Contacts of the helix formed by residues 596 - 605 (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 TYR 596 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594M THR* 3.6 2.6 - - - +
595M LEU* 1.3 80.9 - - + +
597M LEU* 1.3 56.3 + - - +
598M LEU 3.1 2.7 - - - -
599M TYR* 2.7 15.0 + - - -
600M ALA* 2.4 41.2 + - + +
619M ALA* 3.6 30.1 - - + +
623M VAL* 6.2 1.6 - - - -
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Residues in contact with LEU 597 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594M THR* 5.4 8.4 - - - -
596M TYR* 1.3 78.3 - - - +
598M LEU* 1.3 55.9 + - - +
600M ALA* 4.4 2.0 - - - -
601M GLN* 2.7 40.0 + - + +
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Residues in contact with LEU 598 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562M THR* 5.7 9.2 - - - -
594M THR* 6.0 3.1 - - - -
596M TYR 2.8 4.8 + - - -
597M LEU* 1.3 75.2 - - - +
599M TYR* 1.3 57.3 + - - +
601M GLN* 4.4 0.2 - - - +
602M LEU* 2.9 32.3 + - - +
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Residues in contact with TYR 599 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577M ARG* 6.4 2.7 - - + -
580M PHE* 5.6 10.3 - - + -
581M GLU* 5.7 11.0 - - + +
595M LEU 5.1 7.2 - - - +
596M TYR* 2.7 10.1 + - - +
598M LEU* 1.3 74.7 - - - +
600M ALA* 1.3 57.8 + - - +
602M LEU* 3.8 5.6 - - - +
603M GLU* 2.9 30.5 + - - +
615M VAL* 5.1 1.9 - - + +
110p SER* 6.2 4.0 - - - -
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Residues in contact with ALA 600 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596M TYR* 2.4 49.1 + - + +
597M LEU* 4.3 2.2 - - - +
599M TYR* 1.3 66.3 - - - +
601M GLN* 1.3 58.7 + - - +
603M GLU* 3.3 4.9 + - - +
604M GLU* 2.9 29.6 + - - +
612M ALA* 5.5 1.6 - - - +
615M VAL* 4.6 23.0 - - + +
616M TYR* 5.6 2.0 - - - +
619M ALA* 4.6 2.2 - - + -
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Residues in contact with GLN 601 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597M LEU* 2.7 26.5 + - + +
598M LEU 4.4 0.2 - - - +
600M ALA* 1.3 75.2 - - - +
602M LEU* 1.3 60.5 + - - +
604M GLU* 3.8 6.2 - - - +
605M GLU* 2.9 32.4 + - - +
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Residues in contact with LEU 602 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598M LEU 2.9 24.1 + - - +
599M TYR* 3.9 5.6 - - - +
601M GLN* 1.3 77.6 - - - +
603M GLU* 1.3 57.6 + - - +
605M GLU* 3.6 4.7 + - - +
606M TRP* 3.2 25.8 + - - +
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Residues in contact with GLU 603 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599M TYR 2.9 20.3 + - - +
600M ALA 3.8 3.4 - - - +
602M LEU* 1.3 74.8 - - - +
604M GLU* 1.3 65.0 + - - +
606M TRP* 3.4 17.8 + - - +
608M LEU* 3.8 16.1 + - - +
611M HIS* 4.8 11.1 - - + +
612M ALA* 4.6 4.3 + - - +
615M VAL* 4.5 17.5 - - + -
110p SER* 5.2 9.9 - - - -
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Residues in contact with GLU 604 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600M ALA 2.9 17.9 + - - +
601M GLN* 3.4 6.7 + - - +
603M GLU* 1.3 77.4 - - - +
605M GLU* 1.3 58.8 + - - +
606M TRP 3.6 0.7 + - - -
607M GLY* 4.0 6.4 + - - -
608M LEU 4.7 3.7 + - - +
612M ALA* 3.9 21.7 - - + +
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Residues in contact with GLU 605 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601M GLN 2.9 18.9 + - - +
602M LEU* 3.8 5.4 - - - +
603M GLU 3.3 0.2 - - - -
604M GLU* 1.3 73.4 - - - +
606M TRP* 1.3 62.2 + - - +
607M GLY* 3.2 3.8 + - - -
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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