Contacts of the helix formed by residues 659 - 665 (chain D) in PDB entry 2QMR
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 ILE 659 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D TYR* 4.1 29.4 - - + -
648D LEU 4.7 2.0 - - - +
651D LEU* 4.3 10.5 - - + -
652D ALA* 3.8 34.1 - - + +
655D LEU* 4.5 15.5 - - + +
656D GLY* 4.5 1.6 - - - +
657D GLY* 2.9 19.0 - - - +
658D ASN* 1.3 77.8 - - - +
660D GLU* 1.3 66.1 - - - +
661D GLN 3.3 2.0 - - - -
662D LEU* 2.9 26.1 + - + +
663D VAL* 3.2 23.1 + - + +
694D LEU* 4.7 2.2 - - + -
697D ALA* 4.1 17.3 - - + -
698D CYS* 4.7 2.0 - - - -
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Residues in contact with GLU 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657D GLY* 3.0 19.1 + - - +
658D ASN* 3.3 1.5 - - - +
659D ILE* 1.3 79.2 - - - +
661D GLN* 1.3 78.6 + - - +
663D VAL* 3.5 0.7 + - - +
664D ALA* 3.2 18.4 + - - +
698D CYS* 3.9 18.6 - - + -
700D GLN* 3.7 24.7 + - - +
701D HIS* 3.0 34.9 + - - +
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Residues in contact with GLN 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D GLU* 5.0 3.5 - - - +
658D ASN 4.5 4.2 + - - +
659D ILE 3.1 1.2 + - - -
660D GLU* 1.3 96.1 - - - +
662D LEU* 1.3 73.9 + - + +
664D ALA* 3.5 5.1 + - - +
665D ARG* 3.2 70.7 + - - +
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Residues in contact with LEU 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605D CYS* 3.9 28.0 - - + -
606D GLU* 3.4 34.8 - - + +
609D TYR* 3.2 44.5 + - + -
610D GLN* 5.5 9.7 - - + +
651D LEU* 6.5 0.2 - - + -
655D LEU* 5.9 0.2 - - + -
658D ASN 5.1 3.1 - - - +
659D ILE* 2.9 21.1 + - + +
661D GLN* 1.3 86.9 - - + +
663D VAL* 1.3 62.4 + - - +
665D ARG* 3.6 9.0 + - - +
666D SER* 2.9 22.2 + - - -
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Residues in contact with VAL 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D TYR* 3.3 12.6 - - + +
659D ILE* 3.2 28.6 + - + +
660D GLU 3.7 6.3 - - - +
661D GLN 3.3 0.2 - - - -
662D LEU* 1.3 76.3 - - - +
664D ALA* 1.3 60.5 + - - +
666D SER* 2.7 22.0 + - - +
668D ILE* 3.8 18.6 - - + +
669D LEU* 4.8 10.2 - - + +
694D LEU* 3.7 34.5 - - + -
698D CYS* 3.9 17.9 - - - -
701D HIS* 4.5 13.7 - - + -
702D VAL* 6.2 0.9 - - + -
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Residues in contact with ALA 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660D GLU* 3.2 9.8 + - - +
661D GLN* 3.7 7.9 - - - +
662D LEU 3.4 0.2 - - - -
663D VAL* 1.3 79.5 - - - +
665D ARG* 1.3 61.3 + - + +
666D SER 3.2 8.0 + - - +
701D HIS* 3.6 34.0 - - + +
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Residues in contact with ARG 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D GLN* 5.1 8.3 - - - +
661D GLN* 3.2 57.0 + - - +
662D LEU* 3.6 6.0 + - - +
663D VAL 3.3 1.2 - - - -
664D ALA* 1.3 78.5 - - + +
666D SER* 1.3 58.3 + - - +
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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