Contacts of the helix formed by residues 701 - 713 (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 GLY 701 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319 SER* 6.1 4.7 - - - -
699M THR 3.4 3.2 + - - -
700M THR* 1.3 79.9 - - - +
702M ALA* 1.3 60.4 + - - +
703M PHE 3.5 2.7 - - - +
704M TRP* 3.9 11.3 + - - +
705M GLN* 3.6 20.8 + - - +
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Residues in contact with ALA 702 (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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700M THR* 3.3 7.5 + - - +
701M GLY* 1.3 77.2 - - - +
703M PHE* 1.3 59.9 + - - +
705M GLN* 3.5 4.2 + - - +
706M THR* 2.9 31.9 + - - -
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Residues in contact with PHE 703 (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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669M LEU* 6.3 2.7 - - + -
700M THR* 5.7 4.0 - - - -
701M GLY* 3.5 2.5 - - - +
702M ALA* 1.3 79.3 - - - +
704M TRP* 1.3 58.4 + - - +
706M THR* 3.9 4.4 - - - -
707M TRP* 2.9 30.8 + - - +
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Residues in contact with TRP 704 (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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701M GLY* 3.9 12.8 + - - +
702M ALA 3.3 0.8 - - - -
703M PHE* 1.3 79.8 - - - +
705M GLN* 1.3 56.9 + - - +
707M TRP* 3.5 4.3 + - - +
708M LYS* 2.9 30.0 + - - +
728M ARG* 5.1 14.4 - - + -
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Residues in contact with GLN 705 (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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701M GLY 3.6 14.3 + - - +
702M ALA* 3.5 5.4 + - - +
704M TRP* 1.3 76.9 - - - +
706M THR* 1.3 61.5 + - - +
708M LYS* 3.8 5.6 - - - +
709M ASP* 2.9 30.1 + - - +
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Residues in contact with THR 706 (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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702M ALA 2.9 19.4 + - - -
703M PHE* 4.0 5.2 - - - -
705M GLN* 1.3 75.4 - - - +
707M TRP* 1.3 59.6 + - - +
709M ASP* 3.5 5.0 + - - +
710M PHE* 2.9 29.3 + - - +
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Residues in contact with TRP 707 (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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684M ALA 5.8 0.9 - - - +
688M TYR* 4.8 18.4 - - + -
703M PHE 2.9 20.5 + - - +
704M TRP* 3.9 4.5 - - - +
706M THR* 1.3 74.5 - - - +
708M LYS* 1.3 60.7 + - - +
710M PHE* 3.8 6.1 - - - +
711M GLU* 2.9 28.6 + - - +
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Residues in contact with LYS 708 (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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704M TRP 2.9 18.8 + - - +
705M GLN* 3.8 6.7 - - - +
707M TRP* 1.3 75.4 - - - +
709M ASP* 1.3 61.0 + - - +
711M GLU* 3.3 7.4 + - - +
712M VAL* 2.9 26.9 + - - +
721M LYS* 6.1 0.7 - - - +
724M LEU* 6.1 4.7 - - + -
725M ARG* 5.6 12.6 - - + +
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Residues in contact with ASP 709 (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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705M GLN 2.9 17.9 + - - +
706M THR* 3.9 6.3 - - - +
708M LYS* 1.3 73.8 - - - +
710M PHE* 1.3 61.5 + - - +
712M VAL* 3.2 8.1 + - - +
713M ARG* 2.9 28.4 + - - +
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Residues in contact with PHE 710 (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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676M CYS* 5.8 8.5 - - + -
684M ALA* 6.0 4.7 - - + -
706M THR 2.9 17.6 + - - +
707M TRP* 3.8 7.6 - - - +
709M ASP* 1.3 75.4 - - - +
711M GLU* 1.3 62.3 + - - +
713M ARG* 3.4 8.1 + - - +
714M HIS* 3.2 21.3 + - - +
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Residues in contact with GLU 711 (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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707M TRP 2.9 18.3 + - - +
708M LYS* 3.6 7.2 - - - +
709M ASP 3.2 0.4 - - - -
710M PHE* 1.3 73.9 - - - +
712M VAL* 1.3 63.6 + - - +
714M HIS* 3.3 18.5 + - - +
716M ASN* 3.3 24.8 - - + +
721M LYS* 5.8 4.5 - - + -
724M LEU* 5.1 14.8 - - + -
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Residues in contact with VAL 712 (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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708M LYS 2.9 13.8 + - - +
709M ASP* 3.2 11.8 + - - +
711M GLU* 1.3 76.9 - - - +
713M ARG* 1.3 61.5 + - - +
714M HIS 3.4 0.7 + - - -
715M GLY* 3.5 9.4 + - - -
716M ASN* 4.0 3.9 + - - -
717M GLU* 4.2 23.3 + - - +
721M LYS* 5.9 4.0 - - + +
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Residues in contact with ARG 713 (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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709M ASP 2.9 15.3 + - - +
710M PHE* 3.8 8.5 - - - +
711M GLU 3.3 0.6 - - - -
712M VAL* 1.3 76.0 - - - +
714M HIS* 1.3 58.0 + - - +
715M GLY 3.3 3.1 + - - -
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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