Contacts of the helix formed by residues 805 - 814 (chain C) in PDB entry 1JZ3
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 ALA 805 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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792C ASP 3.7 6.7 - - - +
793C ILE 3.4 26.9 - - - +
794C GLY* 4.9 2.5 - - - +
796C SER* 4.3 1.8 - - - -
802C ASP* 3.0 23.5 + - - +
804C ASN* 1.3 80.2 - - - +
806C TRP* 1.4 67.6 + - - +
807C VAL* 4.2 2.7 - - + +
808C GLU* 3.0 18.8 + - + -
809C ARG* 3.0 11.8 + - - +
1001C PRO* 4.7 7.2 - - - -
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Residues in contact with TRP 806 (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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791C ASN 5.1 6.2 + - - -
792C ASP* 3.3 15.1 + - - +
804C ASN 3.6 1.6 + - - -
805C ALA* 1.4 73.3 - - - +
807C VAL* 1.3 65.4 + - - +
809C ARG* 2.7 43.4 + - - +
810C TRP* 3.0 63.6 + + + -
877C PRO* 4.4 5.4 - - + -
878C HIS* 3.4 38.1 - - + -
991C MET* 3.3 26.8 - - + +
1001C PRO* 3.8 21.8 - - + +
1002C SER 5.0 0.2 - - - -
1003C VAL* 4.4 13.1 + - + +
1008C GLN* 3.6 40.2 - - + -
8407C DMS 5.0 1.9 + - - -
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Residues in contact with VAL 807 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C PRO* 3.6 33.4 - - + -
792C ASP* 2.9 24.7 + - + +
793C ILE* 3.6 24.2 - - + +
796C SER* 4.6 0.2 - - - -
805C ALA* 3.1 3.5 - - + -
806C TRP* 1.3 76.9 - - - +
808C GLU* 1.3 78.0 + - + +
810C TRP* 3.4 9.6 + - - +
811C LYS* 2.9 47.5 + - + +
816C TYR* 4.3 9.6 - - + +
968C MET* 5.9 0.4 - - + -
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Residues in contact with GLU 808 (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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796C SER* 2.7 33.4 + - - +
797C GLU 5.4 0.2 - - - -
801C ILE* 3.4 25.5 - - + +
802C ASP 3.0 30.7 - - - +
803C PRO* 3.9 11.9 - - + -
805C ALA* 3.0 6.5 + - + +
807C VAL* 1.3 81.1 - - + +
809C ARG* 1.3 62.5 + - - +
811C LYS* 3.0 31.3 + - - +
812C ALA* 2.7 33.7 + - - +
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Residues in contact with ARG 809 (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 PRO 3.7 15.3 - - - +
804C ASN* 3.5 26.1 + - - +
805C ALA 3.0 11.2 + - - +
806C TRP* 2.7 69.1 + - + +
808C GLU* 1.3 78.0 - - - +
810C TRP* 1.3 63.9 + - - +
812C ALA* 3.8 4.1 - - - +
813C ALA* 3.0 25.1 + - - +
877C PRO* 3.5 22.6 - - + +
1001C PRO* 3.6 15.9 - - - +
8407C DMS 5.1 3.2 + - - -
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Residues in contact with TRP 810 (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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785C THR* 5.7 2.5 - - + -
786C ARG* 4.1 5.2 - - + -
788C PRO* 5.1 0.4 - - + -
792C ASP* 3.6 43.5 - - + -
806C TRP* 3.0 35.8 + + + +
807C VAL* 3.6 9.6 - - + +
809C ARG* 1.3 76.9 - - - +
811C LYS* 1.3 64.5 + - - +
813C ALA 3.2 1.2 + - - -
814C GLY 3.1 3.6 + - - -
815C HIS* 2.9 56.8 + + + +
816C TYR* 3.5 34.3 - + + -
877C PRO* 4.1 8.7 - - + -
878C HIS 2.8 23.9 + - - -
879C PRO* 4.0 2.2 - - - +
880C ALA* 3.7 28.5 - - + -
991C MET* 3.7 26.5 - - - -
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Residues in contact with LYS 811 (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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798C ALA* 6.3 0.2 - - - +
801C ILE* 4.4 9.3 - - - +
807C VAL* 2.9 35.8 + - + +
808C GLU* 3.0 32.1 + - - +
810C TRP* 1.3 77.7 - - - +
812C ALA* 1.3 60.6 + - - +
814C GLY* 3.0 20.1 + - - -
815C HIS 5.0 0.2 - - - +
816C TYR* 3.8 24.7 - - + +
817C GLN* 6.1 1.4 - - - +
844C HIS* 5.5 0.5 - - - -
968C MET* 6.3 1.3 - - + -
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Residues in contact with ALA 812 (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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808C GLU 2.7 22.5 + - - +
809C ARG* 4.1 4.0 - - - +
811C LYS* 1.3 75.1 - - - +
813C ALA* 1.3 58.7 + - - +
814C GLY 3.4 0.7 + - - -
844C HIS* 4.7 7.4 + - - -
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Residues in contact with ALA 813 (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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809C ARG 3.0 17.4 + - - +
810C TRP 3.8 0.2 - - - +
812C ALA* 1.3 76.0 - - - +
814C GLY* 1.3 60.4 + - - +
815C HIS* 3.6 17.2 + - + -
844C HIS* 3.6 12.1 + - - +
847C LYS* 5.7 0.2 - - - +
849C LEU* 3.7 17.7 - - + +
876C THR* 3.7 4.9 - - - +
877C PRO* 3.6 26.2 - - + -
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Residues in contact with GLY 814 (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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811C LYS 3.0 15.5 + - - -
812C ALA 3.1 1.4 + - - -
813C ALA* 1.3 79.3 - - - +
815C HIS* 1.3 68.0 + - - +
816C TYR 3.2 3.4 - - - -
817C GLN* 3.1 6.3 + - - -
818C ALA* 2.9 26.9 + - - +
844C HIS* 3.6 25.8 - - - -
849C LEU* 4.1 3.1 - - - -
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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