Contacts of the strand formed by residues 307 - 312 (chain F) in PDB entry 1Q57
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 VAL 307 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306F GLU* 1.3 81.4 - - - +
308F ILE* 1.3 63.5 + - - +
309F MET* 3.6 4.1 + - + -
446F MET* 4.6 10.8 - - + -
449F LEU* 5.4 1.3 - - + -
450F LYS* 3.6 25.1 - - + +
453F ALA* 3.4 23.1 - - + -
460F LEU* 3.3 23.8 - - + +
462F VAL* 5.3 4.5 - - + -
495F LEU 4.2 4.0 - - - +
496F SER* 3.5 25.9 - - - +
497F ASP* 2.9 25.2 + - - -
498F THR 3.6 3.4 + - - -
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Residues in contact with ILE 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F PHE* 3.7 31.0 - - + -
301F GLY 4.2 1.3 - - - +
302F ALA* 3.9 21.5 - - + -
306F GLU* 3.7 20.6 - - + +
307F VAL* 1.3 72.6 - - - +
309F MET* 1.3 64.7 + - - +
310F VAL* 4.1 1.1 - - + -
459F VAL* 4.6 11.0 - - + -
460F LEU 2.9 7.8 + - - +
461F VAL* 4.2 18.8 - - + -
462F VAL* 2.8 27.9 + - - +
498F THR* 3.4 32.3 - - - +
500F ILE* 3.8 17.7 - - + -
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Residues in contact with MET 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F VAL* 5.0 1.1 - - + -
308F ILE* 1.3 76.4 - - - +
310F VAL* 1.3 66.8 + - - +
311F THR* 3.8 6.0 + - - -
446F MET* 3.5 25.1 - - + -
462F VAL* 3.2 41.7 - - + +
464F CYS* 4.3 11.9 - - + -
486F LEU* 5.6 6.1 - - + -
492F LEU* 3.7 27.8 - - + -
496F SER* 3.7 12.1 - - - +
498F THR 2.8 8.1 + - - -
499F ILE* 3.1 28.2 - - + +
500F ILE 3.0 27.0 + - - +
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Residues in contact with VAL 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F PHE* 6.1 0.4 - - + -
308F ILE* 4.9 6.7 - - + -
309F MET* 1.3 73.7 - - - +
311F THR* 1.3 64.4 + - - +
318F MET* 3.6 13.1 - - + +
321F PHE* 4.1 26.5 - - + -
322F VAL* 3.9 11.9 - - + -
461F VAL* 3.7 27.8 - - + -
462F VAL 3.0 6.1 + - - +
463F ILE* 3.4 12.7 - - + -
464F CYS* 2.9 26.5 + - - +
500F ILE* 3.2 10.3 - - + +
502F LEU* 3.5 25.1 - - + -
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Residues in contact with THR 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F MET* 4.9 7.2 - - - -
310F VAL* 1.3 75.8 - - - +
312F SER* 1.3 71.0 + - - +
318F MET* 3.6 4.3 - - - -
464F CYS* 2.8 27.5 + - - -
466F LEU* 2.8 29.3 - - + +
481F VAL* 4.6 8.3 - - + -
486F LEU* 4.7 8.7 - - + +
499F ILE* 5.0 9.0 - - + -
500F ILE 2.9 8.6 + - - +
501F ALA* 3.2 21.8 - - + -
502F LEU* 3.0 19.4 + - - +
519F LEU* 5.0 1.3 - - + -
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Residues in contact with SER 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311F THR* 1.3 86.0 + - - +
313F GLY* 1.3 72.1 + - - +
315F GLY* 3.8 12.3 - - - -
317F VAL* 5.3 1.0 - - - +
318F MET* 3.0 23.0 + - - +
465F HIS* 4.2 0.5 - - - -
466F LEU* 3.5 28.9 + - - +
481F VAL* 5.3 2.5 - - - -
501F ALA* 5.3 0.2 - - - -
502F LEU* 2.5 40.5 + - - +
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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