Contacts of the helix formed by residues 773 - 787 (chain A) in PDB entry 4GT5
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 SER 773 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A VAL* 5.0 1.6 - - - -
771A ARG 3.9 1.0 + - - -
772A HIS* 1.3 79.2 - - - +
774A ILE* 1.3 69.5 + - - +
775A LYS* 3.2 16.3 + - - +
776A ASP* 3.4 20.4 + - - +
777A VAL* 3.2 20.4 + - - +
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Residues in contact with ILE 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A ALA* 3.8 17.5 - - + +
638A MET* 3.7 28.7 - - + -
639A VAL* 3.9 19.7 - - + -
642A ALA* 4.0 21.3 - - + -
710A VAL* 4.2 21.9 - - + +
713A PHE* 4.1 30.7 - - + -
772A HIS 3.8 0.4 + - - -
773A SER* 1.3 76.6 + - - +
775A LYS* 1.3 64.7 + - + +
777A VAL* 4.4 7.2 - - + -
778A HIS* 2.9 28.8 + - - +
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Residues in contact with LYS 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A VAL* 3.9 33.7 - - + -
643A GLY* 6.4 2.2 - - - -
773A SER* 3.2 10.4 + - - +
774A ILE* 1.3 82.8 - - + +
776A ASP* 1.3 64.2 + - - +
778A HIS* 3.3 5.2 + - - +
779A ALA* 2.9 28.4 + - - +
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Residues in contact with ASP 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A HIS* 4.5 14.8 - - + -
773A SER* 3.4 24.2 + - - +
774A ILE 3.4 0.4 - - - -
775A LYS* 1.3 80.1 - - - +
777A VAL* 1.3 60.5 + - - +
779A ALA* 3.3 7.3 + - - +
780A ARG* 2.9 29.9 + - - +
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Residues in contact with VAL 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710A VAL* 5.2 0.9 - - + -
713A PHE* 3.5 35.4 - - + -
759A ILE* 3.8 24.9 - - + -
763A CYS* 4.1 19.1 - - - -
772A HIS* 4.0 20.9 - - + +
773A SER 3.2 15.8 + - - +
774A ILE* 3.8 12.8 - - + +
776A ASP* 1.3 75.5 - - - +
778A HIS* 1.3 58.0 + - - +
780A ARG* 3.3 5.8 + - - +
781A LEU* 2.9 31.7 + - + +
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Residues in contact with HIS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A SER* 3.2 33.8 + - - -
635A ALA* 3.9 11.8 - - + +
636A ALA* 3.5 29.0 - - + +
639A VAL* 4.0 15.7 - - + +
774A ILE 2.9 18.8 + - - +
775A LYS 3.4 6.3 + - - +
777A VAL* 1.3 78.0 - - - +
779A ALA* 1.3 57.6 + - - +
781A LEU* 3.4 3.2 + - - +
782A GLN* 2.9 63.9 + - - +
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Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A LYS 2.9 17.2 + - - +
776A ASP* 3.5 8.3 - - - +
777A VAL 3.3 0.2 - - - -
778A HIS* 1.3 80.5 + - - +
780A ARG* 1.3 57.7 + - - +
782A GLN* 3.3 7.6 + - - +
783A ALA* 2.9 30.9 + - - +
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Residues in contact with ARG 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759A ILE* 4.3 18.4 - - + -
776A ASP 2.9 16.8 + - - +
777A VAL* 3.6 6.7 - - - +
779A ALA* 1.3 77.6 - - - +
781A LEU* 1.3 57.7 + - - +
783A ALA* 3.3 6.9 + - - +
784A LEU* 2.9 35.3 + - + +
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Residues in contact with LEU 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A LEU* 4.2 23.2 - - + +
631A ALA* 4.1 18.2 - - + +
632A SER* 4.5 12.6 - - - +
635A ALA* 4.3 5.2 - - + -
713A PHE* 3.5 39.0 - - + -
717A LEU* 3.9 20.9 - - + -
721A PHE* 5.9 0.2 - - + -
756A VAL* 5.3 1.8 - - + -
759A ILE* 4.0 20.2 - - + -
777A VAL* 2.9 24.9 + - + +
778A HIS 3.8 3.4 - - - +
780A ARG* 1.3 73.8 - - - +
782A GLN* 1.3 61.3 + - - +
784A LEU* 3.4 5.0 + - - +
785A ALA* 2.9 29.9 + - - +
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Residues in contact with GLN 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A SER* 3.7 16.1 + - - +
778A HIS* 2.9 47.4 + - - +
779A ALA* 3.7 7.2 - - - +
781A LEU* 1.3 73.6 - - - +
783A ALA* 1.3 61.0 - - - +
785A ALA* 3.3 6.9 + - + +
786A GLN* 2.9 37.5 + - - +
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Residues in contact with ALA 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ALA 2.9 16.8 + - - +
780A ARG* 3.5 7.2 - - - +
781A LEU 3.3 0.2 - - - -
782A GLN* 1.3 77.3 - - - +
784A LEU* 1.3 60.4 + - + +
786A GLN* 2.9 22.8 + - - +
787A ALA* 3.0 13.5 + - - +
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Residues in contact with LEU 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A LEU* 3.3 17.2 - - + +
755A GLU* 4.3 19.5 - - + +
756A VAL* 4.1 20.2 - - + -
759A ILE* 3.7 28.5 - - + -
780A ARG* 2.9 18.7 + - + +
781A LEU* 3.8 5.2 - - - +
783A ALA* 1.3 77.0 - - + +
785A ALA* 1.3 57.4 + - - +
787A ALA 3.1 5.6 - - - +
788A PRO* 3.0 34.1 - - - +
789A PRO* 4.3 20.4 - - + -
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Residues in contact with ALA 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A GLY* 4.6 7.5 - - - +
628A LEU* 3.6 33.6 - - + +
629A ALA* 4.3 6.3 - - + +
632A SER* 5.2 2.0 - - - -
781A LEU 2.9 17.9 + - - +
782A GLN* 3.6 9.4 - - + +
783A ALA 3.2 0.2 - - - -
784A LEU* 1.3 75.8 - - - +
786A GLN* 1.3 64.5 + - - +
787A ALA 3.3 0.4 + - - -
788A PRO* 3.9 11.0 - - - +
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Residues in contact with GLN 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782A GLN* 2.9 18.9 + - - +
783A ALA* 2.9 12.5 + - - +
785A ALA* 1.3 83.0 - - - +
787A ALA* 1.3 60.3 + - + +
788A PRO* 3.8 3.2 - - - +
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Residues in contact with ALA 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783A ALA 3.0 9.0 + - - +
784A LEU* 3.1 12.4 - - - +
786A GLN* 1.3 81.6 - - + +
788A PRO* 1.3 67.0 - - - +
789A PRO* 3.4 5.9 - - - +
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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