Contacts of the helix formed by residues 939 - 948 (chain A) in PDB entry 4YZC
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 HIS 939 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A PRO* 3.2 29.6 + - + -
798A GLU* 3.5 19.8 + - - -
803A VAL* 4.0 20.3 - - + +
868A ALA 5.1 9.6 - - - -
869A VAL* 3.7 26.8 + - + -
937A PHE 3.3 0.8 - - - -
938A PRO* 1.3 91.1 - - + +
940A LEU* 1.3 58.1 + - - +
941A LEU 3.5 0.7 - - - -
942A ALA* 4.2 2.2 - - + -
943A HIS* 2.9 33.6 + - + +
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Residues in contact with LEU 940 (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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842A PHE* 3.9 18.8 - - + -
869A VAL* 4.6 14.4 + - + +
897A VAL* 3.9 21.5 - - + -
900A LEU* 4.0 24.0 - - + -
901A LEU* 4.2 7.6 - - + -
904A MET* 3.9 28.5 - - + -
933A PHE* 4.7 8.5 - - + -
934A THR* 5.4 1.8 - - - +
937A PHE* 3.1 29.4 + - + +
938A PRO 3.3 0.4 - - - -
939A HIS* 1.3 77.3 - - - +
941A LEU* 1.3 56.5 + - - +
943A HIS* 3.9 1.0 - - + +
944A THR* 2.6 47.0 + - - +
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Residues in contact with LEU 941 (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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800A HIS* 3.4 33.1 - - + +
804A ILE* 3.9 15.7 - - + -
830A PRO* 4.3 11.4 - - + +
833A TRP* 4.2 10.1 - - + -
838A GLN* 3.7 34.8 - - + +
841A PHE* 3.7 30.7 - - + -
842A PHE* 3.6 23.7 - - + -
934A THR* 4.8 1.5 - - + +
937A PHE 4.7 0.8 + - - -
938A PRO 4.6 1.4 + - - -
939A HIS 3.5 0.2 - - - -
940A LEU* 1.3 78.6 - - - +
942A ALA* 1.3 58.9 + - - +
944A THR* 3.3 0.9 + - - -
945A TYR* 2.8 33.5 + - + +
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Residues in contact with ALA 942 (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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803A VAL* 3.8 24.7 - - + -
804A ILE* 3.7 23.1 - - + +
807A GLU* 4.6 20.1 - - + +
830A PRO* 5.8 0.2 - - - -
938A PRO 5.0 1.2 + - - +
939A HIS* 3.7 4.6 + - + +
940A LEU 3.4 0.4 - - - -
941A LEU* 1.3 78.8 - - - +
943A HIS* 1.3 63.3 + - - +
945A TYR* 3.3 4.8 + - - +
946A ARG* 3.1 28.1 + - - +
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Residues in contact with HIS 943 (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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861A GLN 4.4 4.9 + - - -
862A LEU* 2.6 44.2 + - + +
865A GLY* 3.7 35.4 - - - -
866A GLY 4.5 1.2 + - - -
869A VAL* 3.7 28.4 - - + +
897A VAL* 4.6 4.2 - - + +
939A HIS* 2.9 20.9 + - + +
940A LEU* 3.9 1.8 - - + +
942A ALA* 1.3 77.8 - - - +
944A THR* 1.3 66.8 + - - +
946A ARG* 3.4 4.0 + - - +
947A ALA* 3.0 24.7 + - + +
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Residues in contact with THR 944 (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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841A PHE* 4.1 12.3 - - + -
842A PHE* 4.0 11.6 - - + -
845A VAL* 3.8 30.3 - - + -
862A LEU* 4.0 21.0 - - + +
897A VAL* 4.4 1.7 - - - +
901A LEU* 4.0 7.4 - - + +
940A LEU* 2.6 38.4 + - - +
941A LEU 3.8 2.5 - - - -
943A HIS* 1.3 76.4 - - - +
945A TYR* 1.3 63.9 + - - +
947A ALA* 3.9 0.2 - - - -
948A MET* 3.0 35.3 + - + +
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Residues in contact with TYR 945 (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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807A GLU* 4.8 4.0 - - - -
825A HIS 5.2 1.2 + - - -
828A LYS* 3.5 13.5 + - - +
829A HIS* 4.1 6.3 - + - -
830A PRO* 3.5 29.9 - - + +
833A TRP* 3.5 30.1 - + - -
841A PHE* 3.8 9.1 - + + -
941A LEU* 2.8 18.4 + - + +
942A ALA* 3.6 6.1 - - - +
943A HIS 3.3 0.2 - - - -
944A THR* 1.3 78.0 - - - +
946A ARG* 1.3 91.2 + - + +
948A MET 3.5 1.7 + - - -
949A GLU* 3.6 1.7 + - - +
960A TYR* 2.6 30.0 + - + -
961A TYR* 2.4 63.7 + + - -
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Residues in contact with ARG 946 (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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807A GLU* 2.5 45.7 + - + +
808A LEU* 5.6 0.6 - - - +
811A LYS* 3.6 22.4 - - - +
829A HIS* 3.8 15.6 - - - -
861A GLN* 5.3 1.0 - - - +
942A ALA 3.1 18.7 + - - +
943A HIS* 4.0 3.6 - - - +
945A TYR* 1.3 91.0 - - + +
947A ALA* 1.3 66.1 + - - +
948A MET 3.4 0.3 + - - -
949A GLU* 2.9 49.3 + - - +
961A TYR* 5.8 0.2 - - - -
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Residues in contact with ALA 947 (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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858A ILE* 5.2 2.5 - - - +
861A GLN* 3.5 47.3 - - + +
862A LEU* 3.8 23.1 - - + -
943A HIS* 3.0 21.9 + - + +
944A THR 3.9 3.6 - - - +
946A ARG* 1.3 77.8 - - - +
948A MET* 1.3 62.1 + - + +
949A GLU 3.3 1.7 + - - -
950A LEU* 3.9 12.3 + - - +
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Residues in contact with MET 948 (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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841A PHE* 4.5 4.5 - - + -
845A VAL* 3.8 33.2 - - + -
848A ARG* 4.3 1.6 - - + -
849A ILE* 4.0 25.8 - - + -
858A ILE* 4.3 10.5 - - + +
862A LEU* 5.0 11.7 - - - -
944A THR* 3.0 23.7 + - + +
945A TYR 3.5 0.2 + - - -
946A ARG 3.3 0.4 - - - -
947A ALA* 1.3 77.1 - - + +
949A GLU* 1.3 56.5 + - - +
950A LEU* 3.0 6.5 - - - -
951A CYS* 2.9 54.8 + - - +
952A SER 3.7 1.9 + - - -
957A PHE* 3.9 21.7 - - + -
961A TYR* 3.4 19.1 + - + +
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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