Contacts of the helix formed by residues 746 - 760 (chain A) in PDB entry 3GQL
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 746 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A VAL* 4.4 4.3 - - - -
744A ARG 4.6 0.4 - - - +
745A PRO* 1.3 80.8 - - - +
747A PHE* 1.3 64.0 + - - +
748A LYS* 3.1 15.1 + - - +
749A GLN* 3.0 35.4 + - - +
750A LEU* 2.9 27.8 + - - +
554C ASP* 3.6 32.0 - - + +
555C GLY 4.4 0.4 - - - +
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Residues in contact with PHE 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA* 4.3 10.5 - - + +
611A MET* 3.6 45.8 - - + -
612A GLU* 3.5 22.7 - - + -
615A ALA* 4.4 11.7 - - + -
624A LEU* 4.5 0.2 - - + -
679A HIS* 3.6 17.7 - - + -
682A ASP* 3.5 33.2 - - + -
683A VAL* 3.4 19.5 - - + -
686A PHE* 4.0 24.0 - + + -
746A THR* 1.3 74.7 - - - +
748A LYS* 1.3 56.6 + - - +
750A LEU* 3.8 12.1 - - + +
751A VAL* 2.9 36.4 + - - +
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Residues in contact with LYS 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A GLU* 3.7 19.3 + - - +
746A THR* 3.0 12.6 + - - +
747A PHE* 1.3 79.0 - - - +
749A GLN* 1.3 63.6 + - + +
751A VAL* 3.4 3.6 + - - +
752A GLU* 3.1 42.1 + - - +
476C ASP* 5.5 5.9 + - - +
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Residues in contact with GLN 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A PRO* 3.5 22.4 - - + +
746A THR* 3.0 30.6 + - - +
748A LYS* 1.3 73.3 - - + +
750A LEU* 1.3 58.0 + - - +
752A GLU* 2.6 35.2 + - - +
753A ASP* 2.8 25.7 + - - +
475C ARG* 4.0 13.2 - - - +
554C ASP 2.7 28.6 - - - +
555C GLY* 3.7 4.0 - - - -
556C PRO* 4.5 10.1 - - - +
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Residues in contact with LEU 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA* 4.6 3.8 - - + -
683A VAL* 4.2 17.3 - - + -
686A PHE* 3.7 25.6 - - + -
732A MET* 3.7 33.4 - - + -
736A CYS* 4.0 12.1 - - - -
745A PRO* 4.1 13.9 - - + -
746A THR 2.9 19.6 + - - +
747A PHE* 3.8 22.9 - - + +
749A GLN* 1.3 78.6 - - - +
751A VAL* 1.3 58.4 + - - +
753A ASP* 4.5 7.0 - - - +
754A LEU* 2.8 44.0 + - + +
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Residues in contact with VAL 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A TYR* 3.4 23.1 - - + +
608A ALA* 3.4 38.8 - - + +
609A ARG* 3.8 7.6 - - + +
612A GLU* 3.8 24.7 - - - +
747A PHE 2.9 27.6 + - - +
748A LYS 3.6 5.2 - - - +
749A GLN 3.1 0.4 + - - -
750A LEU* 1.3 75.2 - - - +
752A GLU* 1.3 65.7 + - + +
754A LEU* 4.6 1.3 - - - -
755A ASP* 3.1 20.6 + - + +
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Residues in contact with GLU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A LYS* 3.1 41.8 + - - +
749A GLN* 2.6 21.6 + - - +
751A VAL* 1.3 69.1 - - + +
753A ASP* 1.3 60.0 + - - +
755A ASP* 2.7 33.9 + - - +
756A ARG* 3.1 7.8 + - - +
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Residues in contact with ASP 753 (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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732A MET* 3.5 23.1 - - + +
745A PRO* 6.0 0.9 - - - +
749A GLN* 2.8 31.1 + - - +
750A LEU* 4.0 4.9 + - - +
752A GLU* 1.3 74.7 - - - +
754A LEU* 1.3 57.9 + - - +
756A ARG* 3.1 33.8 + - - +
757A ILE* 2.8 33.8 + - - +
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Residues in contact with LEU 754 (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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601A VAL* 4.3 13.2 - - + +
604A ALA* 3.5 34.3 - - + +
605A TYR* 4.0 17.0 - - + -
608A ALA* 4.0 9.0 - - + -
686A PHE* 3.7 23.6 - - + -
690A LEU* 5.1 0.7 - - + -
729A LEU* 4.3 15.3 - - + -
732A MET* 3.5 28.7 - - + -
750A LEU 2.8 26.4 + - - +
753A ASP* 1.3 73.4 - - - +
755A ASP* 1.3 56.9 + - - +
757A ILE* 4.0 3.3 - - + +
758A VAL* 2.9 37.1 + - - +
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Residues in contact with ASP 755 (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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605A TYR* 3.8 31.3 + - + -
751A VAL* 3.1 16.6 + - + +
752A GLU* 2.7 22.5 + - - +
754A LEU* 1.3 72.0 - - - +
756A ARG* 1.3 60.3 + - - +
758A VAL* 3.6 5.0 + - - +
759A ALA* 3.5 18.2 + - - +
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Residues in contact with ARG 756 (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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728A GLU* 3.0 29.5 + - - +
752A GLU 3.1 7.9 + - - +
753A ASP* 3.1 42.8 + - - +
755A ASP* 1.3 76.4 - - - +
757A ILE* 1.3 75.3 + - - +
759A ALA* 2.9 20.0 + - - +
760A LEU* 3.3 29.8 + - + +
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Residues in contact with ILE 757 (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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601A VAL* 3.6 21.1 - - + -
728A GLU* 3.4 43.1 - - + +
729A LEU* 3.9 21.5 - - + -
732A MET* 3.6 30.7 - - + -
753A ASP 2.8 20.1 + - - +
754A LEU* 4.0 5.2 - - + +
756A ARG* 1.3 84.2 - - - +
758A VAL* 1.3 62.5 + - - +
760A LEU* 3.1 14.5 + - - +
761A THR* 2.9 27.2 + - - +
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Residues in contact with VAL 758 (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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598A LYS* 2.8 47.8 + - + +
601A VAL* 3.4 24.7 - - + +
602A SER* 3.6 35.9 - - - +
605A TYR* 4.2 8.5 - - + -
754A LEU 2.9 29.4 + - - +
755A ASP* 3.9 5.8 - - - +
756A ARG 3.2 0.2 - - - -
757A ILE* 1.3 75.0 - - - +
759A ALA* 1.3 57.0 + - - +
760A LEU 3.1 1.1 + - - -
761A THR* 3.2 11.9 + - - -
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Residues in contact with ALA 759 (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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598A LYS* 4.3 7.8 + - - +
755A ASP 3.5 9.9 + - - +
756A ARG* 2.9 12.8 + - - +
758A VAL* 1.3 78.8 - - - +
760A LEU* 1.3 67.5 + - + +
761A THR 3.5 0.7 + - - +
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Residues in contact with LEU 760 (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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728A GLU* 6.1 0.4 - - - +
756A ARG* 3.7 33.9 - - + +
757A ILE* 3.1 11.1 + - + +
758A VAL 3.1 1.2 - - - -
759A ALA* 1.3 89.8 - - + +
761A THR* 1.3 58.5 + - - +
762A SER 4.2 0.5 + - - -
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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