Contacts of the helix formed by residues 636 - 650 (chain M) in PDB entry 6M6A
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 ASP 636 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565D ILE* 5.9 0.8 - - - +
634M PRO* 4.0 2.5 + - + -
635M PHE* 1.3 81.6 - - - +
637M PRO* 1.3 79.2 - - - +
638M LEU* 3.0 38.5 + - - +
639M LEU* 3.2 43.3 + - + +
640M VAL* 3.4 12.8 + - - +
757M PHE* 4.3 3.1 - - - -
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Residues in contact with PRO 637 (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 PHE* 3.6 25.6 - - + -
636M ASP* 1.3 93.7 - - - +
638M LEU* 1.3 65.9 + - + +
640M VAL* 3.2 15.0 + - + +
641M ARG* 2.9 31.8 + - + +
670M PHE* 5.4 1.8 - - + -
674M LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 638 (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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636M ASP* 3.0 21.9 + - - +
637M PRO* 1.3 83.5 - - + +
639M LEU* 1.3 60.0 + - + +
641M ARG* 3.0 16.3 + - + +
642M GLU* 2.9 41.9 + - - +
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Residues in contact with LEU 639 (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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563D PRO* 6.4 0.4 - - + -
565D ILE* 3.7 37.7 - - + -
566D ILE* 3.8 26.9 - - + -
633M ALA* 5.5 0.7 - - + -
634M PRO* 5.1 9.2 - - + +
636M ASP* 3.2 37.2 + - + +
637M PRO 3.3 0.2 - - - -
638M LEU* 1.3 72.7 - - + +
640M VAL* 1.3 60.9 + - - +
642M GLU* 3.3 24.6 + - - +
643M ALA* 2.9 30.1 + - - +
755M TYR* 5.3 7.7 - - + -
757M PHE* 5.1 11.4 - - + -
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Residues in contact with VAL 640 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635M PHE* 4.5 9.4 - - + -
636M ASP 3.4 16.8 - - - +
637M PRO* 3.2 14.4 - - + +
638M LEU 3.2 0.2 - - - -
639M LEU* 1.3 75.9 - - - +
641M ARG* 1.3 57.6 + - - +
643M ALA* 3.8 4.8 - - - +
644M ILE* 2.9 50.0 + - + +
671M LEU* 6.3 3.4 - - + -
674M LEU* 6.3 2.0 - - + -
675M VAL* 5.8 2.7 - - + -
726M LEU* 3.7 30.7 - - + -
757M PHE* 4.2 13.2 - - + -
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Residues in contact with ARG 641 (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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637M PRO* 2.9 21.8 + - + +
638M LEU* 3.0 20.8 + - + +
640M VAL* 1.3 78.8 - - - +
642M GLU* 1.3 57.4 + - + +
644M ILE* 3.2 7.9 - - - +
645M LEU* 2.9 46.3 + - + +
674M LEU* 2.4 40.7 + - - +
675M VAL* 3.4 26.9 - - - +
676M PRO* 4.6 0.2 - - - +
677M GLU* 3.0 30.3 + - - -
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Residues in contact with GLU 642 (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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563D PRO* 5.2 5.2 - - - +
565D ILE* 3.5 18.0 - - - +
638M LEU* 2.9 35.5 + - - +
639M LEU* 3.3 30.9 + - - +
640M VAL 3.3 0.2 - - - -
641M ARG* 1.3 77.2 - - + +
643M ALA* 1.3 56.6 + - - +
645M LEU* 3.2 9.5 + - + +
646M PHE* 2.9 54.5 + - + -
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Residues in contact with ALA 643 (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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639M LEU 2.9 18.3 + - - +
640M VAL* 3.3 6.5 + - - +
642M GLU* 1.3 77.6 - - - +
644M ILE* 1.3 61.0 + - + +
646M PHE* 3.1 16.2 + - - +
647M GLU* 3.0 26.9 + - - +
650M ARG* 4.8 0.9 + - - -
724M THR* 4.6 7.2 - - - +
726M LEU* 5.1 5.8 - - + -
755M TYR* 3.6 39.2 - - + -
757M PHE* 6.4 0.2 - - + -
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Residues in contact with ILE 644 (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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640M VAL* 2.9 33.1 + - + +
641M ARG* 3.2 35.4 - - - +
643M ALA* 1.3 75.3 - - + +
645M LEU* 1.3 61.8 + - + +
647M GLU* 3.7 7.9 - - - +
648M LEU* 2.9 37.9 + - + +
654M VAL* 4.1 30.4 - - + +
675M VAL* 3.7 28.7 - - + -
706M VAL* 5.2 7.4 - - + -
724M THR* 5.9 0.2 - - - -
726M LEU* 5.4 2.9 - - + -
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Residues in contact with LEU 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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641M ARG* 2.9 34.3 + - + +
642M GLU* 3.3 10.3 - - + +
643M ALA 3.2 0.2 - - - -
644M ILE* 1.3 77.6 - - + +
646M PHE* 1.3 61.5 + - + +
648M LEU* 3.3 31.6 - - + +
649M GLU* 2.8 43.9 + - - +
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Residues in contact with PHE 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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563D PRO* 4.9 17.5 - - + -
642M GLU* 2.9 42.4 + - + -
643M ALA* 3.1 13.2 + - - +
645M LEU* 1.3 75.3 - - + +
647M GLU* 1.3 59.0 + - - +
649M GLU* 3.1 25.8 + - - +
650M ARG* 3.0 57.8 + - - +
753M TYR* 5.0 6.7 - + - -
755M TYR* 3.7 18.8 - + - -
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Residues in contact with GLU 647 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643M ALA 3.0 14.5 + - - +
644M ILE* 3.8 4.9 - - - +
645M LEU 3.3 0.4 - - - -
646M PHE* 1.3 76.7 - - - +
648M LEU* 1.3 56.4 + - - +
650M ARG* 3.1 22.4 + - - +
651M GLY 2.7 3.8 + - - -
652M GLY* 2.4 40.2 + - - +
653M LYS 2.9 31.6 + - - +
654M VAL* 3.8 13.0 - - + -
721M GLU 2.8 27.4 - - - +
723M ASN* 2.9 29.9 + - - +
724M THR* 3.3 12.5 - - + +
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Residues in contact with LEU 648 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644M ILE* 2.9 26.5 + - + +
645M LEU* 3.3 38.4 - - + +
647M GLU* 1.3 74.2 - - - +
649M GLU* 1.3 69.8 + - + +
651M GLY* 3.1 14.9 + - - +
652M GLY 5.5 0.7 - - - -
677M GLU* 5.6 10.8 - - + -
678M ALA* 6.4 1.8 - - + -
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Residues in contact with GLU 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 LEU* 2.8 40.7 + - - +
646M PHE* 3.1 30.6 + - - +
648M LEU* 1.3 82.8 - - + +
650M ARG* 1.3 64.3 + - - +
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Residues in contact with ARG 650 (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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643M ALA 4.8 0.2 + - - -
646M PHE* 3.0 47.6 + - - +
647M GLU* 3.1 41.5 + - - +
649M GLU* 1.3 79.5 + - - +
651M GLY* 1.3 59.5 + - - +
652M GLY* 3.3 9.7 + - - +
723M ASN* 4.1 18.2 - - - +
750M GLU* 6.3 0.7 - - - -
751M GLU 5.5 0.4 + - - -
753M TYR* 3.1 45.1 + - - -
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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