Contacts of the helix formed by residues 655 - 668 (chain B) in PDB entry 1MQB
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 LYS 655 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653B THR* 3.0 19.1 + - + -
654B GLU* 1.3 75.8 - - - +
656B GLN* 1.3 69.6 + - - +
657B ARG* 3.2 4.7 - - - +
658B VAL* 2.9 38.6 + - + +
659B ASP* 2.5 32.9 + - - +
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Residues in contact with GLN 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B GLU* 3.5 14.6 + - - +
624B PHE* 3.2 36.3 - - + -
648B LEU* 4.7 4.7 - - + -
652B TYR* 4.5 5.8 - - + -
653B THR* 3.0 36.9 + - - +
654B GLU 3.4 2.0 - - - +
655B LYS* 1.3 95.8 - - - +
657B ARG* 1.3 67.0 + - - +
659B ASP* 3.6 18.8 + - - +
660B PHE* 2.9 28.5 + - - +
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Residues in contact with ARG 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU* 5.6 6.5 - - - +
648B LEU* 4.2 7.7 - - - +
652B TYR* 4.2 13.4 - - + -
654B GLU* 3.0 37.3 - - + +
655B LYS* 4.0 0.7 - - - +
656B GLN* 1.3 77.3 - - - +
658B VAL* 1.3 77.5 + - - +
660B PHE* 3.7 1.4 - - - +
661B LEU* 3.1 47.6 + - - +
683B SER* 6.0 2.4 - - - -
688B MET* 3.6 29.5 - - + +
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Residues in contact with VAL 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU* 6.2 1.5 - - - +
655B LYS* 2.9 36.8 + - + +
657B ARG* 1.3 98.2 - - + +
659B ASP* 1.3 66.3 + - - +
661B LEU* 4.2 3.4 - - - +
662B GLY* 2.7 34.0 + - - -
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Residues in contact with ASP 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B PHE* 4.2 9.9 - - + -
655B LYS* 2.5 40.8 + - - -
656B GLN* 3.5 26.1 + - - +
658B VAL* 1.3 81.9 - - - +
660B PHE* 1.3 67.2 + - - +
662B GLY* 4.0 1.6 - - - -
663B GLU* 3.5 15.2 + - - +
759B GLY* 5.6 5.5 - - - +
762B ARG* 5.5 4.2 + - - -
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Residues in contact with PHE 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B PHE* 3.6 39.2 - + + -
646B LYS* 3.4 35.0 - - + -
647B THR 3.7 24.5 - - - -
648B LEU* 3.8 23.6 - - + -
656B GLN 2.9 20.3 + - - +
657B ARG 3.7 2.5 - - - +
659B ASP* 1.3 76.8 - - - +
661B LEU* 1.3 91.1 + - + +
662B GLY 3.0 2.1 + - - -
663B GLU* 3.2 10.3 + - - +
688B MET* 4.0 14.4 - - + -
689B MET 4.2 0.9 - - - -
690B ILE* 3.3 40.6 - - + +
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Residues in contact with LEU 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU* 4.7 26.5 - - + +
657B ARG* 3.1 26.4 + - - +
658B VAL* 4.2 3.4 - - - +
660B PHE* 1.3 101.3 - - + +
662B GLY* 1.3 61.6 + - - +
663B GLU 3.2 0.2 - - - -
664B ALA* 3.1 17.6 + - + +
665B GLY* 3.1 10.2 + - - -
681B VAL* 4.9 16.2 - - + -
682B ILE 4.8 5.2 - - - +
683B SER* 4.0 23.8 - - - -
688B MET* 4.2 19.1 - - + -
689B MET 4.8 2.7 - - - +
690B ILE* 4.6 6.3 - - + -
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Residues in contact with GLY 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU* 5.6 5.2 - - - -
658B VAL 2.7 24.1 + - - -
659B ASP* 4.0 3.4 - - - -
660B PHE 3.0 1.2 + - - -
661B LEU* 1.3 72.4 - - - +
663B GLU* 1.3 62.5 - - - +
665B GLY* 3.0 12.6 + - - -
666B ILE* 3.1 22.2 + - - +
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Residues in contact with GLU 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B PHE* 5.2 5.9 - - + -
646B LYS* 2.6 32.2 + - - +
659B ASP 3.5 9.1 + - - +
660B PHE 3.2 11.1 + - - +
662B GLY* 1.3 76.5 - - - +
664B ALA* 1.3 56.1 + - - +
666B ILE* 3.4 10.9 + - - +
667B MET* 3.0 51.8 + - + +
690B ILE* 4.2 8.3 - - + +
757B ASP* 3.4 15.6 + - - +
758B PHE* 2.9 32.4 + - - +
759B GLY* 4.1 14.8 + - - +
1001B ANP 4.4 1.0 + - - -
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Residues in contact with ALA 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B THR* 4.8 5.0 - - + -
660B PHE 3.9 0.8 + - - -
661B LEU* 3.1 12.6 + - + +
663B GLU* 1.3 79.6 - - - +
665B GLY* 1.3 60.5 + - - +
667B MET* 4.4 5.8 - - - -
668B GLY* 2.9 23.7 + - - -
678B LEU* 3.2 22.0 - - + +
681B VAL* 3.5 32.3 - - + -
690B ILE* 3.9 15.3 - - + -
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Residues in contact with GLY 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B LEU* 3.7 32.8 + - - +
604B PHE* 4.0 9.2 - - - +
605B THR* 5.3 3.1 - - - -
661B LEU 3.1 7.5 + - - -
662B GLY 3.0 8.6 + - - -
664B ALA* 1.3 78.8 - - - +
666B ILE* 1.3 61.5 + - - +
669B GLN* 3.4 23.7 + - - +
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Residues in contact with ILE 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B GLY 3.1 17.5 + - - +
663B GLU* 3.6 6.5 - - - +
665B GLY* 1.3 76.2 - - - +
667B MET* 1.3 58.4 + - - +
669B GLN* 3.0 34.1 + - - +
670B PHE* 3.3 30.3 - - + -
735B TYR* 3.7 22.0 - - + +
758B PHE* 4.0 15.5 - - + +
759B GLY 5.6 2.2 - - - +
761B SER* 3.4 38.1 - - - +
762B ARG* 5.9 1.1 - - - +
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Residues in contact with MET 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646B LYS* 6.2 1.1 - - + -
663B GLU* 3.0 54.4 + - + +
664B ALA* 3.5 3.3 + - - +
666B ILE* 1.3 76.4 - - - +
668B GLY* 1.3 59.9 + - - +
669B GLN 3.2 0.2 - - - -
670B PHE* 3.4 30.9 + - - +
676B ILE* 3.6 37.0 - - + +
678B LEU* 3.6 29.2 + - + +
690B ILE* 4.9 4.7 - - + -
692B THR* 3.7 24.9 - - + -
756B SER* 5.8 0.4 - - - +
757B ASP 5.3 1.1 - - - +
758B PHE* 4.0 17.5 - - + -
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Residues in contact with GLY 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B PHE* 3.4 39.3 - - - +
664B ALA 2.9 16.5 + - - -
666B ILE 3.2 0.4 - - - -
667B MET* 1.3 74.7 - - - +
669B GLN* 1.3 59.9 + - - +
670B PHE 3.2 6.4 + - - +
678B LEU* 3.8 13.2 - - - -
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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