Contacts of the helix formed by residues 705 - 716 (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 CYS 705 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669D LEU* 4.6 21.3 - - - -
701D HIS 4.8 2.2 - - - -
702D VAL* 2.8 11.9 + - - +
704D PRO* 1.3 85.4 - - - +
706D ILE* 1.3 60.0 - - - +
707D ALA 3.2 3.4 - - - -
708D ASP* 2.8 37.7 + - + +
709D PHE* 3.0 34.9 + - + -
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Residues in contact with ILE 706 (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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699D PHE* 4.1 6.5 - - + -
702D VAL* 3.4 28.1 + - + -
703D LYS* 3.0 18.8 + - + +
704D PRO 3.7 0.4 - - - -
705D CYS* 1.3 78.6 - - - +
707D ALA* 1.3 60.5 + - + +
709D PHE* 4.4 8.7 - - + +
710D MET* 2.9 42.0 + - + +
735D ILE* 3.7 44.2 - - + -
739D MET* 3.9 26.2 - - + -
743D MET* 5.3 0.4 - - + -
746D TYR* 3.7 20.4 - - + +
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Residues in contact with ALA 707 (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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704D PRO 6.2 0.4 - - - +
705D CYS 3.2 0.4 - - - -
706D ILE* 1.3 81.6 - - + +
708D ASP* 1.3 66.0 + - - +
711D PRO* 3.2 23.1 - - - +
746D TYR* 3.7 27.8 - - + +
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Residues in contact with ASP 708 (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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673D TYR* 3.6 22.2 + - + -
704D PRO 5.1 1.8 - - - +
705D CYS* 2.8 25.3 + - + +
707D ALA* 1.3 87.1 - - - +
709D PHE* 1.3 64.2 + - + +
710D MET 3.5 0.2 - - - -
711D PRO* 3.5 8.2 - - - +
712D ILE* 3.5 18.2 - - - +
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Residues in contact with PHE 709 (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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669D LEU* 3.7 38.8 - - + -
672D MET* 4.6 1.8 - - + -
673D TYR* 4.2 23.3 - + + -
676D MET* 3.6 41.1 - - + -
691D LEU* 4.0 25.4 - - + -
702D VAL* 4.5 7.9 - - + -
705D CYS* 3.0 44.3 + - + +
706D ILE* 3.2 9.8 + - + +
708D ASP* 1.3 78.9 - - + +
710D MET* 1.3 65.1 + - - +
712D ILE* 3.0 7.9 + - + +
713D LEU* 3.0 35.5 + - + +
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Residues in contact with MET 710 (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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706D ILE* 2.9 24.0 + - + +
709D PHE* 1.3 75.4 - - - +
711D PRO* 1.3 65.7 - - + +
713D LEU* 3.2 26.1 + - - +
714D GLY* 2.9 25.8 + - - -
732D ILE* 4.3 18.8 - - + -
735D ILE* 4.2 12.8 - - + -
743D MET* 3.2 40.2 - - + -
746D TYR* 3.6 40.4 - - + +
749D MET* 3.9 12.3 - - - +
750D VAL* 4.7 6.9 - - + +
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Residues in contact with PRO 711 (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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707D ALA 3.2 23.8 - - - +
708D ASP* 3.5 9.9 - - - +
710D MET* 1.3 92.5 - - + +
712D ILE* 1.3 53.5 + - + +
714D GLY* 3.3 2.5 + - - +
715D THR* 2.6 38.2 + - - +
746D TYR* 5.9 0.2 - - + -
749D MET* 3.8 19.3 - - + -
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Residues in contact with ILE 712 (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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673D TYR* 2.9 43.7 - - + +
676D MET* 3.7 36.1 - - + +
677D GLN* 5.2 4.0 - - + +
688D PHE* 4.0 4.9 - - + -
708D ASP 3.5 18.4 - - - +
709D PHE* 3.0 8.4 + - + +
711D PRO* 1.3 75.8 - - + +
713D LEU* 1.3 66.9 + - - +
715D THR* 3.1 8.3 + - - +
716D ASN* 2.9 42.3 + - - +
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Residues in contact with LEU 713 (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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688D PHE* 3.6 31.0 - - + -
691D LEU* 3.7 18.4 - - + -
709D PHE* 3.0 21.4 + - + +
710D MET* 3.5 28.9 - - - +
712D ILE* 1.3 76.6 - - - +
714D GLY* 1.3 60.4 + - - +
716D ASN* 3.3 3.6 + - - +
717D LEU* 3.2 27.1 + - - +
728D ALA* 3.7 29.1 - - - +
731D ALA* 3.9 4.3 - - + -
732D ILE* 3.9 16.2 - - + -
735D ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 714 (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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710D MET 2.9 13.0 + - - -
711D PRO* 3.6 5.6 - - - -
712D ILE 3.2 0.2 - - - -
713D LEU* 1.3 76.9 - - - +
715D THR* 1.3 60.3 + - - +
716D ASN 3.2 0.9 + - - -
717D LEU* 3.3 14.1 + - - +
749D MET* 4.6 5.2 - - - -
750D VAL* 4.4 8.2 - - - +
753D GLN* 3.0 37.3 + - - -
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Residues in contact with THR 715 (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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711D PRO* 2.6 26.4 + - - +
712D ILE* 3.1 13.5 + - - +
714D GLY* 1.3 72.8 - - - +
716D ASN* 1.3 65.1 + - - +
717D LEU 3.4 1.1 + - - -
718D ASN* 4.3 10.2 + - - +
753D GLN* 5.1 1.9 + - - +
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Residues in contact with ASN 716 (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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676D MET 4.0 8.5 + - - -
684D ARG* 3.0 30.4 + - - -
688D PHE* 3.4 34.9 - - + -
712D ILE* 2.9 33.6 + - - +
713D LEU 3.3 4.2 + - - +
714D GLY 3.1 0.2 - - - -
715D THR* 1.3 84.4 - - - +
717D LEU* 1.3 51.4 + - - +
718D ASN* 2.7 22.1 + - - +
724D VAL* 3.6 9.5 - - + +
725D CYS* 3.7 19.4 + - - -
728D ALA* 4.4 4.4 - - + +
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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