Contacts of the helix formed by residues 755 - 771 (chain Z) in PDB entry 5GJQ
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 ASP 755 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753Z ALA* 3.5 3.2 - - - +
754Z LYS* 1.3 81.8 - - + +
756Z PRO* 1.3 53.7 - - - +
757Z ASN* 4.0 6.1 - - + +
758Z ASN* 3.0 21.0 + - + +
759Z LEU* 2.3 40.3 + - - +
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Residues in contact with PRO 756 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369Z ARG* 5.4 7.7 - - + +
370Z MET* 5.7 2.9 - - - +
755Z ASP* 1.3 72.0 - - - +
757Z ASN* 1.3 53.1 + - - +
759Z LEU* 3.5 9.2 - - + +
760Z PHE* 2.5 32.2 + - - +
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Residues in contact with ASN 757 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755Z ASP* 3.1 5.6 - - + +
756Z PRO* 1.3 76.5 - - - +
758Z ASN* 1.3 55.2 + - - +
760Z PHE* 3.1 8.3 - - - +
761Z MET* 2.4 39.1 + - - +
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Residues in contact with ASN 758 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723Z TYR* 6.4 1.3 - - - +
726Z ILE* 5.1 5.1 - - + +
752Z HIS 4.3 0.9 - - - +
753Z ALA* 4.8 1.1 - - - -
754Z LYS* 4.3 8.7 - - + +
755Z ASP* 3.0 28.9 + - + +
757Z ASN* 1.3 76.9 - - - +
759Z LEU* 1.3 52.2 + - - +
761Z MET* 2.8 7.0 + - - +
762Z VAL* 2.2 43.6 + - + +
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Residues in contact with LEU 759 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752Z HIS 3.6 14.2 + - - -
753Z ALA* 3.4 19.0 - - + +
755Z ASP 2.3 30.6 + - - +
756Z PRO* 3.5 11.0 - - + +
758Z ASN* 1.3 66.2 - - - +
760Z PHE* 1.3 54.8 + - - +
763Z ARG* 2.6 38.4 + - - +
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Residues in contact with PHE 760 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369Z ARG 4.5 15.7 - - - +
370Z MET* 5.7 4.0 - - - +
373Z ALA* 3.4 22.3 - - + +
756Z PRO 2.5 23.8 + - - +
757Z ASN* 3.1 11.4 - - + +
759Z LEU* 1.3 72.9 - - - +
761Z MET* 1.3 52.0 + - - +
763Z ARG* 4.5 0.9 - - - -
764Z LEU* 2.7 32.5 + - - +
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Residues in contact with MET 761 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723Z TYR* 4.3 24.0 - - + +
726Z ILE* 4.4 9.6 - - + +
727Z PHE* 4.9 6.9 - - + +
757Z ASN 2.4 30.5 + - - +
758Z ASN* 3.5 6.7 - - - +
760Z PHE* 1.3 69.8 - - - +
762Z VAL* 1.3 51.0 + - - +
764Z LEU* 3.0 9.2 - - - +
765Z ALA* 2.4 38.9 + - - +
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Residues in contact with VAL 762 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726Z ILE* 4.7 6.0 - - + +
751Z TYR* 4.5 15.9 - - + +
752Z HIS* 3.1 31.2 - - - +
758Z ASN* 2.2 30.8 + - + +
759Z LEU 3.7 1.1 - - - +
761Z MET* 1.3 65.1 - - - +
763Z ARG* 1.3 59.0 + - - +
765Z ALA* 2.8 8.3 + - - +
766Z GLN* 2.3 42.9 + - + +
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Residues in contact with ARG 763 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361Z SER* 5.8 2.3 - - - -
370Z MET 5.4 2.2 - - - +
373Z ALA* 4.2 11.4 - - + -
374Z SER* 4.8 12.3 - - - +
377Z VAL* 4.3 9.7 - - + +
759Z LEU 2.6 22.4 + - - +
760Z PHE* 3.6 4.5 - - - +
762Z VAL* 1.3 70.4 - - - +
764Z LEU* 1.3 54.5 + - - +
766Z GLN* 4.8 2.9 - - - -
767Z GLY* 2.7 32.6 + - - +
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Residues in contact with LEU 764 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373Z ALA* 3.9 14.1 - - + +
