Contacts of the helix formed by residues 662 - 679 (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 GLU 662 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661M ASP* 1.3 78.1 - - + +
663M HIS* 1.3 58.4 + - - +
664M ALA 3.5 1.8 - - - -
665M ARG* 3.9 9.0 - - + -
666M GLU* 2.9 34.4 + - + +
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Residues in contact with HIS 663 (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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627M GLN* 5.2 10.3 - - + +
655M ALA 5.0 0.9 - - - +
658M VAL 4.6 8.3 - - - +
659M LEU* 4.7 0.2 - - - -
660M SER* 4.2 22.0 - - - +
661M ASP 3.4 2.4 - - - +
662M GLU* 1.3 76.6 - - - +
664M ALA* 1.3 58.4 + - - +
666M GLU* 4.0 2.3 - - - +
667M MET* 2.9 34.9 + - - +
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Residues in contact with ALA 664 (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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655M ALA 4.2 10.1 - - - -
656M ILE* 4.0 19.2 - - + +
658M VAL 4.2 2.8 + - - +
659M LEU* 3.6 28.1 - - + +
660M SER 5.0 0.2 - - - +
661M ASP 5.0 2.5 + - - +
662M GLU 3.5 0.2 - - - -
663M HIS* 1.3 79.3 - - - +
665M ARG* 1.3 58.2 + - - +
668M CYS* 2.8 35.5 + - + +
694M ILE* 5.1 12.3 - - + -
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Residues in contact with ARG 665 (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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661M ASP 5.0 2.8 + - - +
662M GLU* 3.4 14.8 + - + +
663M HIS 3.2 0.6 - - - -
664M ALA* 1.3 77.2 - - - +
666M GLU* 1.3 59.9 + - - +
668M CYS* 3.9 2.4 - - - +
669M LEU* 2.9 31.8 + - - +
691M CYS* 6.5 0.9 - - - +
694M ILE* 5.3 4.8 - - + +
695M CYS* 3.7 37.5 - - + +
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Residues in contact with GLU 666 (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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662M GLU* 2.9 20.4 + - + +
663M HIS* 4.1 2.5 - - - +
665M ARG* 1.3 74.6 - - - +
667M MET* 1.3 62.0 + - - +
669M LEU* 3.7 4.4 - - - +
670M ARG* 2.9 31.4 + - - +
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Residues in contact with MET 667 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632M PHE* 6.0 6.1 - - + -
652M TYR* 6.0 0.7 - - - -
655M ALA* 3.8 32.3 - - + +
663M HIS 2.9 19.1 + - - +
664M ALA 4.5 0.9 - - - +
666M GLU* 1.3 76.6 - - - +
668M CYS* 1.3 58.5 + - - +
670M ARG* 3.4 3.7 + - - +
671M PHE* 2.9 34.0 + - - +
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Residues in contact with CYS 668 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652M TYR* 5.6 2.5 - - - -
656M ILE* 4.6 18.5 - - + +
664M ALA 2.8 22.8 + - - +
665M ARG* 4.2 2.9 - - - +
667M MET* 1.3 77.6 - - - +
669M LEU* 1.3 49.4 + - - +
671M PHE* 4.8 2.9 - - - -
672M ALA* 2.7 37.9 + - - +
687M ILE* 4.7 8.9 - - + +
690M PHE* 5.9 6.7 - - + -
691M CYS* 6.2 4.5 - - + +
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Residues in contact with LEU 669 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665M ARG 2.9 21.9 + - - +
666M GLU* 3.7 5.2 - - - +
667M MET 3.2 0.2 - - - -
668M CYS* 1.3 76.5 - - - +
670M ARG* 1.3 59.1 + - - +
672M ALA* 3.2 5.4 + - - +
673M ASP* 2.9 29.6 + - - +
703M PHE* 6.3 2.7 - - + -
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Residues in contact with ARG 670 (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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666M GLU 2.9 17.2 + - - +
667M MET* 4.0 4.0 - - - +
669M LEU* 1.3 77.4 - - - +
671M PHE* 1.3 57.3 + - - +
673M ASP* 3.3 4.8 + - - +
674M MET* 2.9 29.6 + - - +
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Residues in contact with PHE 671 (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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648M THR 5.1 2.0 - - - +
652M TYR* 3.7 33.1 - - + +
667M MET 2.9 18.3 + - - +
668M CYS* 4.5 2.9 - - - +
670M ARG* 1.3 76.9 - - - +
672M ALA* 1.3 57.3 + - - +
674M MET* 3.9 6.9 - - - +
675M GLU* 2.9 30.3 + - - +
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Residues in contact with ALA 672 (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 2.7 24.2 + - - +
669M LEU* 3.4 8.3 - - - +
670M ARG 3.1 0.2 - - - -
671M PHE* 1.3 75.5 - - - +
673M ASP* 1.3 59.5 + - - +
675M GLU* 3.4 4.1 + - - +
676M CYS* 2.9 30.5 + - - +
683M ARG 5.3 1.1 - - - +
684M ALA* 5.0 5.0 - - - +
687M ILE* 3.6 28.7 - - + +
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Residues in contact with ASP 673 (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 2.9 16.5 + - - +
670M ARG* 3.9 4.7 - - - +
672M ALA* 1.3 73.8 - - - +
674M MET* 1.3 61.4 + - - +
676M CYS* 3.8 4.8 - - - +
677M LYS* 2.9 32.4 + - - +
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Residues in contact with MET 674 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670M ARG 2.9 18.7 + - - +
671M PHE* 4.0 7.9 - - - +
673M ASP* 1.3 75.7 - - - +
675M GLU* 1.3 61.8 + - - +
677M LYS* 3.7 5.3 + - - +
678M LEU* 3.5 21.7 + - - +
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Residues in contact with GLU 675 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671M PHE 2.9 20.1 + - - +
672M ALA* 3.9 3.6 - - - +
674M MET* 1.3 76.8 - - - +
676M CYS* 1.3 57.8 + - - +
678M LEU* 4.9 1.1 - - - -
679M GLY* 2.7 36.5 + - - +
680M GLU 4.0 2.0 - - - +
683M ARG* 4.4 20.8 - - + +
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Residues in contact with CYS 676 (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 2.9 19.4 + - - +
673M ASP* 4.0 6.1 - - - +
675M GLU* 1.3 75.7 - - - +
677M LYS* 1.3 63.7 + - - +
678M LEU 3.4 0.5 + - - -
679M GLY 3.5 10.7 - - - +
680M GLU 4.1 10.5 - - - +
681M ILE* 5.7 0.8 - - - -
684M ALA* 3.8 26.4 - - + +
710M PHE* 5.8 7.4 - - + -
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Residues in contact with LYS 677 (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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673M ASP 2.9 18.2 + - - +
674M MET* 4.1 6.7 - - - +
675M GLU 3.3 0.2 - - - -
676M CYS* 1.3 76.7 - - - +
678M LEU* 1.3 58.0 + - - +
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Residues in contact with LEU 678 (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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674M MET 3.5 14.6 + - - +
675M GLU* 3.4 2.4 + - - +
676M CYS 3.2 0.2 - - - -
677M LYS* 1.3 80.2 - - - +
679M GLY* 1.3 65.5 + - - +
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Residues in contact with GLY 679 (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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675M GLU* 2.7 17.0 + - - +
676M CYS 3.5 11.3 - - - +
678M LEU* 1.3 82.1 - - - +
680M GLU* 1.3 67.1 + - - +
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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