Contacts of the helix formed by residues 650 - 666 (chain G) in PDB entry 1MVW
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 SER 650 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475G PHE* 4.3 6.3 - - - -
479G CYS* 5.7 0.4 - - - -
533G PHE* 4.1 27.7 - - - -
537G GLU* 2.6 25.0 + - - +
599G ASN* 2.7 29.5 + - - -
648G THR* 3.3 1.2 - - - -
649G VAL* 1.0 81.1 - - - +
651G ALA* 1.3 64.7 + - - +
652G LEU 3.2 3.2 + - - -
653G PHE* 3.6 10.5 - - - +
654G ARG* 3.2 28.1 + - - +
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Residues in contact with ALA 651 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537G GLU* 3.9 11.0 - - - +
641G LYS* 5.0 10.8 - - - +
646G PHE* 5.4 2.2 - - + -
647G GLN 4.9 4.5 - - - +
648G THR* 2.9 39.2 + - + +
650G SER* 1.3 78.9 + - - +
652G LEU* 1.3 62.3 + - + +
654G ARG* 4.1 9.9 + - - +
655G GLU* 3.7 18.6 + - - +
1V ASP 5.5 0.2 + - - -
4V GLU* 4.9 11.6 - - + +
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Residues in contact with LEU 652 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646G PHE* 2.6 54.1 - - + -
648G THR 4.9 4.0 - - - +
649G VAL* 5.6 8.7 - - + +
650G SER* 3.2 1.0 - - - +
651G ALA* 1.3 76.2 - - + +
653G PHE* 1.3 57.8 - - - +
654G ARG 2.8 2.2 - - - -
655G GLU* 2.3 45.1 + - - +
656G ASN* 2.6 36.5 + - - +
4V GLU* 5.3 1.3 - - - +
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Residues in contact with PHE 653 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268G TYR* 5.5 10.1 - + + -
269G LEU* 3.6 30.1 - - + -
479G CYS* 3.2 57.2 - - + -
482G PHE* 4.2 7.0 - + - -
483G THR* 3.3 13.7 - - + -
533G PHE* 4.8 6.3 - + - -
649G VAL 4.3 6.0 + - - +
650G SER* 3.6 19.5 - - - +
652G LEU* 1.3 76.5 - - - +
654G ARG* 1.3 60.1 + - + +
656G ASN* 3.8 7.6 - - + +
657G LEU* 2.7 57.6 + - + +
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Residues in contact with ARG 654 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482G PHE* 4.7 10.8 - - + -
527G GLU* 3.9 25.9 + - + +
528G MLY 5.2 1.8 + - - -
529G PRO* 6.1 0.2 - - - +
533G PHE* 3.5 44.2 - - + +
534G SER* 4.9 7.5 + - - +
537G GLU* 2.9 35.5 + - - -
650G SER 3.2 17.0 + - - +
651G ALA* 4.1 10.7 + - - +
652G LEU 2.8 0.6 + - - -
653G PHE* 1.3 81.9 - - + +
655G GLU* 1.3 50.4 + - - +
657G LEU* 3.0 7.3 + - - +
658G ASN* 2.6 46.8 + - - +
350V SER 4.9 3.0 + - - -
353V GLN* 4.9 13.7 - - - +
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Residues in contact with GLU 655 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651G ALA 3.7 8.7 + - - +
652G LEU* 2.3 39.6 + - + +
654G ARG* 1.3 72.2 - - - +
656G ASN* 1.3 63.8 + - - +
658G ASN* 3.7 7.9 - - - +
659G MLY 3.2 24.4 + - - +
1V ASP* 1.5 63.7 + - + +
2V GLU* 4.4 8.3 - - - +
4V GLU* 3.2 19.0 - - - +
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Residues in contact with ASN 656 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266G GLU* 4.6 4.3 - - - +
268G TYR* 4.2 26.3 + - + -
652G LEU* 2.6 36.0 + - - +
653G PHE* 3.8 7.5 + - - +
655G GLU* 1.3 76.2 - - - +
657G LEU* 1.3 58.9 + - - +
658G ASN 3.0 9.0 + - - -
659G MLY 3.1 31.6 + - - +
660G LEU* 3.0 23.5 + - - +
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Residues in contact with LEU 657 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268G TYR* 5.0 1.9 - - - -
482G PHE* 3.5 40.4 - - + -
483G THR* 3.9 31.0 - - + +
486G MLY 4.3 11.3 - - + -
653G PHE* 2.7 41.5 + - + +
654G ARG* 3.3 7.2 - - - +
656G ASN* 1.3 72.9 - - - +
658G ASN* 1.3 62.4 + - - +
660G LEU* 3.9 16.6 - - + -
661G MET* 3.4 32.8 + - + +
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Residues in contact with ASN 658 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486G MLY 3.1 34.8 - - - -