376Z PHE* 6.1 3.4 - - + -
377Z VAL* 5.9 1.3 - - - +
380Z PHE* 4.9 1.6 - - - +
727Z PHE* 6.0 3.6 - - + -
760Z PHE 2.7 18.4 + - - +
761Z MET* 3.0 14.6 - - - +
763Z ARG* 1.3 73.9 - - - +
765Z ALA* 1.3 52.6 + - - +
767Z GLY* 3.3 1.3 - - - -
768Z LEU* 2.5 37.1 + - - +
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Residues in contact with ALA 765 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726Z ILE* 3.1 33.2 - - + +
727Z PHE* 4.3 3.6 - - - +
730Z GLY* 3.6 10.0 - - - +
748Z LEU* 5.3 7.9 - - + -
761Z MET 2.4 31.4 + - - +
762Z VAL* 2.8 10.0 + - - +
764Z LEU* 1.3 67.0 - - - +
766Z GLN* 1.3 49.2 - - - +
768Z LEU* 2.8 10.5 + - - +
769Z THR* 2.2 38.9 + - - -
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Residues in contact with GLN 766 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361Z SER* 4.3 20.1 - - - -
748Z LEU* 5.0 15.1 - - + +
751Z TYR 5.4 3.1 - - - +
762Z VAL* 2.3 32.1 + - + +
763Z ARG* 4.5 2.5 - - - +
765Z ALA* 1.3 65.9 - - - +
767Z GLY* 1.3 59.1 + - - +
769Z THR* 3.2 13.0 - - - -
770Z HIS* 2.8 30.1 + - - +
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Residues in contact with GLY 767 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361Z SER* 4.7 5.8 - - - -
377Z VAL* 4.2 12.6 - - - -
380Z PHE* 3.5 17.7 - - - +
381Z VAL* 3.8 4.1 + - - -
763Z ARG 2.7 25.1 + - - -
764Z LEU 3.3 1.3 - - - -
766Z GLN* 1.3 72.1 - - - +
768Z LEU* 1.3 49.4 + - - -
770Z HIS* 3.0 5.5 + - - -
771Z LEU* 2.4 36.2 + - - -
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Residues in contact with LEU 768 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380Z PHE* 3.9 4.2 - - + +
727Z PHE 5.3 0.7 - - - +
730Z GLY* 3.4 16.8 - - - +
731Z MET* 4.3 1.1 - - - +
734Z SER* 2.5 44.9 - - - -
764Z LEU 2.5 17.3 + - - +
765Z ALA* 2.8 11.2 + - - +
767Z GLY* 1.3 70.3 - - - -
769Z THR* 1.3 57.0 + - - +
771Z LEU* 2.9 14.9 + - - -
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Residues in contact with THR 769 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729Z MET 5.9 0.2 - - - -
730Z GLY* 4.2 3.3 + - - -
733Z GLY* 3.9 12.9 - - - +
734Z SER* 4.4 7.0 - - - +
737Z ASN* 5.0 4.6 - - - +
745Z LEU* 6.0 5.4 - - - -
748Z LEU* 4.7 14.4 - - - -
765Z ALA 2.2 26.6 + - - -
766Z GLN* 3.2 19.1 - - - -
768Z LEU* 1.3 71.1 - - - +
770Z HIS* 1.3 57.1 + - - +
771Z LEU 4.3 0.3 - - - +
774Z GLY* 3.4 16.8 - - - -
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Residues in contact with HIS 770 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358Z PHE* 4.4 9.2 - - + -
359Z GLY 3.4 26.7 - - - +
361Z SER* 5.4 4.0 - - - +
381Z VAL* 3.2 17.5 - - + +
766Z GLN 2.8 18.3 + - - +
767Z GLY* 3.1 3.6 - - - +
769Z THR* 1.3 70.9 - - - +
771Z LEU* 1.3 60.5 + - - +
773Z LYS* 2.8 25.3 + - - -
774Z GLY* 3.2 10.1 - - - +
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Residues in contact with LEU 771 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380Z PHE* 3.1 22.9 - - + +
383Z ALA* 5.7 1.3 - - + -
734Z SER* 3.8 14.9 - - - +
767Z GLY 2.4 21.3 + - - +
768Z LEU* 2.9 26.7 + - - +
770Z HIS* 1.3 68.9 - - - +
772Z GLY* 1.3 58.5 + - - +
774Z GLY* 3.1 16.3 + - - -
775Z THR 3.8 2.4 + - - -
776Z LEU* 4.7 8.7 - - - +
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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