Contacts of the helix formed by residues 649 - 657 (chain B) in PDB entry 6QHD
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 649 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B TYR* 5.1 11.9 - - - -
579B LEU* 4.7 5.3 - - - +
645B LEU* 4.5 1.8 - - - -
648B MET* 1.3 80.9 - - - +
650B PHE* 1.3 52.0 + - - +
651B ALA* 3.3 9.5 + - - +
652B GLU* 2.7 28.6 + - - +
653B ILE* 2.6 35.7 + - - +
686B TYR 4.2 8.5 + - - -
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Residues in contact with PHE 650 (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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575B TYR* 6.1 0.2 - - - +
576B ILE* 3.9 27.5 - - + +
579B LEU* 5.5 3.4 - - + -
585B ILE* 5.3 4.9 - - + -
608B LEU* 3.8 22.9 - - + -
609B ARG 5.4 0.4 - - - -
619B VAL* 4.0 43.3 - - + -
620B THR 3.8 24.0 - - - -
621B PHE* 4.8 7.6 - + + -
640B TYR* 4.2 16.2 - + - -
645B LEU* 4.2 12.7 - - + +
648B MET 3.7 1.6 + - - -
649B SER* 1.3 71.4 - - - +
651B ALA* 1.3 53.2 + - - +
653B ILE* 3.2 16.4 - - + +
654B ILE* 2.6 69.2 + - + +
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Residues in contact with ALA 651 (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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579B LEU* 3.3 29.7 - - + +
649B SER* 3.3 5.2 + - - +
650B PHE* 1.3 77.2 - - - +
652B GLU* 1.4 57.3 + - - +
654B ILE* 3.5 12.0 - - - +
655B MET* 2.9 34.7 + - - +
683B PHE* 4.2 22.4 - - + +
686B TYR* 4.1 18.4 - - + +
687B CYS* 4.2 2.0 - - - -
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Residues in contact with GLU 652 (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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648B MET* 3.4 31.9 - - + +
649B SER* 2.7 29.1 + - - +
651B ALA* 1.4 72.3 - - - +
653B ILE* 1.3 51.7 + - - +
655B MET* 3.5 1.2 - - - +
656B GLY* 2.5 34.5 + - - -
686B TYR 4.2 3.0 + - - +
687B CYS* 3.6 16.7 - - - +
688B ARG* 2.9 49.2 + - - +
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Residues in contact with ILE 653 (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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710A PHE* 4.8 19.3 - - + -
621B PHE* 5.8 0.2 - - - -
640B TYR* 4.1 42.8 - - + +
645B LEU* 5.7 3.1 - - + -
648B MET* 3.5 31.8 - - + +
649B SER 2.6 15.8 + - - +
650B PHE* 3.2 37.2 - - + +
652B GLU* 1.3 71.3 - - - +
654B ILE* 1.3 55.8 + - - +
657B TYR* 2.6 41.8 + - + +
711B ILE* 4.6 11.7 - - + -
712B CYS* 5.5 4.7 - - - -
713B VAL* 6.0 1.8 - - + +
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Residues in contact with ILE 654 (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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606B PHE* 4.6 4.5 - - + -
608B LEU* 3.5 32.3 - - + -
621B PHE* 4.6 13.9 - - + -
650B PHE* 2.6 53.4 + - + +
651B ALA* 3.5 9.4 - - - +
652B GLU 3.4 0.2 - - - -
653B ILE* 1.3 76.1 - - + +
655B MET* 1.3 65.7 + - + +
657B TYR* 3.3 19.1 + - - +
669B PRO* 5.0 2.4 - - - +
670B LEU* 3.9 28.7 - - + +
679B LYS* 6.1 0.2 - - + -
683B PHE* 4.3 30.3 - - + -
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Residues in contact with MET 655 (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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651B ALA 2.9 15.1 + - - +
652B GLU 4.0 0.7 - - - +
654B ILE* 1.3 79.2 - - + +
656B GLY* 1.3 59.6 + - - +
657B TYR 3.7 4.0 + - - +
658B LYS* 4.6 2.9 + - - -
669B PRO* 5.5 2.5 - - - +
679B LYS* 3.8 45.8 - - + +
680B GLU* 3.2 42.8 - - - +
683B PHE* 3.8 14.1 - - + -
687B CYS* 3.5 29.4 - - - -
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Residues in contact with GLY 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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648B MET* 4.4 2.7 - - - -
652B GLU 2.5 23.7 + - - -
653B ILE 3.1 2.4 + - - -
655B MET* 1.3 72.3 - - - +
657B TYR* 1.3 60.0 + - - +
658B LYS* 2.6 27.8 + - - -
711B ILE* 3.2 25.6 - - - +
713B VAL* 3.4 2.5 - - - +
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Residues in contact with TYR 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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706A LEU* 4.8 6.9 - - - +
621B PHE* 4.0 35.5 - + + -
623B TRP* 3.4 42.7 - + - -
637B VAL* 5.0 9.8 - - + +
640B TYR* 5.0 3.8 - + - -
653B ILE* 2.6 22.5 + - + +
654B ILE* 3.3 14.4 + - - +
655B MET 4.2 3.5 - - - +
656B GLY* 1.3 76.5 - - - +
658B LYS* 1.3 83.1 + - - +
659B ILE* 4.2 19.5 - - + +
669B PRO* 3.1 34.7 - - + +
670B LEU* 4.9 7.9 - - + -
713B VAL* 3.5 28.3 - - + -
714B THR* 5.0 1.9 + - - -
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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