Contacts of the helix formed by residues 681 - 698 (chain A) in PDB entry 2PY3
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 681 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A ILE* 3.8 5.8 - - - -
651A ILE* 3.8 11.0 - - + -
673A GLU* 4.9 1.6 + - - -
679A VAL* 5.1 9.9 - - + -
680A TYR* 1.3 86.9 - - - +
682A HIS* 1.3 59.6 + - - +
683A GLN* 3.1 24.0 + - - +
684A SER* 2.7 30.7 + - - +
685A ASP 3.4 2.9 + - - -
744A PRO* 5.2 3.5 - - - +
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Residues in contact with HIS 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 3.5 45.4 + - + +
621A LYS* 3.9 10.5 - - - +
622A CYS 3.6 30.4 + - - -
623A ILE* 3.7 15.7 - - + +
651A ILE* 4.3 16.1 - - + +
681A THR* 1.3 75.1 - - - +
683A GLN* 1.3 69.0 + - + +
685A ASP* 3.1 11.1 + - - +
686A VAL* 3.1 27.4 + - - +
750A PHE* 3.8 5.4 - - + -
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Residues in contact with GLN 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A THR* 3.0 13.1 - - - +
682A HIS* 1.3 88.2 - - + +
684A SER* 1.3 61.7 + - - +
686A VAL* 2.8 29.7 - - + +
687A TRP 3.3 1.2 + - - -
744A PRO* 3.6 32.6 - - + +
745A SER* 4.8 4.8 - - - +
747A ARG* 2.8 36.2 + - - +
748A PRO 3.0 21.2 - - - +
749A THR* 4.1 21.8 - - - +
750A PHE 5.2 0.4 - - - +
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Residues in contact with SER 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA* 3.8 9.7 - - - +
673A GLU* 3.0 28.4 + - - +
674A ALA* 5.1 0.6 - - - +
679A VAL* 4.4 0.3 + - - +
680A TYR* 3.5 34.1 + - - -
681A THR* 2.7 28.7 + - - +
683A GLN* 1.3 78.8 - - - +
685A ASP* 1.3 61.9 + - - +
687A TRP* 3.2 18.2 + - - +
688A SER* 3.3 9.9 + - - -
747A ARG* 3.7 2.2 - - - +
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Residues in contact with ASP 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A MET* 3.4 17.5 - - + +
622A CYS 4.3 1.4 - - - +
623A ILE* 3.4 10.4 - - - +
624A HIS* 2.9 26.3 + - - +
625A ARG* 3.0 14.6 + - - -
626A ASP 4.9 0.2 + - - -
627A LEU* 4.1 7.0 - - - +
680A TYR* 2.7 30.6 + - - -
681A THR 3.4 1.4 + - - -
682A HIS* 3.1 15.1 + - - +
684A SER* 1.3 78.5 - - - +
686A VAL* 1.3 59.2 + - - +
688A SER* 3.1 8.6 + - - -
689A PHE* 2.9 25.3 + - - +
750A PHE* 3.7 16.8 - - + -
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Residues in contact with VAL 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A HIS 3.1 14.3 + - - +
683A GLN* 2.8 34.5 - - - +
685A ASP* 1.3 73.2 - - - +
687A TRP* 1.3 66.2 + - - +
689A PHE* 3.1 5.8 + - - +
690A GLY 3.0 17.0 + - - -
739A CYS* 3.3 13.9 - - - +
747A ARG* 3.6 29.6 - - + -
748A PRO 3.6 18.6 - - - +
749A THR 4.6 0.4 - - - -
750A PHE* 3.5 36.3 - - + +
753A LEU* 4.7 6.5 - - + -
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Residues in contact with TRP 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LYS 5.2 1.4 + - - -
669A TRP 3.7 9.9 + - - -
670A MET 3.4 9.5 + - - -
671A ALA* 3.6 24.5 - - + -
672A PRO* 3.5 39.0 - - + -
684A SER 3.2 10.7 + - - +
685A ASP 3.2 0.6 - - - -
