Contacts of the helix formed by residues 594 - 601 (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 GLY 594 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547G ASP* 2.9 13.8 + - - -
593G SER* 1.3 74.1 - - - +
595G TRP* 1.3 65.7 + - - +
596G LEU 3.2 2.5 - - - -
597G GLU* 3.1 12.8 + - - +
598G MLY 2.7 48.4 + - - +
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Residues in contact with TRP 595 (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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473G ASN 4.5 1.8 - - - -
474G SER* 2.8 20.9 + - - -
475G PHE* 3.0 41.0 - + + +
478G LEU* 4.0 29.2 - - + -
532G ILE* 5.3 1.3 - - + -
536G LEU* 3.9 27.4 - - + -
547G ASP* 4.0 0.6 + - - +
550G PHE* 4.1 22.4 - + + -
579G PHE* 4.4 16.8 - + - -
590G TYR* 4.3 16.2 - - + -
591G ASN 2.8 31.7 + - - -
592G ILE* 3.5 9.9 - - + -
593G SER 3.1 17.9 - - - +
594G GLY* 1.3 82.5 - - - +
596G LEU* 1.3 55.4 - - - +
598G MLY 3.6 7.2 - - - +
599G ASN* 2.6 41.3 + - - +
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Residues in contact with LEU 596 (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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536G LEU* 3.8 18.6 - - + -
539G GLU* 4.6 11.7 - - + +
540G CYS* 3.8 13.6 - - - -
545G ALA* 3.8 27.8 - - + +
546G THR* 3.5 30.7 - - - +
547G ASP* 3.4 13.2 + - - +
550G PHE* 3.8 27.8 - - + -
594G GLY 3.2 0.4 - - - -
595G TRP* 1.3 80.1 - - - +
597G GLU* 1.3 63.7 + - - +
599G ASN* 3.4 3.3 + - - +
600G MLY 3.2 40.3 + - - +
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Residues in contact with GLU 597 (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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594G GLY* 3.1 14.1 + - - +
596G LEU* 1.3 76.5 - - + +
598G MLY 1.3 60.0 + - - +
599G ASN 2.9 1.8 - - - -
600G MLY 2.5 33.1 + - - -
601G ASP 3.2 9.0 + - - -
602G PRO* 3.3 31.8 - - + +
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Residues in contact with MLY 598 (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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272G MLY 4.8 10.4 - - - -
431G MLY 6.4 2.0 - - - -
472G PHE* 5.8 2.9 - - - -
474G SER* 4.2 16.9 + - - -
475G PHE* 3.9 22.3 - - + +
476G GLU* 2.7 40.2 + - + +
593G SER 3.6 23.8 - - - -
594G GLY* 2.7 30.6 + - - +
595G TRP* 3.6 6.1 - - - +
597G GLU* 1.3 75.8 - - - +
599G ASN* 1.3 61.2 + - - +
600G MLY 3.4 0.2 + - - -
601G ASP* 3.7 6.3 + - - +
602G PRO* 5.5 0.7 - - - -
649G VAL* 3.2 18.6 - - - +
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Residues in contact with ASN 599 (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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475G PHE* 3.6 8.5 - - + -
536G LEU* 3.6 26.4 + - + +
537G GLU* 4.4 0.8 - - - +
540G CYS* 4.0 10.7 - - - -
595G TRP 2.6 18.7 + - - +
596G LEU 3.6 5.6 - - - +
598G MLY 1.3 77.2 + - - +
600G MLY 1.3 60.4 + - - +
647G GLN 4.6 0.3 - - - +
648G THR* 2.8 19.0 + - - +
649G VAL* 2.0 83.7 + - + +
650G SER* 2.7 24.3 + - - -
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Residues in contact with MLY 600 (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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539G GLU 3.8 4.0 - - - -
540G CYS* 3.3 44.9 - - + +
541G MET 4.7 0.4 - - - -
542G PHE 2.8 34.3 - - - -
543G PRO* 4.1 13.7 - - - -
545G ALA* 4.7 13.7 - - - -
596G LEU* 3.2 27.8 - - - +
597G GLU* 2.5 23.5 + - - +
599G ASN* 1.3 74.3 + - - +
601G ASP* 1.3 68.2 + - - +
602G PRO* 3.9 11.0 - - + -
640G LYS* 3.2 29.3 + - - +
646G PHE 5.3 1.6 - - - +
647G GLN 5.4 4.5 - - - +
649G VAL* 4.8 0.2 - - - -
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Residues in contact with ASP 601 (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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272G MLY 3.5 39.0 + - - -
428G ALA* 6.0 0.3 - - - +
432G ALA* 5.5 0.5 - - - +
436G MLY 3.6 19.4 - - - -
597G GLU 3.2 1.8 + - - -
598G MLY 3.7 3.8 + - - +
599G ASN 3.5 1.2 - - - -
600G MLY 1.3 81.3 + - - +
602G PRO* 1.3 73.3 - - - +
603G LEU* 3.4 24.8 + - - +
640G LYS* 5.0 1.4 + - - -
646G PHE* 6.6 0.2 - - + -
649G VAL* 4.0 16.2 - - + -
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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