - - - +
374B ILE* 1.3 63.1 + - - +
375B ILE* 3.4 26.1 + - + +
384B ILE* 4.4 2.0 - - - -
385B CYS* 3.0 29.1 + - - +
387B PHE* 3.6 24.0 - - + -
407B ILE* 4.0 6.5 - - - +
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Residues in contact with ILE 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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347B GLU* 4.6 2.6 - - - +
356B ARG* 4.4 7.2 - - - +
360B SER* 2.6 36.7 + - - +
361B GLU 4.8 0.6 + - - -
373B LYS* 1.3 71.9 - - - +
375B ILE* 1.3 64.4 + - - +
382B ARG* 3.6 33.7 + - + -
383B HIS 3.4 9.2 - - - +
384B ILE* 4.3 4.5 - - + -
404B VAL* 3.5 28.5 - - + +
405B ILE 3.7 7.2 - - - +
406B GLY* 3.4 36.8 - - - +
407B ILE* 4.1 13.4 - - + +
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Residues in contact with ILE 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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347B GLU* 3.9 26.0 - - + +
373B LYS* 3.4 31.2 - - + +
374B ILE* 1.3 80.1 - - - +
376B SER* 1.3 67.4 + - - +
382B ARG* 4.1 7.0 - - - +
383B HIS 3.1 23.6 + - - +
385B CYS* 3.8 5.6 - - + -
387B PHE* 4.3 7.0 - - + -
394B CYS* 3.6 25.6 - - - -
396B PHE* 3.5 32.3 - - + -
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Residues in contact with SER 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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347B GLU* 5.1 1.6 + - - -
375B ILE* 1.3 78.3 - - - +
377B ASN* 1.3 72.5 + - - +
380B GLY* 3.6 7.1 - - - -
381B TYR 3.8 3.4 - - - -
382B ARG* 3.9 26.2 - - - +
396B PHE* 3.7 10.1 - - - -
588B ASP* 2.6 31.2 + - - -
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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