Contacts of the helix formed by residues 681 - 694 (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 ILE 681 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676M CYS* 5.7 0.9 - - - +
680M GLU* 1.3 74.8 - - - +
682M ASP* 1.3 64.0 + - - +
683M ARG 3.4 0.9 - - - -
684M ALA* 3.3 13.4 + - + +
685M ARG* 3.1 22.9 + - - +
711M GLU* 6.3 0.7 - - - -
714M HIS* 4.1 26.2 - - + -
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Residues in contact with ASP 682 (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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680M GLU* 3.3 10.0 - - + +
681M ILE* 1.3 77.0 - - - +
683M ARG* 1.3 58.6 + - - +
685M ARG* 3.3 5.1 + - - +
686M ALA* 2.9 32.6 + - - +
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Residues in contact with ARG 683 (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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672M ALA* 5.1 2.9 - - - +
675M GLU* 4.4 22.4 - - + -
680M GLU* 4.2 8.3 + - - +
681M ILE 3.4 0.4 - - - -
682M ASP* 1.3 77.8 - - - +
684M ALA* 1.3 50.1 + - - +
686M ALA* 4.6 4.9 - - - -
687M ILE* 2.7 38.8 + - - +
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Residues in contact with ALA 684 (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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672M ALA* 5.0 4.5 - - - +
676M CYS* 3.8 29.3 - - + +
680M GLU 4.5 1.0 + - - -
681M ILE* 3.3 17.9 + - + +
682M ASP 3.1 0.8 - - - -
683M ARG* 1.3 77.9 - - - +
685M ARG* 1.3 59.2 + - - +
687M ILE* 3.7 3.4 - - - +
688M TYR* 2.9 28.2 + - - +
707M TRP* 5.8 0.7 - - - +
710M PHE* 6.0 4.9 - - + -
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Residues in contact with ARG 685 (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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681M ILE 3.1 15.8 + - - +
682M ASP* 3.9 4.7 - - - +
684M ALA* 1.3 74.8 - - - +
686M ALA* 1.3 60.3 + - - +
688M TYR* 3.1 8.1 + - - +
689M SER* 2.9 27.2 + - - -
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Residues in contact with ALA 686 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682M ASP 2.9 17.7 + - - +
683M ARG* 4.5 3.6 - - - +
685M ARG* 1.3 76.5 - - - +
687M ILE* 1.3 57.3 + - - +
689M SER* 3.3 8.5 + - - -
690M PHE* 2.9 27.5 + - - +
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Residues in contact with ILE 687 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668M CYS* 4.7 7.5 - - + +
672M ALA* 3.6 31.7 - - + +
683M ARG 2.7 24.3 + - - +
684M ALA* 3.8 4.3 - - - +
686M ALA* 1.3 75.6 - - - +
688M TYR* 1.3 58.6 + - - +
690M PHE* 3.5 7.9 + - - +
691M CYS* 2.9 26.2 + - - +
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Residues in contact with TYR 688 (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 2.9 18.1 + - - +
685M ARG* 3.1 8.7 + - - +
687M ILE* 1.3 76.5 - - - +
689M SER* 1.3 61.0 + - - +
691M CYS* 3.0 10.2 + - - +
692M SER* 2.9 26.3 + - - -
707M TRP* 4.8 18.4 - - + -
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Residues in contact with SER 689 (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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685M ARG 2.9 12.7 + - - -
686M ALA* 3.7 11.2 - - - -
688M TYR* 1.3 75.8 - - - +
690M PHE* 1.3 61.9 + - - +
692M SER* 3.2 21.2 + - - +
693M GLN* 3.4 8.3 + - - +
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Residues in contact with PHE 690 (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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668M CYS* 5.9 7.0 - - + -
686M ALA 2.9 17.6 + - - +
687M ILE* 3.8 8.3 - - - +
689M SER* 1.3 76.5 - - - +
691M CYS* 1.3 61.6 + - - +
693M GLN* 3.5 7.2 + - - +
694M ILE* 3.3 23.0 + - - +
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Residues in contact with CYS 691 (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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665M ARG* 6.5 1.3 - - - +
668M CYS* 6.2 4.7 - - + +
687M ILE 2.9 17.9 + - - +
688M TYR* 3.0 11.2 + - - +
690M PHE* 1.3 76.2 - - - +
692M SER* 1.3 56.7 + - - +
693M GLN 3.5 0.2 - - - -
694M ILE* 2.8 24.1 - - - +
695M CYS* 4.0 11.0 - - + +
703M PHE* 6.3 2.7 - - + -
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Residues in contact with SER 692 (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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688M TYR 2.9 10.4 + - - -
689M SER* 3.4 13.9 - - - -
690M PHE 3.2 0.6 - - - -
691M CYS* 1.3 78.1 - - - +
693M GLN* 1.3 63.5 + - - +
694M ILE 3.3 5.6 - - - +
731M GLN* 4.9 17.5 - - - -
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Residues in contact with GLN 693 (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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689M SER 3.4 7.9 + - - +
690M PHE* 3.5 8.2 + - - +
692M SER* 1.3 79.1 - - - +
694M ILE* 1.3 58.5 + - + +
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Residues in contact with ILE 694 (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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664M ALA* 5.1 16.2 - - + -
665M ARG* 5.3 6.5 - - + +
690M PHE 3.3 13.9 + - - +
691M CYS* 2.8 20.0 - - - +
692M SER 3.5 6.9 - - - +
693M GLN* 1.3 77.7 - - + +
695M CYS* 1.3 70.6 + - + +
696M ASP* 3.7 1.7 - - - -
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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