Contacts of the helix formed by residues 644 - 658 (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 644 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639M ALA 4.3 3.4 - - - +
640M ALA 5.8 2.2 - - - -
642M ILE 3.1 5.1 + - - -
643M TYR* 1.3 81.6 - - - +
645M VAL* 1.3 66.2 + - - -
646M THR 3.4 2.5 - - - -
647M HIS* 3.0 13.5 + - - +
648M THR* 3.1 12.3 + - - -
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Residues in contact with VAL 645 (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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644M GLY* 1.3 69.4 - - - -
646M THR* 1.3 57.1 + - - +
648M THR* 2.7 31.1 + - - -
649M ARG* 2.9 10.9 + - - +
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Residues in contact with THR 646 (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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644M GLY 3.4 0.6 - - - -
645M VAL* 1.3 78.1 - - - +
647M HIS* 1.3 57.3 + - - +
649M ARG* 3.2 10.2 + - - +
650M GLY* 2.9 24.4 + - - -
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Residues in contact with HIS 647 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639M ALA* 4.2 17.6 - - + +
643M TYR* 3.4 28.9 - - + -
644M GLY 3.0 12.0 + - - +
646M THR* 1.3 77.7 - - - +
648M THR* 1.3 57.2 + - - +
650M GLY* 3.4 1.4 + - - -
651M ILE* 2.9 29.9 + - - +
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Residues in contact with THR 648 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639M ALA* 4.8 8.6 + - - -
640M ALA* 6.0 3.1 - - - -
644M GLY 3.1 8.6 + - - -
645M VAL* 2.7 20.5 + - - -
647M HIS* 1.3 71.3 - - - +
649M ARG* 1.3 56.0 + - - -
651M ILE* 3.6 7.2 + - - +
652M TYR* 2.9 26.9 + - - +
671M PHE* 5.1 2.3 - - - +
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Residues in contact with ARG 649 (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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645M VAL 2.9 11.1 + - - +
646M THR* 3.2 12.1 + - - +
648M THR* 1.3 75.0 - - - +
650M GLY* 1.3 60.4 + - - +
652M TYR* 3.1 8.8 + - - +
653M GLN* 2.9 28.2 + - - +
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Residues in contact with GLY 650 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646M THR 2.9 15.7 + - - -
647M HIS* 3.9 2.7 - - - -
649M ARG* 1.3 75.1 - - - +
651M ILE* 1.3 57.7 + - - +
653M GLN* 3.4 6.2 + - - +
654M LYS* 2.9 29.7 + - - +
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Residues in contact with ILE 651 (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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635M TYR* 5.2 2.5 - - + +
636M ILE* 4.9 13.9 - - + -
639M ALA* 4.3 17.7 - - + -
647M HIS 2.9 18.5 + - - +
648M THR* 3.7 6.5 - - - +
650M GLY* 1.3 75.5 - - - +
652M TYR* 1.3 57.8 + - - +
654M LYS* 4.2 5.8 - - - +
655M ALA* 2.9 31.0 + - - +
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Residues in contact with TYR 652 (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 2.9 18.4 + - - +
649M ARG* 3.1 10.5 + - - +
651M ILE* 1.3 75.6 - - - +
653M GLN* 1.3 59.6 + - - +
655M ALA* 3.5 4.4 + - - +
656M ILE* 2.9 29.6 + - - +
667M MET 6.0 0.6 - - - -
668M CYS* 5.6 3.2 - - - -
671M PHE* 3.7 29.2 - - + +
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Residues in contact with GLN 653 (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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649M ARG 2.9 14.9 + - - +
650M GLY* 4.0 6.5 - - - +
652M TYR* 1.3 73.4 - - - +
654M LYS* 1.3 60.5 + - - +
656M ILE* 3.4 5.3 + - - +
657M GLU* 2.9 28.2 + - - +
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Residues in contact with LYS 654 (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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650M GLY 2.9 17.7 + - - +
651M ILE* 4.2 5.6 - - - +
653M GLN* 1.3 75.6 - - - +
655M ALA* 1.3 63.7 + - - +
657M GLU* 3.3 14.9 + - - +
658M VAL* 3.3 15.4 + - - +
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Residues in contact with ALA 655 (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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632M PHE* 6.2 4.0 - - + -
651M ILE 2.9 21.7 + - - +
652M TYR* 3.9 5.4 - - - +
654M LYS* 1.3 75.9 - - - +
656M ILE* 1.3 56.9 + - - +
658M VAL* 2.9 23.6 - - - +
663M HIS* 4.9 0.7 - - - +
664M ALA* 4.2 7.8 - - - -
667M MET* 3.8 26.9 - - + +
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Residues in contact with ILE 656 (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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652M TYR 2.9 18.8 + - - +
653M GLN* 3.9 6.3 - - - +
654M LYS 3.3 0.2 - - - -
655M ALA* 1.3 74.7 - - - +
657M GLU* 1.3 65.7 + - - +
658M VAL 4.2 0.2 - - - -
659M LEU* 4.7 1.7 - - - +
664M ALA* 4.0 21.7 - - + +
667M MET* 5.3 0.4 - - - +
668M CYS* 4.6 17.7 - - + +
690M PHE* 6.5 1.3 - - + -
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Residues in contact with GLU 657 (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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653M GLN 2.9 17.7 + - - +
654M LYS* 3.6 9.0 - - - +
655M ALA 3.3 0.6 - - - -
656M ILE* 1.3 79.9 - - - +
658M VAL* 1.3 62.0 + - - +
659M LEU* 3.4 5.7 + - - +
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Residues in contact with VAL 658 (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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654M LYS 3.3 11.3 + - - +
655M ALA* 2.9 20.9 - - - +
656M ILE 4.2 0.7 - - - -
657M GLU* 1.3 76.0 - - - +
659M LEU* 1.3 59.4 + - - +
663M HIS* 4.6 4.4 - - - +
664M ALA* 4.2 4.7 + - - +
103p GLU 4.7 13.7 - - - +
104p GLY 5.7 2.7 - - - +
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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