Contacts of the helix formed by residues 721 - 737 (chain A) in PDB entry 3ZJU
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 721 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A PRO* 5.8 5.8 - - + -
715A ASP* 2.9 17.2 + - - +
719A ARG* 3.2 41.6 + - + +
720A GLN* 1.3 76.2 - - - +
722A PHE* 1.3 64.4 + - - +
723A ASN* 3.2 12.6 - - - -
724A THR* 2.9 33.1 + - - -
725A ALA 3.1 6.9 + - - -
1861A MG 4.3 13.5 - - - -
15B A 5.1 1.1 - - - +
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Residues in contact with PHE 722 (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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58A ILE* 4.5 8.1 - - + -
61A VAL* 3.8 29.8 - - + -
62A ILE* 4.1 23.8 - - + -
564A LEU* 5.0 2.9 - - + -
647A MET* 3.6 31.9 - - + +
652A ALA* 4.2 25.5 - - + +
715A ASP 5.1 0.2 - - - -
716A ILE* 3.9 30.3 - - + -
720A GLN* 3.6 35.9 - - + -
721A THR* 1.3 70.9 - - - +
723A ASN* 1.3 58.7 + - - +
725A ALA* 3.1 10.3 - - - +
726A ILE* 3.0 31.6 + - - +
764A PHE* 3.9 11.0 - + + -
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Residues in contact with ASN 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A MET 3.4 13.1 + - - +
648A PHE* 3.1 35.5 + - + +
650A SER* 4.2 5.8 + - - +
651A PRO* 3.7 31.6 - - - +
721A THR* 3.5 14.0 - - - -
722A PHE* 1.3 75.0 - - - +
724A THR* 1.3 76.9 + - - +
726A ILE* 3.4 3.5 + - - +
727A ALA* 3.0 21.8 + - - +
1861A MG 3.6 21.2 - - - -
13B G 4.6 7.1 + - - -
14B A 4.4 5.5 + - - -
22B A 5.3 3.4 + - - -
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Residues in contact with THR 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LYS* 5.4 2.3 - - - +
715A ASP* 2.6 26.2 + - - -
719A ARG* 3.9 3.8 + - - -
721A THR* 2.9 19.8 + - - -
723A ASN* 1.3 89.0 - - - +
725A ALA* 1.3 64.9 + - - +
727A ALA* 3.0 8.2 + - - +
728A ALA* 2.9 23.6 + - - +
1861A MG 4.3 5.4 - - - -
14B A 3.7 36.6 - - - +
15B A 4.5 2.7 - - - +
22B A 4.2 9.0 - - + -
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Residues in contact with ALA 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LYS 6.0 0.2 - - - -
712A VAL* 3.6 15.5 - - + +
715A ASP* 3.6 14.2 + - + -
716A ILE* 4.0 23.3 - - + -
721A THR 3.1 9.8 + - - +
722A PHE* 3.1 18.8 + - - +
724A THR* 1.3 75.6 + - - +
726A ILE* 1.3 63.3 + - - +
728A ALA* 3.2 14.1 + - - +
729A ILE* 3.2 18.1 + - - +
764A PHE* 4.4 7.2 - - + -
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Residues in contact with ILE 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU* 3.9 26.5 - - + -
647A MET* 3.7 5.6 - - + -
648A PHE* 3.5 45.8 - - + +
669A PHE* 5.7 1.1 - - + -
722A PHE 3.0 19.6 + - - +
723A ASN 3.8 4.0 - - - +
724A THR 3.3 0.2 - - - -
725A ALA* 1.3 77.7 - - - +
727A ALA* 1.3 62.0 + - - +
729A ILE* 3.1 11.4 + - + +
730A MET* 3.0 33.5 + - + +
761A LEU* 5.2 4.7 - - + -
764A PHE* 3.6 41.3 - - + -
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Residues in contact with ALA 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PHE* 4.3 5.8 - - + -
723A ASN 3.0 13.6 + - - +
724A THR 3.0 8.9 + - - +
726A ILE* 1.3 77.7 - - - +
728A ALA* 1.3 57.7 + - - +
730A MET* 3.4 2.5 + - - +
731A GLU* 2.8 31.0 + - - +
22B A 3.7 29.8 - - + +
23B C 3.8 28.1 - - - +
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Residues in contact with ALA 728 (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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708A THR* 4.0 11.3 + - + +
711A LYS* 4.0 30.3 - - + +
712A VAL* 4.1 13.0 - - + -
724A THR 2.9 11.9 + - - +
725A ALA* 3.2 8.7 + - - +
727A ALA* 1.3 78.1 - - - +
729A ILE* 1.3 56.3 + - - +
731A GLU* 3.2 10.6 + - - +
732A LEU* 2.9 30.8 + - - +
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Residues in contact with ILE 729 (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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669A PHE* 4.4 5.6 - - + -
708A THR* 4.5 6.3 - - - -
712A VAL* 3.9 15.5 - - + -
725A ALA 3.3 16.2 - - - +
726A ILE* 3.1 12.9 + - - +
728A ALA* 1.3 75.6 - - - +
