Contacts of the helix formed by residues 377 - 383 (chain M) in PDB entry 6FF7
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 THR 377 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347M SER* 3.9 28.0 - - - -
365M ALA 5.6 1.0 - - - +
368M GLN 5.3 3.4 - - - -
369M GLY 5.8 1.8 - - - -
373M GLU* 5.3 12.5 - - - +
374M ILE* 5.0 3.0 - - - +
376M ASN* 1.3 77.5 - - - +
378M TYR* 1.3 56.0 + - - +
379M THR 3.1 0.7 - - - -
380M GLU* 2.9 16.0 + - - +
381M ALA* 2.9 24.8 + - - +
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Residues in contact with TYR 378 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369M GLY 5.9 0.8 + - - -
370M ARG 5.4 7.9 - - - +
375M ILE* 5.6 3.1 - - - -
376M ASN 2.8 6.5 + - - +
377M THR* 1.3 76.6 - - - +
379M THR* 1.3 58.7 + - - +
381M ALA* 3.1 11.8 + - + +
382M VAL* 2.9 26.0 + - - +
404M PHE* 5.3 16.7 - - + +
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Residues in contact with THR 379 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376M ASN 2.9 13.0 + - - -
378M TYR* 1.3 78.6 - - - +
380M GLU* 1.3 56.4 + - - +
382M VAL* 3.2 9.8 + - - +
383M GLN* 2.8 27.6 + - - +
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Residues in contact with GLU 380 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M SER* 5.7 1.1 - - - +
351M ARG* 4.6 23.6 - - + +
365M ALA* 5.3 6.4 - - - +
376M ASN 4.2 0.6 + - - -
377M THR* 2.9 19.9 + - - +
379M THR* 1.3 75.8 - - - +
381M ALA* 1.3 64.8 + - - +
383M GLN* 3.1 28.3 - - - +
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Residues in contact with ALA 381 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362M LYS* 4.6 17.3 - - - +
365M ALA* 4.8 5.1 + - - +
366M LEU* 3.6 37.4 - - + +
377M THR 2.9 11.7 + - - +
378M TYR* 3.1 15.0 + - - +
380M GLU* 1.3 77.8 - - - +
382M VAL* 1.3 60.3 + - - +
383M GLN 3.2 3.5 + - - +
384M THR* 5.8 0.5 - - - -
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Residues in contact with VAL 382 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378M TYR 2.9 12.7 + - - +
379M THR* 3.2 11.2 + - - +
381M ALA* 1.3 75.2 - - - +
383M GLN* 1.3 59.3 + - - +
384M THR* 3.6 5.4 + - - -
401M PHE* 4.0 28.7 - - + +
404M PHE* 6.2 2.5 - - + -
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Residues in contact with GLN 383 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351M ARG 5.7 0.9 - - - +
362M LYS* 5.7 2.3 - - - +
379M THR 2.8 15.0 + - - +
380M GLU* 3.1 23.1 + - - +
381M ALA 4.2 2.9 - - - +
382M VAL* 1.3 76.0 - - - +
384M THR* 1.3 59.5 + - - +
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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