Contacts of the helix formed by residues 741 - 751 (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 LEU 741 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702Z PRO* 4.9 7.9 - - + -
703Z ARG 4.4 9.2 - - - +
704Z LEU* 5.2 0.4 - - - -
732Z VAL* 5.1 6.1 - - + +
733Z GLY* 5.3 0.7 - - - -
736Z THR* 2.7 29.6 - - - +
737Z ASN* 3.9 1.6 - - - -
738Z ASN 2.6 19.8 + - - -
740Z ARG* 1.3 72.9 - - - +
742Z ALA* 1.3 62.1 + - - +
743Z ALA 3.3 2.7 - - - +
744Z MET* 3.0 30.4 + - + +
745Z LEU 3.2 6.6 + - - -
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Residues in contact with ALA 742 (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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213I GLU* 5.8 3.8 - - - +
704Z LEU* 5.0 2.4 - - + +
738Z ASN* 3.5 11.9 + - - +
739Z ALA* 4.1 18.8 - - - +
740Z ARG 3.5 3.4 + - - -
741Z LEU* 1.3 73.3 - - - +
743Z ALA* 1.3 58.5 + - - +
744Z MET 3.0 8.9 + - - -
745Z LEU* 3.7 2.1 + - - +
746Z ARG* 3.4 22.0 + - - +
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Residues in contact with ALA 743 (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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704Z LEU* 3.7 35.2 - - + +
707Z LEU* 4.1 12.0 - - + +
708Z ASP* 4.7 11.6 + - + +
741Z LEU* 3.3 0.8 - - - +
742Z ALA* 1.3 77.9 - - - +
744Z MET* 1.3 61.0 + - - +
746Z ARG* 4.3 7.3 - - - +
747Z GLN* 4.0 13.9 + - - +
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Residues in contact with MET 744 (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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707Z LEU* 4.2 16.9 - - + +
729Z MET* 4.8 17.3 - - + +
732Z VAL* 6.0 2.7 - - + -
733Z GLY* 5.1 11.9 - - - +
741Z LEU* 3.0 27.5 + - + +
742Z ALA 3.0 0.8 - - - -
743Z ALA* 1.3 76.6 - - - +
745Z LEU* 1.3 69.1 + - - +
746Z ARG 3.1 2.5 + - - -
747Z GLN* 3.2 14.7 + - - +
748Z LEU* 3.4 12.1 + - - +
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Residues in contact with LEU 745 (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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733Z GLY* 5.8 1.8 - - - -
737Z ASN* 4.0 26.2 - - + +
738Z ASN* 4.2 11.0 - - + +
741Z LEU 3.2 3.6 + - - +
742Z ALA 4.4 2.5 - - - +
744Z MET* 1.3 77.1 - - - +
746Z ARG* 1.3 57.7 + - - +
748Z LEU* 3.6 6.3 + - - +
749Z ALA* 2.8 32.6 + - - +
769Z THR* 6.0 5.2 - - - -
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Residues in contact with ARG 746 (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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742Z ALA 3.4 16.9 + - - +
743Z ALA* 4.3 8.5 - - - +
744Z MET 3.1 0.4 + - - -
745Z LEU* 1.3 77.5 - - - +
747Z GLN* 1.3 51.9 + - - +
749Z ALA* 2.9 11.0 + - - +
750Z GLN* 2.7 35.1 + - - +
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Residues in contact with GLN 747 (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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707Z LEU 5.5 4.0 - - - +
708Z ASP* 6.4 0.4 - - - -
711Z SER* 5.2 14.4 - - - -
729Z MET* 5.8 4.9 - - + -
743Z ALA 4.0 9.5 + - - +
744Z MET* 3.2 10.3 + - - +
746Z ARG* 1.3 77.6 - - - +
748Z LEU* 1.3 51.4 + - - +
750Z GLN* 2.2 35.3 + - - +
751Z TYR* 2.3 17.5 + - + -
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Residues in contact with LEU 748 (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* 5.7 0.7 - - - +
729Z MET* 4.9 15.6 - - + +
730Z GLY 5.5 1.6 - - - +
744Z MET 3.4 8.4 + - - +
745Z LEU* 3.9 7.2 - - - +
747Z GLN* 1.3 78.4 - - - +
749Z ALA* 1.3 55.2 + - - +
751Z TYR* 2.6 44.2 + - + +
765Z ALA* 5.3 9.9 - - + -
766Z GLN* 5.0 12.4 - - + +
769Z THR* 4.7 19.5 - - - -
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Residues in contact with ALA 749 (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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745Z LEU 2.8 16.8 + - - +
746Z ARG* 3.1 14.1 - - - +
748Z LEU* 1.3 75.3 - - - +
750Z GLN* 1.3 55.8 + - - +
751Z TYR 4.3 2.8 - - - +
752Z HIS* 6.0 0.2 - - - +
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Residues in contact with GLN 750 (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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746Z ARG 2.7 9.8 + - - +
747Z GLN* 2.2 26.7 + - - +
749Z ALA* 1.3 68.2 - - - +
751Z TYR* 1.3 58.4 + - - -
752Z HIS* 3.8 3.5 + - - +
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Residues in contact with TYR 751 (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* 5.4 11.7 - - + -
747Z GLN* 2.3 17.4 + - + +
748Z LEU* 2.6 39.1 + - + +
749Z ALA 4.3 3.0 - - - +
750Z GLN* 1.3 69.8 - - - +
752Z HIS* 1.3 60.9 + - - +
762Z VAL* 4.5 16.3 - - + +
766Z GLN* 5.4 4.3 - - - +
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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