730A MET* 1.3 57.1 + - - +
732A LEU* 3.1 5.6 + - - +
733A MET* 2.8 27.3 + - + +
757A VAL* 3.9 31.9 - - + -
760A MET* 3.9 31.2 - - + +
761A LEU* 3.5 35.2 - - + -
764A PHE* 4.6 7.2 - - + -
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Residues in contact with MET 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU* 4.9 5.6 - - + -
648A PHE* 3.7 28.9 - - + -
665A GLY 5.3 1.6 - - - +
666A ALA* 5.2 7.4 - - + +
669A PHE* 3.6 55.9 - - + -
726A ILE* 3.0 23.2 + - + +
727A ALA 3.7 6.1 - - - +
729A ILE* 1.3 73.0 - - - +
731A GLU* 1.3 67.9 + - - +
733A MET* 3.2 0.7 + - - +
734A ASN* 2.9 30.8 + - - +
23B C 3.2 32.1 - - - +
24B A 4.1 22.4 - - - +
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Residues in contact with GLU 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LYS* 6.3 0.7 - - - -
727A ALA* 2.8 21.3 + - - +
728A ALA* 3.5 9.3 - - - +
730A MET* 1.3 74.8 - - - +
732A LEU* 1.3 65.7 + - - +
734A ASN* 3.2 14.1 + - - +
735A LYS* 3.4 32.5 + - - +
22B A 2.5 38.8 + - - +
23B C 3.6 28.0 - - - +
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Residues in contact with LEU 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A LEU* 4.7 2.2 - - + -
704A ASP* 4.4 12.6 - - + -
705A VAL* 3.9 44.2 - - + +
708A THR* 3.7 33.9 - - + +
728A ALA 2.9 13.1 + - - +
729A ILE* 3.5 7.4 - - - +
731A GLU* 1.3 77.1 - - - +
733A MET* 1.3 56.8 + - - +
735A LYS* 3.0 14.5 + - + +
736A LEU* 3.0 37.7 + - + +
753A ALA 5.5 0.2 - - - +
757A VAL* 4.1 20.9 - - + -
760A MET* 4.5 4.7 - - + -
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Residues in contact with MET 733 (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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669A PHE* 4.0 26.7 - - + -
672A ARG* 4.2 6.3 - - + +
673A VAL* 3.8 33.9 - - + +
676A LEU* 3.5 30.5 - - + -
729A ILE 2.8 21.1 + - - +
730A MET 3.2 4.5 + - - +
732A LEU* 1.3 68.7 - - - +
734A ASN* 1.3 68.7 + - - +
736A LEU* 3.7 19.2 - - - +
737A ALA* 3.1 26.8 + - + +
754A LEU* 4.6 6.7 - - - -
757A VAL* 4.0 27.6 - - + -
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Residues in contact with ASN 734 (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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669A PHE* 5.5 1.4 - - - -
672A ARG* 4.7 13.3 + - - -
730A MET* 2.9 21.4 + - - +
731A GLU* 3.2 10.0 + - - +
733A MET* 1.3 79.4 - - - +
735A LYS* 1.3 59.8 + - - +
737A ALA* 3.9 5.8 + - - +
738A LYS* 3.7 32.5 + - - +
23B C 3.9 8.1 + - - -
24B A 3.0 36.5 + - - -
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Residues in contact with LYS 735 (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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701A LEU* 4.5 15.3 - - + +
704A ASP* 3.2 34.8 + - + +
731A GLU* 3.4 31.7 + - - +
732A LEU* 3.0 14.5 + - + +
734A ASN* 1.3 74.4 - - - +
736A LEU* 1.3 67.0 + - - +
738A LYS* 3.1 17.9 + - + +
739A ALA* 3.4 10.9 + - - +
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Residues in contact with LEU 736 (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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676A LEU* 3.8 15.8 - - + +
701A LEU* 4.1 24.5 - - + -
705A VAL* 4.6 0.2 - - + -
732A LEU* 3.0 27.6 + - + +
733A MET* 3.3 17.9 + - - +
735A LYS* 1.3 76.9 - - - +
737A ALA* 1.3 63.2 + - - +
738A LYS 3.0 0.2 - - - -
739A ALA* 3.0 14.5 + - - +
741A THR* 5.7 0.2 - - - +
749A LEU* 5.8 0.4 - - + -
750A MET* 3.4 31.8 - - + +
753A ALA* 3.7 34.1 - - + -
754A LEU* 4.3 9.2 - - + -
757A VAL* 4.0 23.3 - - + -
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Residues in contact with ALA 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A LEU* 3.7 20.0 - - + +
733A MET* 3.1 15.5 + - + +
734A ASN* 4.1 7.2 - - - +
736A LEU* 1.3 77.0 - - - +
738A LYS* 1.3 61.7 + - + +
739A ALA 3.4 3.2 + - - +
41B C 5.6 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
------------------------------------------------------------
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