Contacts of the helix formed by residues 372 - 377 (chain F) in PDB entry 6VVT
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 GLN 372 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D LYS* 4.2 21.6 - - - +
405D LEU* 6.1 0.5 - - - +
361F LEU 3.9 5.2 - - - +
362F ASP* 3.7 34.0 + - - +
363F GLN 3.1 16.4 - - - +
364F THR* 4.3 8.4 + - - +
365F ILE 4.7 0.7 - - - -
371F SER* 1.3 79.4 - - - +
373F LEU* 1.3 67.0 + - - +
374F GLY* 3.3 1.3 - - - +
375F ASP* 3.0 31.1 + - - +
376F PHE* 4.3 6.5 - - - -
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Residues in contact with LEU 373 (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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330D LEU* 4.0 31.0 - - + -
336D ALA* 5.5 0.4 - - + -
359F ILE* 4.9 9.9 - - + -
360F SER 4.1 15.0 - - - +
361F LEU* 3.3 21.7 + - + +
363F GLN* 2.9 28.6 + - + +
365F ILE* 4.4 22.1 - - + +
372F GLN* 1.3 72.5 - - - +
374F GLY* 1.3 64.3 + - - +
375F ASP 3.0 1.4 + - - -
376F PHE* 3.1 24.7 + - + +
377F ILE* 4.2 8.7 - - + +
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Residues in contact with GLY 374 (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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1041C SER* 3.9 0.5 + - - -
1043C ILE* 2.9 31.4 - - - +
361F LEU* 3.1 37.4 + - - -
372F GLN* 3.3 2.5 - - - +
373F LEU* 1.3 75.3 - - - +
375F ASP* 1.3 64.1 + - - +
376F PHE 3.1 1.0 + - - -
377F ILE* 3.2 11.3 + - - +
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Residues in contact with ASP 375 (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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1041C SER* 3.4 20.6 + - - -
1043C ILE* 5.0 0.8 - - - +
1044C THR* 5.3 11.2 - - + +
1048C LEU* 3.3 16.0 - - + +
371F SER* 3.2 13.7 + - - -
372F GLN* 3.0 40.7 + - - +
373F LEU 3.0 1.4 + - - -
374F GLY* 1.3 78.1 - - - +
376F PHE* 1.3 67.9 + - + +
377F ILE 3.3 1.1 - - - -
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Residues in contact with PHE 376 (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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1048C LEU* 3.2 29.8 - - + +
1051C LYS* 5.6 6.5 - - + +
421D ARG* 6.3 1.1 - - - -
365F ILE* 4.9 9.4 - - + -
366F GLY* 4.9 16.6 - - - -
371F SER* 4.1 29.2 - - - -
372F GLN 4.3 5.8 - - - -
373F LEU* 3.1 18.8 + - + +
375F ASP* 1.3 82.8 - - + +
377F ILE* 1.3 64.9 + - + +
378F GLU* 3.5 3.5 + - - +
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Residues in contact with ILE 377 (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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1041C SER* 3.2 7.3 + - - -
1042C MET* 2.8 44.1 + - + -
1043C ILE* 4.5 2.5 - - + -
1048C LEU* 3.5 1.3 - - - -
328D VAL* 4.0 25.4 - - + -
330D LEU* 3.9 32.3 - - + -
331D ASP* 5.3 1.3 - - - +
361F LEU* 4.1 18.4 - - + -
373F LEU* 4.2 11.9 - - + +
374F GLY* 3.2 20.2 + - - +
375F ASP 3.3 0.6 - - - -
376F PHE* 1.3 79.8 - - + +
378F GLU* 1.3 73.4 + - - +
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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