Contacts of the helix formed by residues 739 - 755 (chain A) in PDB entry 3WAJ
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 739 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A GLU* 3.0 40.2 + - + +
727A GLU* 2.8 29.6 + - - +
731A ARG* 3.5 32.4 - - - +
737A SER 3.8 0.4 + - - -
738A PRO* 1.3 72.8 - - - +
740A MET* 1.3 61.8 + - - +
742A THR* 2.9 9.4 + - - -
743A GLN 2.9 22.9 + - - -
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Residues in contact with MET 740 (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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612A ILE* 3.4 25.8 - - + +
613A GLU* 3.5 42.6 - - + +
616A THR* 3.6 22.6 - - - +
617A GLY* 5.0 5.4 - - - +
702A PRO* 5.9 1.1 - - + -
704A GLU* 3.9 1.2 + - - +
738A PRO 3.7 0.2 + - - -
739A THR* 1.3 74.0 - - - +
741A GLY* 1.3 57.9 + - - +
743A GLN* 3.0 21.6 + - - +
744A GLU* 2.9 24.6 + - - +
770A TYR* 4.0 14.1 - - + +
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Residues in contact with GLY 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 3.5 15.6 - - - +
702A PRO* 3.8 8.2 - - - +
704A GLU* 2.9 17.8 + - - -
705A TRP* 3.3 15.4 - - - -
740A MET* 1.3 76.8 - - - +
742A THR* 1.3 61.0 + - - +
744A GLU* 3.4 5.9 + - - +
745A VAL* 3.1 26.2 + - - +
767A PRO* 4.8 3.8 - - - +
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Residues in contact with THR 742 (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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705A TRP* 3.1 18.9 + - - +
724A ALA* 3.5 35.0 - - + +
727A GLU* 2.6 32.7 + - - +
738A PRO* 3.6 17.0 - - + -
739A THR* 2.9 11.4 + - - -
741A GLY* 1.3 73.0 - - - +
743A GLN* 1.3 60.3 + - - +
745A VAL* 3.1 6.1 + - - +
746A LEU* 2.8 35.6 + - + +
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Residues in contact with GLN 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A THR* 3.6 23.9 - - + -
617A GLY* 4.7 4.2 + - - -
667A LEU* 3.4 41.3 - - + +
737A SER* 3.6 14.8 + - - -
738A PRO* 2.8 26.9 + - + +
739A THR 2.9 15.3 + - - +
740A MET* 3.0 22.6 + - - +
742A THR* 1.3 77.6 - - - +
744A GLU* 1.3 56.1 + - - +
746A LEU* 3.2 2.1 + - - +
747A TYR* 2.8 40.0 + - + -
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Residues in contact with GLU 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 3.8 14.6 - - + +
615A GLU* 2.7 38.9 - - - +
616A THR* 4.4 1.5 - - + +
683A HIS* 3.8 5.1 + - - -
684A LEU* 5.1 0.2 - - + -
740A MET 2.9 12.4 + - - +
741A GLY* 3.6 8.3 - - - +
742A THR 3.2 0.2 - - - -
743A GLN* 1.3 74.9 - - - +
745A VAL* 1.3 65.0 + - - +
747A TYR* 3.2 11.0 + - - +
748A LYS* 2.9 55.2 + - + +
766A ALA 3.6 1.5 - - - +
767A PRO* 3.5 4.4 - - + -
768A SER* 2.8 40.0 + - - +
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Residues in contact with VAL 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A TRP* 4.0 12.6 - - + -
720A VAL* 3.9 22.9 - - + -
721A LEU* 4.5 6.7 - - + -
724A ALA* 3.6 24.7 - - + -
741A GLY 3.1 18.4 + - - +
742A THR 3.1 7.2 + - - +
744A GLU* 1.3 77.2 - - - +
746A LEU* 1.3 58.0 + - - +
748A LYS* 3.3 9.4 + - - +
749A TYR* 2.9 25.5 + - - +
765A ILE* 3.8 22.7 - - + +
766A ALA 4.0 3.6 - - - -
767A PRO* 4.0 20.4 - - + -
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Residues in contact with LEU 746 (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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641A PHE* 4.3 10.3 - - + -
665A ILE* 4.4 9.0 - - + -
667A LEU* 4.0 23.6 - - + -
669A ILE* 5.1 5.8 - - + -
721A LEU* 4.4 9.4 - - + -
724A ALA* 4.4 12.3 - - + -
725A LEU* 3.6 31.0 - - + +
728A ALA* 4.0 26.5 - - + -
738A PRO* 4.2 3.8 - - + -
742A THR* 2.8 30.8 + - + +
743A GLN 3.7 4.3 - - - +
745A VAL* 1.3 70.8 - - - +
747A TYR* 1.3 60.2 + - - +
749A TYR* 3.2 8.0 + - + +
750A ALA* 2.8 32.3 + - - +
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Residues in contact with TYR 747 (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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615A GLU* 3.6 12.3 - - + -
616A THR* 3.9 32.9 + - + -
619A TYR* 6.0 0.2 - - - +
637A TYR* 4.5 9.4 - - - -
667A LEU* 4.0 24.3 - - + +
