Contacts of the helix formed by residues 690 - 706 (chain A) in PDB entry 1CEZ
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 VAL 690 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ASP* 5.0 1.0 + - - -
554A VAL* 6.5 1.1 - - + -
686A SER 3.3 23.3 + - - +
687A VAL* 3.6 21.8 - - + +
688A THR 3.6 1.2 + - - -
689A VAL* 1.3 74.3 - - - +
691A ALA* 1.3 67.3 + - - +
692A ALA 3.1 1.2 + - - -
693A VAL* 3.1 12.0 + - - +
694A GLU* 3.2 17.9 + - + +
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Residues in contact with ALA 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A SER* 6.2 0.2 - - - -
550A LEU* 2.9 31.8 - - + +
552A ASP* 3.4 39.1 + - + +
689A VAL 3.4 0.4 - - - -
690A VAL* 1.3 81.9 - - - +
692A ALA* 1.3 60.8 + - - +
694A GLU* 3.7 8.1 + - - +
695A ALA 3.4 9.5 + - - -
865A PRO* 5.2 0.3 - - - +
866A ALA 5.8 1.8 - - - +
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ILE* 4.9 10.8 - - + -
546A PHE* 3.9 29.4 - - + -
547A SER* 5.4 3.5 - - - +
550A LEU* 4.5 0.7 - - - -
552A ASP* 4.8 1.9 + - - +
689A VAL* 3.0 23.3 + - + +
691A ALA* 1.3 76.4 - - - +
693A VAL* 1.3 66.3 + - - +
695A ALA* 3.1 6.7 + - - +
696A MET* 3.1 37.6 + - + +
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Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A TRP* 3.9 38.8 - - + -
685A VAL* 4.6 1.6 - - + +
686A SER* 4.2 23.1 - - - +
689A VAL* 3.1 19.4 + - + +
690A VAL* 3.1 9.0 + - - +
692A ALA* 1.3 76.1 - - - +
694A GLU* 1.3 63.9 + - - +
696A MET* 3.1 18.1 + - + +
697A ASN* 3.0 37.2 + - - +
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Residues in contact with GLU 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 VAL* 3.2 14.5 + - + +
691A ALA* 4.0 11.4 - - - +
692A ALA 3.2 0.2 - - - -
693A VAL* 1.3 81.2 - - - +
695A ALA* 1.3 57.0 + - - +
697A ASN* 3.4 8.5 + - + +
698A TRP* 3.0 27.8 + - - +
863A ALA 4.6 6.2 - - - +
865A PRO* 3.7 30.1 - - + +
866A ALA 4.9 1.7 + - - -
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Residues in contact with ALA 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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546A PHE* 4.1 19.3 - - + -
550A LEU* 3.6 28.5 - - + +
691A ALA 3.4 1.8 + - - -
692A ALA 3.1 9.9 + - - +
694A GLU* 1.3 78.5 - - - +
696A MET* 1.3 63.2 + - - +
698A TRP* 3.5 8.6 + - - +
699A LEU* 3.0 29.9 + - + +
842A LEU* 4.6 11.0 - - + -
865A PRO* 4.5 6.0 - - + +
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Residues in contact with MET 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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543A ILE* 5.4 8.3 - - + -
546A PHE* 3.8 27.1 - - + -
638A ALA* 5.5 9.9 - - - -
639A TYR* 5.3 11.7 - - - -
682A TRP* 5.9 6.1 - - + -
689A VAL* 5.5 2.7 - - + -
692A ALA* 3.1 38.0 + - + +
693A VAL* 3.1 22.0 + - + +
695A ALA* 1.3 75.1 - - - +
697A ASN* 1.3 64.2 + - - +
699A LEU* 3.1 5.5 + - - +
700A LYS* 2.8 38.7 + - + +
779A ALA* 4.0 22.0 - - + -
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Residues in contact with ASN 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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682A TRP* 5.6 6.4 - - - -
693A VAL* 3.0 30.2 + - - +
694A GLU* 3.8 11.7 - - + +
696A MET* 1.3 74.7 - - - +
698A TRP* 1.3 61.4 + - - +
700A LYS* 3.2 21.8 + - - +
701A SER* 2.8 35.8 + - - +
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Residues in contact with TRP 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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694A GLU* 3.0 17.9 + - + +
695A ALA* 3.6 10.5 - - - +
696A MET 3.2 0.2 - - - -
697A ASN* 1.3 77.1 - - - +
699A LEU* 1.3 79.9 + - + +
701A SER* 3.2 7.1 + - - -
702A ALA* 3.1 21.3 + - - +
842A LEU* 4.3 21.9 + - + +
845A PHE* 4.5 8.7 - - - -
846A TYR* 3.3 36.8 - + + -
849A PHE* 4.0 15.5 - + - -
861A MET* 3.9 16.4 - - - +
862A PRO* 3.2 35.4 - - + -
