Contacts of the helix formed by residues 527 - 544 (chain q) in PDB entry 6FF7
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 527 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454q PRO* 4.7 20.2 - - - -
499q ASP* 6.1 1.1 - - - -
525q GLU* 3.3 5.1 - - - +
526q ARG* 1.3 83.2 - - - +
528q LEU* 1.3 66.3 + - - +
529q HIS* 3.3 8.5 - - - -
530q THR* 3.4 12.3 + - - -
531q ASP* 2.9 21.2 + - - +
755q GLU* 4.1 7.9 - - - -
756q ILE 5.4 0.4 - - - -
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Residues in contact with LEU 528 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527q THR* 1.3 73.3 - - - +
529q HIS* 1.3 65.3 + - - +
531q ASP* 2.9 8.7 + - - +
532q ILE* 2.9 23.3 + - - +
755q GLU* 3.7 17.3 - - + +
756q ILE* 4.9 12.8 - - + +
759q THR* 5.7 6.3 - - - -
764q VAL* 6.0 6.7 - - + -
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Residues in contact with HIS 529 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499q ASP* 3.7 25.7 - - + +
500q GLY* 3.7 19.7 - - - +
503q LEU* 5.1 9.2 - - + +
527q THR* 3.3 4.9 - - - -
528q LEU* 1.3 79.3 - - - +
530q THR* 1.3 58.4 + - - +
532q ILE* 3.3 6.7 + - - +
533q LEU* 2.9 28.6 + - - +
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Residues in contact with THR 530 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454q PRO* 6.2 1.6 - - - -
499q ASP* 4.1 12.2 - - - +
520q VAL* 5.9 7.2 - - - -
521q ASP 5.8 2.7 - - - -
522q GLU 5.8 1.1 - - - -
523q ALA* 5.5 10.3 - - - -
526q ARG* 5.0 4.3 - - - -
527q THR* 3.4 22.7 + - - -
528q LEU 3.2 0.4 - - - -
529q HIS* 1.3 76.7 - - - +
531q ASP* 1.3 65.1 + - - +
533q LEU* 3.0 9.1 + - - +
534q PHE* 2.9 24.1 + - - +
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Residues in contact with ASP 531 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526q ARG* 5.3 3.8 - - + +
527q THR 2.9 12.6 + - - +
528q LEU* 2.9 12.8 + - - +
530q THR* 1.3 77.6 - - - +
532q ILE* 1.3 62.3 + - - +
534q PHE* 3.3 8.3 + - - +
535q GLY* 3.1 17.2 + - - -
756q ILE* 5.3 11.2 - - + -
780q ASP 5.5 0.9 - - - +
781q PHE* 5.5 9.5 - - + -
782q LEU* 5.5 12.8 + - + +
783q ASP 6.3 0.2 - - - +
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Residues in contact with ILE 532 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503q LEU* 5.9 5.2 - - + -
528q LEU 2.9 12.6 + - - +
529q HIS* 3.8 8.7 - - - +
531q ASP* 1.3 77.1 - - - +
533q LEU* 1.3 58.3 + - - +
535q GLY* 2.9 4.0 + - - -
536q LEU* 2.9 29.8 + - - +
764q VAL* 6.6 0.2 - - + -
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Residues in contact with LEU 533 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499q ASP* 5.6 6.5 - - + +
502q LEU* 6.3 3.6 - - + -
503q LEU* 6.0 6.9 - - + +
520q VAL* 5.8 8.3 - - + -
529q HIS 2.9 14.5 + - - +
530q THR* 3.2 14.4 - - - +
532q ILE* 1.3 75.2 - - - +
534q PHE* 1.3 57.3 + - - +
536q LEU* 3.2 5.9 + - - +
537q ILE* 2.8 34.2 + - - +
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Residues in contact with PHE 534 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530q THR 2.9 11.7 + - - +
531q ASP* 3.6 11.9 - - - +
533q LEU* 1.3 77.3 - - - +
535q GLY* 1.3 62.8 - - - +
537q ILE* 3.5 5.3 + - - +
538q LYS* 3.1 21.3 + - - +
782q LEU* 6.2 3.8 - - + -
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Residues in contact with GLY 535 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531q ASP 3.1 6.8 + - - -