686A VAL* 1.3 82.7 - - - +
688A SER* 1.3 64.6 + - - +
690A GLY 2.9 10.7 + - - -
691A VAL* 3.3 19.9 + - + +
704A TYR* 4.1 17.9 + - - -
716A LEU* 4.1 12.5 - - + +
721A ARG* 3.8 29.2 - - - -
739A CYS 3.4 15.7 - - - +
740A TRP* 3.2 50.3 + + + -
741A HIS 4.0 4.5 - - - -
742A ALA* 4.8 0.7 - - - -
747A ARG* 3.8 17.3 - - - +
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A ARG 5.3 1.7 + - - -
627A LEU* 3.9 33.9 + - - +
669A TRP* 2.7 26.9 + - - +
670A MET* 4.8 1.4 - - - -
671A ALA 4.9 0.2 + - - -
680A TYR* 3.7 11.8 + - - -
684A SER 3.3 10.1 + - - -
685A ASP* 3.1 9.7 + - - -
687A TRP* 1.3 78.2 - - - +
689A PHE* 1.3 64.2 + - - +
691A VAL* 3.0 8.5 + - - +
692A LEU* 2.9 21.4 + - - +
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Residues in contact with PHE 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A THR* 3.5 29.8 - - + -
610A LEU* 3.7 15.9 - - + -
611A ALA* 3.5 29.8 - - + -
614A MET* 4.3 2.0 - - + -
627A LEU* 4.1 11.0 - - + +
685A ASP 2.9 12.6 + - - +
686A VAL* 3.1 11.4 + - + +
688A SER* 1.3 76.4 - - - +
690A GLY* 1.3 52.1 + - - +
692A LEU* 3.2 20.0 + - + +
693A MET* 2.7 61.0 + - + +
696A ILE* 6.2 0.7 - - + -
739A CYS* 4.5 1.6 - - - -
750A PHE* 3.7 23.1 - + + -
753A LEU* 4.1 20.9 - - + -
757A LEU* 4.5 5.8 - - + -
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Residues in contact with GLY 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A VAL 3.0 6.3 + - - -
687A TRP 2.9 10.5 + - - -
689A PHE* 1.3 76.1 - - - +
691A VAL* 1.3 61.3 - - - +
693A MET* 3.0 12.4 + - - +
694A TRP 3.0 17.0 + - - -
736A MET* 4.1 3.7 - - - +
739A CYS* 3.9 18.3 - - - +
740A TRP* 3.4 23.4 - - - -
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Residues in contact with VAL 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LYS 3.7 21.3 - - - +
669A TRP* 3.3 38.4 - - + +
687A TRP* 3.8 18.4 - - + +
688A SER 3.0 6.4 + - - +
690A GLY* 1.3 73.7 - - - +
692A LEU* 1.3 64.5 + - - +
694A TRP* 2.8 15.3 + - - +
695A GLU* 2.9 13.5 + - + +
703A PRO* 3.9 22.0 - - + -
704A TYR* 4.7 3.1 - - - +
722A MET* 4.2 7.2 - - + -
740A TRP* 3.3 23.0 - - + +
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Residues in contact with LEU 692 (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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572A LEU* 4.4 1.1 - - + -
610A LEU* 4.1 20.4 - - + -
614A MET* 6.2 0.2 - - + -
627A LEU* 4.1 21.5 - - + -
628A ALA* 3.7 8.1 - - - -
629A ALA* 3.3 37.0 - - + +
632A VAL* 4.3 8.5 - - + -
669A TRP* 4.6 0.6 - - - -
688A SER 2.9 13.0 + - - +
689A PHE* 3.2 32.1 - - + +
691A VAL* 1.3 77.0 - - - +
693A MET* 1.3 62.0 - - - +
695A GLU* 3.1 12.1 + - - +
696A ILE* 2.9 43.4 + - + +
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Residues in contact with MET 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A THR* 3.9 19.3 - - + -
689A PHE* 2.7 49.9 + - + +
690A GLY* 3.0 11.2 + - - +
692A LEU* 1.3 73.1 - - - +
694A TRP* 1.3 63.6 + - - +
696A ILE* 3.2 9.1 + - + +
697A PHE* 3.0 39.5 + - + -
732A LEU* 3.8 29.8 - - + +