527G GLU* 4.7 2.0 + - - +
654G ARG* 2.6 31.0 + - - +
655G GLU* 3.7 8.3 - - - +
656G ASN 3.0 0.4 - - - -
657G LEU* 1.3 77.3 - - - +
659G MLY 1.3 63.8 + - - +
660G LEU 2.9 4.9 - - - -
661G MET* 3.9 2.5 - - - +
662G ALA* 3.1 26.2 + - - +
665G ARG* 5.6 0.7 + - - -
2V GLU* 5.9 2.8 + - - +
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Residues in contact with MLY 659 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266G GLU* 2.5 43.2 + - - +
655G GLU 3.2 14.5 + - - +
656G ASN* 3.5 27.8 - - - +
658G ASN* 1.3 80.0 + - - +
660G LEU* 1.3 58.9 + - - +
662G ALA* 3.8 6.1 - - - +
663G ASN* 3.3 34.0 + - - +
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Residues in contact with LEU 660 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G PHE* 3.9 28.7 - - + -
266G GLU* 6.0 0.2 - - - -
268G TYR* 3.5 34.3 - - + +
462G LEU* 4.3 18.6 - - + -
464G ILE* 4.5 8.5 - - + -
483G THR* 5.2 2.9 - - + -
487G LEU* 5.5 2.7 - - + -
656G ASN 3.0 16.2 + - - +
657G LEU* 3.8 20.0 - - + +
659G MLY 1.3 76.0 + - - -
661G MET* 1.3 54.2 + - + +
662G ALA 2.9 4.0 - - - -
663G ASN* 2.8 26.8 + - - +
664G LEU* 2.8 35.1 + - + +
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Residues in contact with MET 661 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486G MLY 4.2 27.6 - - + +
487G LEU* 3.6 35.4 - - - -
490G PHE* 4.1 31.4 - - + -
657G LEU* 3.4 31.2 + - + +
658G ASN* 3.5 3.3 + - - +
660G LEU* 1.3 79.7 - - + +
662G ALA* 1.3 56.6 + - - +
664G LEU* 3.5 14.5 - - + +
665G ARG* 3.1 54.1 + - - +
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Residues in contact with ALA 662 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658G ASN 3.1 19.5 + - - +
659G MLY 3.8 7.9 - - - +
660G LEU 2.9 0.4 - - - -
661G MET* 1.3 73.6 - - - +
663G ASN* 1.3 66.2 + - - +
664G LEU 3.1 2.0 - - - -
665G ARG* 3.3 21.2 + - - +
666G SER* 3.1 17.3 + - - -
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Residues in contact with ASN 663 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G PHE* 4.2 21.7 - - + -
251G ARG* 3.6 38.1 + - - +
458G PHE* 4.3 12.6 - - + -
659G MLY 3.3 26.4 + - - +
660G LEU* 2.8 10.4 + - - +
662G ALA* 1.3 80.6 - - - +
664G LEU* 1.3 61.6 + - - +
665G ARG 3.4 0.3 + - - -
666G SER* 3.7 11.5 + - - -
667G THR* 2.7 21.0 + - - -
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Residues in contact with LEU 664 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G SER* 4.7 14.4 - - - +
176G LEU* 4.4 13.0 - - + -
249G PHE* 4.0 29.4 - - + -
462G LEU* 4.7 6.1 - - + -
487G LEU* 3.9 15.9 - - + -
490G PHE* 3.3 33.5 - - + -
660G LEU* 2.8 28.1 + - + +
661G MET* 3.5 34.5 - - + +
663G ASN* 1.3 79.7 - - - +
665G ARG* 1.3 54.4 + - - +
667G THR* 2.8 24.1 - - - +
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Residues in contact with ARG 665 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486G MLY 4.8 18.4 + - - -
489G GLN* 5.8 2.2 + - - -
490G PHE* 4.3 18.4 - - + -
658G ASN 5.6 0.6 + - - -
661G MET* 3.1 48.8 + - - +
662G ALA* 3.3 15.1 + - - +
663G ASN 3.2 0.6 - - - -
664G LEU* 1.3 72.7 - - - +
666G SER* 1.3 54.0 + - - +
667G THR 2.6 25.1 + - - +
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Residues in contact with SER 666 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G ASN* 3.2 30.6 + - - +
458G PHE* 5.0 4.3 - - - -
662G ALA 3.1 15.3 + - - -
663G ASN* 3.9 9.4 + - - -
664G LEU 3.6 0.4 - - - -
665G ARG* 1.3 72.1 - - - +
667G THR* 1.3 60.3 + - - +
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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