863A ALA 3.4 23.1 - - - +
864A LEU* 3.3 24.0 - - + +
865A PRO* 4.1 12.6 - - + -
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Residues in contact with LEU 699 (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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546A PHE* 3.8 23.1 - - + -
695A ALA 3.0 20.7 + - - +
696A MET 3.1 5.8 + - - +
698A TRP* 1.3 85.4 - - + +
700A LYS* 1.3 61.2 + - - +
702A ALA* 3.5 6.1 + - - +
703A ALA* 3.1 17.2 + - - +
778A ILE* 3.5 25.5 - - + +
779A ALA* 4.1 14.4 - - + -
782A PHE* 3.8 38.6 - - + -
842A LEU* 4.6 5.4 - - + -
845A PHE* 3.5 35.6 - - + -
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Residues in contact with LYS 700 (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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696A MET* 2.8 32.3 + - + +
697A ASN* 3.2 24.8 + - - +
699A LEU* 1.3 74.3 - - - +
701A SER* 1.3 65.0 + - - +
703A ALA* 3.1 5.3 + - - +
704A LYS* 3.0 22.6 + - - +
775A GLU* 3.3 42.3 + - - +
776A SER* 4.8 7.7 - - - +
778A ILE* 3.8 12.6 - - + -
779A ALA* 5.0 5.4 - - + -
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Residues in contact with SER 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ASN* 2.8 21.3 + - - +
698A TRP* 3.5 5.6 - - - -
700A LYS* 1.3 75.7 - - - +
702A ALA* 1.3 64.4 + - - +
704A LYS* 3.2 16.2 + - - +
705A LEU* 3.2 20.1 + - - +
861A MET* 3.3 32.3 + - - -
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Residues in contact with ALA 702 (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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698A TRP* 3.1 10.6 + - - +
699A LEU* 3.7 7.6 - - - +
700A LYS 3.2 0.2 - - - -
701A SER* 1.3 80.1 - - - +
703A ALA* 1.3 61.9 + - - +
705A LEU* 3.5 3.3 + - - +
706A LEU* 3.0 34.4 + - + +
845A PHE* 4.3 13.9 - - + -
849A PHE* 3.5 37.1 - - + -
861A MET* 3.6 11.1 - - - +
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Residues in contact with ALA 703 (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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699A LEU 3.1 12.7 + - - +
700A LYS 3.1 10.0 + - - +
702A ALA* 1.3 78.2 - - - +
704A LYS* 1.3 62.3 + - - +
706A LEU* 3.3 2.6 + - - +
707A ALA* 3.0 27.1 + - - +
725A VAL* 4.2 20.0 - - + -
774A GLN* 4.5 2.9 - - - +
775A GLU* 3.7 25.4 - - - +
778A ILE* 3.9 15.9 - - + -
845A PHE* 6.1 0.2 - - - -
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Residues in contact with LYS 704 (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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700A LYS 3.0 11.2 + - - +
701A SER* 3.2 11.6 + - - +
703A ALA* 1.3 76.7 - - - +
705A LEU* 1.3 68.0 + - + +
707A ALA* 3.7 4.5 + - - +
708A ALA* 3.1 26.0 + - + +
771A ALA 5.8 0.7 - - - -
775A GLU* 2.8 49.5 + - - +
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Residues in contact with LEU 705 (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 SER* 3.2 12.5 + - - +
702A ALA* 4.0 4.3 - - - +
703A ALA 3.2 0.8 - - - -
704A LYS* 1.3 88.0 - - + +
706A LEU* 1.3 63.5 + - + +
707A ALA 3.2 0.7 - - - -
708A ALA* 3.2 12.6 + - + +
720A ARG* 2.8 26.0 + - - -
854A HIS* 5.6 9.7 + - + +
858A LEU* 5.9 4.3 - - - -
859A ASP 4.7 8.7 - - - +
861A MET* 3.2 43.3 - - + -
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Residues in contact with LEU 706 (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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702A ALA* 3.0 28.3 + - + +
703A ALA 3.3 4.0 + - - +
705A LEU* 1.3 78.0 - - + +
707A ALA* 1.3 58.3 + - - +
720A ARG* 3.3 9.8 + - - +
723A CYS* 2.8 47.9 + - + +
724A ALA 5.0 3.8 - - - +
725A VAL* 3.5 40.6 - - + -
726A HIS 5.5 0.2 - - - +
845A PHE* 5.1 0.4 - - + -
849A PHE* 3.6 25.1 - - + -
853A LEU* 3.2 38.4 - - + -
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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