735A MET* 3.7 37.2 - - - +
736A MET* 3.9 20.2 - - + -
739A CYS* 4.7 1.6 - - - -
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Residues in contact with TRP 694 (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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690A GLY 3.0 10.7 + - - +
691A VAL 2.8 11.3 + - - +
693A MET* 1.3 75.7 - - - +
695A GLU* 1.3 59.3 + - + +
697A PHE 3.6 0.7 + - - -
698A THR* 2.7 58.5 + - + +
701A GLY* 3.8 13.5 - - - -
702A SER 3.4 34.8 - - - -
703A PRO* 3.6 7.6 - - + -
705A PRO* 4.2 15.5 - - + -
722A MET* 3.5 44.2 - - + +
723A ASP 3.1 24.7 + - - -
725A PRO* 3.4 24.0 - - + +
733A TYR* 5.4 0.2 - + - -
736A MET* 4.0 17.7 - - - -
740A TRP* 4.1 3.8 - + + -
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Residues in contact with GLU 695 (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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573A ARG* 4.2 13.7 - - - -
576A LEU* 4.5 0.9 - - - -
628A ALA* 3.6 1.7 - - - -
629A ALA* 2.9 41.1 + - + +
630A ARG* 4.7 1.7 + - - +
669A TRP* 2.7 42.6 + - - +
691A VAL* 2.9 19.4 + - + +
692A LEU* 3.1 13.2 + - - +
694A TRP* 1.3 77.3 - - + +
696A ILE* 1.3 59.9 + - - +
698A THR* 2.9 11.9 + - - -
700A GLY* 2.7 32.3 + - - -
701A GLY 3.9 18.3 - - - +
703A PRO* 4.6 5.0 - - + +
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Residues in contact with ILE 696 (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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572A LEU* 3.9 17.5 - - + -
576A LEU* 3.7 10.7 - - + +
603A LEU* 3.7 36.6 - - + +
606A CYS* 3.9 21.8 - - - -
607A THR* 3.8 28.5 - - + +
610A LEU* 4.0 17.9 - - + -
629A ALA* 5.6 0.2 - - + -
689A PHE* 6.2 0.7 - - + -
692A LEU* 2.9 29.6 + - + +
693A MET* 3.2 10.7 + - - +
695A GLU* 1.3 76.5 - - + +
697A PHE* 1.3 63.3 + - + +
699A LEU* 2.9 20.4 + - - +
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Residues in contact with PHE 697 (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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600A PHE* 4.0 9.4 - + - -
603A LEU* 3.7 33.5 - - + +
604A VAL* 4.1 9.6 - - + -
607A THR* 3.6 20.2 - - - -
693A MET* 3.0 40.7 + - + +
696A ILE* 1.3 77.8 - - + +
698A THR* 1.3 58.9 + - - +
699A LEU* 3.2 2.9 + - - +
725A PRO* 4.0 21.8 - - + +
727A ASN* 3.3 48.5 + - - +
728A CYS* 4.1 11.4 - - + -
732A LEU* 3.5 34.3 - - + -
736A MET* 4.0 13.5 - - + -
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Residues in contact with THR 698 (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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580A ARG* 3.1 17.3 + - - -
694A TRP* 2.7 55.7 + - + +
695A GLU* 2.9 9.9 + - - -
697A PHE* 1.3 75.5 - - - +
699A LEU* 1.3 68.3 + - - +
701A GLY* 3.0 20.7 + - - -
725A PRO* 3.7 19.3 - - + -
727A ASN* 5.1 2.5 - - - +
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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
------------------------------------------------------------
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