532q ILE* 2.9 7.5 + - - -
534q PHE* 1.3 81.8 - - - +
536q LEU* 1.3 63.4 + - - +
538q LYS* 3.1 18.1 + - - +
539q ASP* 3.5 5.2 + - - +
780q ASP* 3.9 26.7 - - - +
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Residues in contact with LEU 536 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506q PHE* 5.9 7.6 - - + -
510q PRO 6.0 1.6 - - - +
532q ILE 2.9 12.3 + - - +
533q LEU* 3.7 9.6 - - - +
535q GLY* 1.3 74.9 - - - +
537q ILE* 1.3 64.1 + - - +
539q ASP* 3.0 10.2 + - - +
540q VAL* 2.9 21.4 + - - +
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Residues in contact with ILE 537 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518q VAL* 6.5 0.9 - - + -
533q LEU 2.8 18.7 + - - +
534q PHE* 3.9 5.8 - - - +
536q LEU* 1.3 74.9 - - - +
538q LYS* 1.3 67.5 + - - +
540q VAL* 3.8 8.8 - - - +
541q ALA* 2.9 26.0 + - - +
549q VAL* 5.4 12.6 - - + -
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Residues in contact with LYS 538 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534q PHE 3.1 12.2 + - - +
535q GLY* 3.1 14.9 + - - +
537q ILE* 1.3 78.9 - - - +
539q ASP* 1.3 61.1 + - - +
541q ALA* 3.4 15.6 - - - +
542q ARG* 3.8 3.5 + - - +
564q PHE 5.9 3.1 - - - +
780q ASP* 6.1 3.8 - - + -
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Residues in contact with ASP 539 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535q GLY 3.5 4.8 + - - +
536q LEU* 3.0 10.1 + - - +
538q LYS* 1.3 76.0 - - - +
540q VAL* 1.3 66.1 + - - +
541q ALA 3.0 1.6 - - - -
542q ARG* 2.9 24.2 + - - +
543q PHE* 3.5 3.6 + - - +
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Residues in contact with VAL 540 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510q PRO 4.7 13.9 - - - +
511q ASP* 4.8 12.6 - - - +
536q LEU* 2.9 15.2 + - + +
537q ILE* 3.1 11.4 + - - +
539q ASP* 1.3 76.0 - - - +
541q ALA* 1.3 58.2 + - - +
543q PHE* 2.8 26.8 + - + +
544q ARG* 2.9 16.4 + - + +
547q LEU* 6.0 0.9 - - - -
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Residues in contact with ALA 541 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417q GLN* 5.5 11.2 - - + -
418q VAL* 6.5 0.7 - - + -
537q ILE 2.9 10.8 + - - +
538q LYS* 3.4 13.9 - - - +
539q ASP 3.0 0.4 - - - -
540q VAL* 1.3 78.8 - - - +
542q ARG* 1.3 62.2 + - - +
544q ARG 3.1 24.2 - - - +
545q PRO* 4.1 2.3 - - - +
547q LEU* 5.5 8.7 - - - +
549q VAL* 6.6 0.2 - - + -
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Residues in contact with ARG 542 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538q LYS 3.8 2.7 + - - +
539q ASP* 2.9 15.8 + - - +
541q ALA* 1.3 82.5 - - - +
543q PHE* 1.3 62.0 + - - +
544q ARG 4.7 1.0 - - - -
545q PRO* 4.9 1.2 - - - +
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Residues in contact with PHE 543 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511q ASP* 6.1 5.4 - - + -
539q ASP 3.5 1.5 + - - +
540q VAL* 2.8 16.6 + - - +
542q ARG* 1.3 81.8 - - - +
544q ARG* 1.3 58.2 + - + +
545q PRO 4.0 1.4 - - - -
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Residues in contact with ARG 544 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511q ASP* 5.8 7.2 - - + +
540q VAL* 2.9 12.6 + - + +
541q ALA* 3.1 15.5 - - - +
543q PHE* 1.3 79.6 - - + +
545q PRO* 1.3 63.0 - - - +
546q GLU* 3.3 8.2 + - + +
547q LEU* 3.4 32.2 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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