Contacts of the helix formed by residues 939 - 948 (chain C) in PDB entry 4YZ9
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797C PRO* 3.1 29.7 + - + +
798C GLU* 3.7 24.1 + - - -
803C VAL* 3.8 23.6 - - + +
869C VAL* 4.1 24.5 + - + +
937C PHE 3.0 1.0 + - - -
938C PRO* 1.3 79.2 - - + +
940C LEU* 1.3 55.7 + - - +
941C LEU 3.4 1.8 - - - -
942C ALA* 4.1 3.6 - - + -
943C HIS* 2.7 39.0 + - + +
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Residues in contact with LEU 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C PHE* 4.0 17.5 - - + -
869C VAL* 3.9 15.7 - - + +
897C VAL* 4.0 22.7 - - + -
900C LEU* 4.0 23.8 - - + -
901C LEU* 4.0 9.9 - - + -
904C MET* 3.8 30.5 - - + -
933C PHE* 4.9 8.1 - - + +
934C THR* 5.7 2.7 - - + +
937C PHE* 2.9 25.1 + - + +
938C PRO 3.4 0.4 - - - -
939C HIS* 1.3 76.4 - - - +
941C LEU* 1.3 57.1 + - - +
943C HIS* 3.8 0.7 - - + +
944C THR* 2.7 46.3 + - - +
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Residues in contact with LEU 941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C HIS* 3.5 35.8 + - + +
804C ILE* 3.9 14.1 - - + -
830C PRO* 4.2 13.2 - - + +
833C TRP* 4.2 9.9 - - + -
838C GLN* 3.8 31.0 - - + +
841C PHE* 3.5 32.3 - - + -
842C PHE* 3.7 21.4 - - + -
934C THR* 5.1 0.8 - - + +
937C PHE 4.8 0.2 + - - -
939C HIS 3.4 0.2 - - - -
940C LEU* 1.3 75.9 - - - +
942C ALA* 1.3 57.7 + - - +
945C TYR* 2.7 40.8 + - + +
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Residues in contact with ALA 942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803C VAL* 3.8 30.3 - - + +
804C ILE* 3.7 19.4 - - + +
807C GLU* 5.6 11.5 - - + -
938C PRO 5.2 1.0 + - - +
939C HIS* 3.5 7.5 + - + +
940C LEU 3.4 0.4 - - - -
941C LEU* 1.3 77.1 - - - +
943C HIS* 1.3 58.9 + - - +
945C TYR* 3.7 6.1 - - - +
946C ARG* 2.9 31.7 + - - +
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Residues in contact with HIS 943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861C GLN 4.0 6.7 + - - -
862C LEU* 2.6 43.7 + - + -
864C ARG* 5.0 1.6 - - + -
865C GLY* 3.9 25.8 - - - -
866C GLY* 4.7 1.2 + - - -
869C VAL* 3.5 30.5 - - + +
897C VAL* 4.6 8.5 - - + -
939C HIS* 2.7 28.0 + - + +
940C LEU 3.8 2.2 - - - +
942C ALA* 1.3 74.5 - - - +
944C THR* 1.3 58.4 + - - +
946C ARG* 3.8 4.9 - - - +
947C ALA* 2.9 29.7 + - + +
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Residues in contact with THR 944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C PHE* 3.8 17.7 - - + -
842C PHE* 4.1 7.7 - - + -
845C VAL* 3.7 29.8 - - + -
862C LEU* 4.0 16.0 - - + +
897C VAL* 4.7 0.2 - - - +
901C LEU* 3.8 16.1 - - + +
940C LEU* 2.7 42.5 + - - +
941C LEU 3.9 2.2 - - - -
943C HIS* 1.3 73.9 - - - +
945C TYR* 1.3 63.4 + - - +
948C MET* 3.0 34.1 + - + +
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Residues in contact with TYR 945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804C ILE* 6.4 0.2 - - + -
807C GLU* 4.4 24.0 - - - -
811C LYS* 5.2 4.3 - - - -
825C HIS* 4.8 11.1 + - - -
828C LYS 4.9 0.9 + - - -
829C HIS* 4.5 10.6 - + - -
830C PRO* 3.5 43.6 - - + +
833C TRP* 3.8 12.8 - + - -
841C PHE* 3.8 11.2 - + + -
941C LEU* 2.7 25.3 + - + +
942C ALA* 3.7 7.6 - - - +
944C THR* 1.3 72.9 - - - +
946C ARG* 1.3 65.8 + - - +
949C GLU* 4.2 8.0 - - - +
960C TYR 3.3 26.3 + - - -
961C TYR* 2.7 53.8 + + - -
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Residues in contact with ARG 946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807C GLU* 5.1 9.2 - - - +
861C GLN* 4.9 1.4 - - - +
942C ALA 2.9 16.8 + - - +
943C HIS* 3.8 4.0 - - - +
945C TYR* 1.3 79.5 - - + +
947C ALA* 1.3 66.7 + - - +
949C GLU* 3.2 29.4 + - - +
950C LEU* 5.5 0.3 - - - +
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Residues in contact with ALA 947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858C ILE* 5.6 1.7 - - - +
861C GLN* 3.3 30.6 - - + +
862C LEU* 3.9 39.9 - - + +
943C HIS* 2.9 18.8 + - + +
944C THR 4.0 3.4 - - - +
946C ARG* 1.3 77.8 - - - +
948C MET* 1.3 60.2 + - + +
949C GLU 3.2 4.2 + - - -
950C LEU* 3.7 10.7 + - - +
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Residues in contact with MET 948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C PHE* 4.6 0.4 - - + -
845C VAL* 3.8 39.5 - - + -
848C ARG* 4.2 8.7 - - + -
849C ILE* 4.4 9.2 - - + -
858C ILE* 4.4 16.6 - - + +
862C LEU* 4.9 10.5 - - + -
944C THR* 3.0 21.1 + - + +
946C ARG 3.2 0.2 - - - -
947C ALA* 1.3 75.0 - - - +
949C GLU* 1.3 64.2 + - - +
950C LEU* 3.0 3.8 - - - +
951C CYS* 2.9 44.3 + - + +
952C SER 3.5 5.7 + - - -
957C PHE* 3.8 24.6 - - + -
961C TYR* 3.3 22.9 + - + +
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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