Contacts of the helix formed by residues 566 - 575 (chain M) in PDB entry 6D6Q
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 THR 566 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233M ARG* 4.2 6.6 + - - -
264M VAL* 5.4 7.4 - - + +
564M HIS* 3.4 30.7 - - + +
565M LEU* 1.3 82.0 - - - +
567M TYR* 1.3 69.4 + - - +
568M ASN* 4.5 6.6 - - - +
569M MET* 3.3 25.8 + - - +
570M VAL* 3.2 23.9 + - - +
854M ARG* 5.3 4.9 - - - -
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Residues in contact with TYR 567 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566M THR* 1.3 70.6 - - - +
568M ASN* 1.3 65.0 + - - +
570M VAL* 2.8 20.3 + - + +
571M LEU* 2.9 22.6 + - + +
854M ARG* 3.2 54.3 + - + -
857M VAL* 4.7 8.3 - - + +
858M LEU* 4.9 11.4 - - + -
884M ASP* 4.2 16.6 - - - -
885M GLU* 2.9 22.9 - - + +
886M LEU* 3.1 39.8 - - + +
942M ILE* 5.7 3.0 - - + +
946M SER* 5.5 2.8 - - - -
951M LEU* 4.4 11.6 - - - +
958M TYR* 5.5 6.2 - + - -
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Residues in contact with ASN 568 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ARG* 4.6 13.6 - - - +
566M THR* 3.6 6.5 + - - +
567M TYR* 1.3 77.1 - - - +
569M MET* 1.3 62.8 + - - +
571M LEU* 4.7 5.5 - - - +
572M ASN* 2.9 42.7 + - - +
877M ALA 4.1 2.6 - - - +
878M CYS* 4.9 2.1 - - - +
880M ILE 2.7 23.9 - - - +
881M SER* 3.6 28.8 + - - +
883M ALA 4.5 1.6 + - - -
885M GLU* 2.7 34.4 + - - +
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Residues in contact with MET 569 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ARG* 3.7 7.9 - - - +
237M TYR* 3.8 9.2 - - - +
264M VAL* 5.9 3.8 - - + -
268M GLU* 3.2 26.7 - - + +
563M PHE* 5.6 3.6 - - + -
565M LEU* 3.9 33.9 - - + -
566M THR* 3.3 20.6 + - - +
567M TYR 3.0 0.8 + - - -
568M ASN* 1.3 80.2 - - - +
570M VAL* 1.3 79.5 + - + +
573M LEU* 2.8 46.8 + - + +
581M PRO* 4.5 16.2 - - + -
584M MET* 4.9 13.2 - - + -
585M LEU* 5.0 5.6 - - + -
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Residues in contact with VAL 570 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565M LEU* 4.9 3.8 - - + -
566M THR 3.2 15.7 - - - +
567M TYR* 2.8 13.9 + - - +
569M MET* 1.3 91.5 - - + +
571M LEU* 1.3 56.3 + - - +
573M LEU* 3.2 5.3 + - - +
574M LEU* 2.9 36.6 + - + +
581M PRO* 4.8 5.5 - - + +
851M LEU* 4.3 20.4 - - + -
854M ARG* 5.0 12.3 - - + -
855M LYS* 4.9 16.2 - - + +
858M LEU* 3.9 26.2 - - + -
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Residues in contact with LEU 571 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567M TYR* 2.9 23.8 + - + +
568M ASN* 3.9 4.7 - - - +
570M VAL* 1.3 72.5 - - - +
572M ASN* 1.3 56.7 + - - +
573M LEU 2.9 4.0 - - - -
574M LEU* 2.7 33.6 + - + +
575M ARG* 3.0 10.0 + - - +
858M LEU* 4.0 31.0 - - + -
863M PHE* 3.9 25.4 - - + +
870M ILE* 4.7 3.1 - - + +
874M GLY* 4.4 10.3 - - - +
877M ALA* 3.8 28.9 - - + -
878M CYS* 3.4 21.8 - - - +
885M GLU* 4.5 9.2 - - + +
886M LEU* 5.1 1.6 - - + -
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Residues in contact with ASN 572 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ARG* 5.3 1.2 - - - +
237M TYR* 3.7 45.0 - - + +
568M ASN* 2.9 33.6 + - - +
569M MET 4.0 0.7 - - - +
571M LEU* 1.3 76.1 - - - +
573M LEU* 1.3 60.8 + - - +
574M LEU 3.4 0.2 - - - -
575M ARG* 3.6 33.5 + - - +
576M VAL* 3.8 11.3 - - - +
878M CYS* 3.1 39.9 + - - +
881M SER* 6.1 2.0 - - - -
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Residues in contact with LEU 573 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237M TYR* 3.8 34.5 - - + +
268M GLU* 4.2 1.1 - - - +
272M LEU* 5.4 1.6 - - + -
569M MET* 2.8 46.9 + - + +
570M VAL 3.5 5.2 - - - +
572M ASN* 1.3 76.2 - - - +
574M LEU* 1.3 63.2 + - - +
575M ARG 3.2 0.7 - - - -
576M VAL* 3.2 18.9 + - + +
579M ILE* 3.4 57.3 - - + +
580M ASN* 4.5 6.0 - - - +
581M PRO* 4.3 17.4 - - + +
584M MET* 4.7 10.8 - - + -
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Residues in contact with LEU 574 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570M VAL* 2.9 26.7 + - + +
571M LEU* 2.7 32.5 + - + +
573M LEU* 1.3 70.2 - - - +
575M ARG* 1.3 65.3 + - - +
576M VAL 3.1 7.6 + - - +
581M PRO* 5.8 5.8 - - + -
855M LYS* 4.5 18.2 - - - +
858M LEU* 4.8 3.4 - - + -
863M PHE 4.7 1.8 - - - +
864M ALA* 4.4 22.2 - - + -
868M ASP* 4.0 24.2 - - + +
869M VAL* 5.0 0.8 - - - -
870M ILE* 4.6 27.1 + - + +
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Residues in contact with ARG 575 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H VAL* 4.3 23.6 - - - +
81H GLY* 4.0 26.5 - - - +
237M TYR* 6.0 1.6 - - - +
238M ARG* 3.5 33.3 - - - +
571M LEU 3.0 12.6 + - - +
572M ASN* 3.6 26.9 + - - +
574M LEU* 1.3 79.5 - - - +
576M VAL* 1.3 63.9 + - + +
577M GLU* 4.1 0.3 + - - +
870M ILE* 4.5 17.2 - - + +
875M ARG* 4.3 31.7 + - - +
878M CYS* 3.2 32.3 + - - +
879M GLU* 3.5 25.1 + - - +
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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