Contacts of the helix formed by residues 640 - 653 (chain O) in PDB entry 5MQF
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 CYS 640 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639O ASN* 1.3 75.1 - - - +
641O THR* 1.3 57.0 + - - +
642O SER 3.2 0.2 - - - -
643O TRP* 3.3 9.0 + - - +
644O ILE* 2.9 29.3 + - - +
674O MET 4.5 10.2 + - - +
675O PRO 3.8 23.3 - - - +
676O GLU* 4.6 9.2 - - + -
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Residues in contact with THR 641 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606O ASN* 4.3 19.0 - - - -
639O ASN* 3.1 8.2 - - - +
640O CYS* 1.3 78.3 - - - +
642O SER* 1.3 58.1 + - - +
644O ILE* 3.8 7.3 - - - +
645O LYS* 2.9 30.8 + - - +
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Residues in contact with SER 642 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604O PRO 5.0 0.4 - - - -
605O LYS* 4.6 1.6 - - - -
606O ASN* 3.5 33.1 - - - +
609O PHE* 4.8 12.5 - - - +
610O LYS 5.9 0.4 + - - +
637O PRO* 3.6 28.3 - - - -
638O GLU 4.7 2.2 - - - -
639O ASN 3.2 6.4 + - - -
641O THR* 1.3 78.1 - - - +
643O TRP* 1.3 58.2 + - - +
645O LYS* 4.2 2.0 - - - +
646O PHE* 2.9 30.9 + - - +
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Residues in contact with TRP 643 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637O PRO* 4.2 18.5 - - + +
639O ASN 3.8 1.0 + - - -
640O CYS* 3.3 14.5 + - - +
642O SER* 1.3 76.3 - - - +
644O ILE* 1.3 60.3 + - - +
646O PHE* 3.8 5.9 - - - +
647O ALA* 2.9 28.6 + - - +
666O ALA* 5.7 8.3 - - + -
675O PRO 5.3 6.5 - - - +
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Residues in contact with ILE 644 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640O CYS 2.9 16.4 + - - +
641O THR* 3.3 8.3 + - - +
642O SER 3.3 0.2 - - - -
643O TRP* 1.3 76.0 - - - +
645O LYS* 1.3 59.1 + - - +
647O ALA* 3.1 7.1 + - - +
648O GLU* 2.9 27.0 + - - +
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Residues in contact with LYS 645 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606O ASN 5.2 1.8 - - - +
610O LYS* 3.7 32.3 - - + +
641O THR 2.9 17.4 + - - +
642O SER* 4.2 3.6 - - - +
644O ILE* 1.3 76.1 - - - +
646O PHE* 1.3 57.6 + - - +
648O GLU* 3.1 7.3 + - - +
649O LEU* 2.9 31.8 + - - +
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Residues in contact with PHE 646 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609O PHE* 6.3 3.1 - - + -
610O LYS* 5.7 1.7 - - - +
613O ILE* 5.7 4.9 - - - -
637O PRO* 6.2 1.1 - - + -
642O SER 2.9 22.5 + - - +
643O TRP* 4.0 7.0 - - - +
645O LYS* 1.3 78.0 - - - +
647O ALA* 1.3 51.0 + - - +
649O LEU* 4.7 2.9 - - - +
650O GLU* 2.7 41.7 + - + +
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Residues in contact with ALA 647 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643O TRP 2.9 19.7 + - - +
644O ILE* 3.1 8.3 + - - +
646O PHE* 1.3 76.4 - - - +
648O GLU* 1.3 54.6 + - - +
650O GLU* 4.4 3.6 - - - -
651O THR* 2.7 38.3 + - - -
685O PHE* 5.4 1.4 - - - +
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Residues in contact with GLU 648 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644O ILE 2.9 13.3 + - - +
645O LYS* 3.1 10.7 + - - +
647O ALA* 1.3 75.0 - - - +
649O LEU* 1.3 60.6 + - - +
651O THR* 3.8 2.4 - - - -
652O ILE* 2.9 29.8 + - - +
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Residues in contact with LEU 649 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610O LYS* 5.4 3.1 - - - +
613O ILE* 4.5 23.3 - - + +
614O GLU* 4.9 13.2 - - + +
617O LEU* 6.2 2.5 - - + -
645O LYS 2.9 14.2 + - - +
646O PHE* 4.6 1.3 - - - +
648O GLU* 1.3 75.2 - - - +
650O GLU* 1.3 61.3 + - - +
652O ILE* 3.2 6.9 + - - +
653O LEU* 2.9 30.3 + - - +
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Residues in contact with GLU 650 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613O ILE* 6.0 0.2 - - - +
646O PHE 2.7 24.7 + - - +
647O ALA* 4.4 3.1 - - - -
649O LEU* 1.3 77.8 - - - +
651O THR* 1.3 60.2 + - - +
653O LEU 3.2 0.3 - - - -
654O GLY 2.8 16.4 + - - +
655O ASP* 2.5 39.8 + - + +
659O ALA* 5.1 9.2 - - + -
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Residues in contact with THR 651 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647O ALA* 2.7 23.9 + - - +
648O GLU* 4.0 3.1 - - - -
650O GLU* 1.3 76.5 - - - +
652O ILE* 1.3 60.5 + - - +
653O LEU 5.1 0.2 - - - -
655O ASP* 3.5 17.0 - - - +
685O PHE* 4.5 22.7 - - - -
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Residues in contact with ILE 652 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648O GLU 2.9 19.3 + - - +
649O LEU* 3.6 8.1 - - - +
650O GLU 3.1 0.2 - - - -
651O THR* 1.3 78.9 - - - +
653O LEU* 1.3 59.3 + - + +
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Residues in contact with LEU 653 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617O LEU* 5.0 16.6 - - + -
625O CYS* 6.4 2.2 - - + -
649O LEU 2.9 13.0 + - - +
650O GLU 3.2 3.1 - - - -
651O THR 5.0 0.4 - - - +
652O ILE* 1.3 81.3 - - + +
654O GLY* 1.3 59.3 + - - +
655O ASP 3.5 3.0 + - - +
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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