668A ARG 4.2 9.1 + - - -
669A ILE* 5.0 1.6 - - + -
670A PRO* 3.6 35.8 - - + +
674A TYR* 3.6 30.1 - + - -
675A TYR* 2.6 27.5 + - - +
684A LEU* 3.6 15.9 - - + -
743A GLN* 2.8 31.0 + - - -
744A GLU* 3.3 9.6 - - - +
746A LEU* 1.3 73.2 - - - +
748A LYS* 1.3 57.8 - - - +
750A ALA* 3.4 2.4 + - - +
751A TYR 3.0 15.1 + - - -
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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
----------------------------------------------------------
683A HIS 5.1 0.6 + - - -
684A LEU* 3.4 47.3 + - + +
686A ASP* 5.0 4.6 + - - -
744A GLU* 2.9 42.4 + - + +
745A VAL* 3.5 7.4 - - - +
747A TYR* 1.3 73.1 - - - +
749A TYR* 1.3 65.6 + - - +
751A TYR* 3.3 7.7 + - - +
752A THR* 3.1 28.7 + - - +
763A VAL* 3.9 13.0 - - + +
764A LYS 3.3 23.9 + - - +
765A ILE* 4.5 6.7 - - + -
766A ALA* 2.8 29.0 + - - +
767A PRO 4.4 0.6 + - - -
768A SER* 4.3 9.3 - - - -
805A ARG* 5.3 1.2 - - - +
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Residues in contact with TYR 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PHE* 3.7 33.9 - + - -
649A PHE* 3.3 32.4 - + - -
721A LEU* 3.7 46.6 - - + +
725A LEU* 5.1 5.0 - - + +
745A VAL 2.9 14.7 + - - +
746A LEU* 3.5 12.6 - - + +
748A LYS* 1.3 75.4 - - - +
750A ALA* 1.3 60.7 + - - +
752A THR* 2.8 20.6 + - - -
753A GLN* 3.1 40.9 + - + +
765A ILE* 3.8 20.6 - - + +
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Residues in contact with ALA 750 (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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641A PHE* 3.9 21.3 - - + -
669A ILE* 3.5 32.1 - - + -
675A TYR* 3.9 4.3 - - + +
746A LEU 2.8 20.4 + - - +
747A TYR* 3.5 6.3 - - - +
749A TYR* 1.3 72.1 - - - +
751A TYR* 1.3 58.1 + - - +
753A GLN* 3.2 1.9 + - - +
754A LEU* 2.8 40.8 + - + +
755A TYR* 5.0 0.9 - - - -
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Residues in contact with TYR 751 (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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675A TYR* 3.4 49.7 + + + -
684A LEU* 5.1 0.4 - - + -
685A PHE* 3.4 18.8 - + - -
747A TYR 3.0 7.6 + - - +
748A LYS* 3.5 8.5 - - - +
749A TYR 3.2 0.6 - - - -
750A ALA* 1.3 75.7 - - - +
752A THR* 1.3 62.4 + - - +
755A TYR* 3.0 24.4 + - + -
756A GLU* 2.8 61.6 + - + +
757A LYS 4.9 0.2 + - - -
760A GLY* 4.2 2.3 - - - -
761A ILE* 2.7 43.1 + - - +
763A VAL* 3.7 20.0 - - + -
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Residues in contact with THR 752 (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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748A LYS 3.1 15.4 + - - +
749A TYR* 2.8 20.1 + - - -
751A TYR* 1.3 75.2 - - - +
753A GLN* 1.3 76.2 + - - +
756A GLU* 3.3 35.3 + - - +
763A VAL* 4.1 24.5 - - + +
765A ILE* 4.0 15.7 - - + +
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Residues in contact with GLN 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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641A PHE* 5.5 3.6 - - + -
749A TYR* 3.1 52.1 + - + +
750A ALA* 3.9 3.8 - - - +
752A THR* 1.3 95.3 + - - +
754A LEU* 1.3 71.0 + - + +
765A ILE* 5.9 0.4 - - - +
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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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641A PHE* 5.0 3.8 - - + -
651A TYR* 3.6 59.7 - - + -
669A ILE* 4.3 1.8 - - + -
672A GLU* 5.1 0.2 - - - +
750A ALA* 2.8 34.1 + - + +
753A GLN* 1.3 86.5 - - + +
755A TYR* 1.3 91.8 + - + +
756A GLU 5.5 0.9 - - - -
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Residues in contact with TYR 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLY* 5.3 0.9 - - - -
651A TYR* 3.8 20.1 + - - -
669A ILE* 5.2 0.7 - - + -
670A PRO 3.5 23.3 + - - -
671A SER* 3.7 4.0 - - - -
672A GLU* 3.6 55.4 + - + +
675A TYR* 3.7 24.0 - + + -
750A ALA 4.9 0.4 - - - -
751A TYR* 3.0 25.5 + - + +
753A GLN 3.8 0.2 - - - -
754A LEU* 1.3 113.1 - - + +
756A GLU* 1.3 70.0 + - - +
757A LYS* 2.9 21.8 + - - +
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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