Contacts of the helix formed by residues 874 - 884 (chain C) in PDB entry 2CKJ
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 LEU 874 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C ILE* 3.9 20.0 - - + -
803C GLU* 4.0 29.8 - - + +
804C THR* 4.1 18.2 - - + +
873C ASP* 1.3 88.3 + - - +
875C SER* 1.3 49.7 + - - -
876C GLN* 2.7 18.0 + - - -
877C SER* 3.0 24.3 + - - +
878C ILE* 3.1 17.2 + - + +
911C ALA* 4.5 14.6 - - + +
915C PHE* 4.5 21.3 - - + -
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Residues in contact with SER 875 (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 HIS* 2.9 35.5 + - - -
866C SER* 5.0 1.2 + - - -
868C VAL* 3.3 28.8 - - - +
872C GLN* 2.8 23.1 + - - -
873C ASP* 3.1 4.9 + - - -
874C LEU* 1.3 73.9 - - - +
876C GLN* 1.3 59.9 + - - +
878C ILE* 3.5 8.1 - - - +
879C MET 3.2 16.1 + - - -
901C LEU* 3.6 17.2 - - - +
909C ASN 4.0 5.5 + - - -
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Residues in contact with GLN 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C LEU* 4.3 19.7 - - + +
872C GLN* 4.0 27.5 + - + +
873C ASP 4.4 1.5 + - - +
874C LEU 2.7 1.7 + - - -
875C SER* 1.3 76.2 - - - +
877C SER* 1.3 67.9 + - - +
878C ILE 2.9 1.6 - - - -
879C MET* 3.0 15.6 + - - +
880C GLU* 3.0 37.0 + - - +
901C LEU* 3.9 18.9 - - + +
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Residues in contact with SER 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C LEU* 3.0 17.7 + - - +
876C GLN* 1.3 80.4 - - - +
878C ILE* 1.4 60.2 + - - +
880C GLU* 3.3 17.3 - - - +
881C ARG* 3.1 21.8 + - - +
915C PHE* 4.7 16.1 - - - -
1011C THR* 4.0 21.8 + - - +
1012C VAL* 5.0 10.0 - - - +
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Residues in contact with ILE 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C HIS* 3.5 31.0 - - + +
843C PHE* 5.1 7.4 - - + -
874C LEU* 3.1 19.9 + - + +
875C SER* 3.5 7.6 - - - +
876C GLN 2.9 0.2 - - - -
877C SER* 1.4 73.5 - - - +
879C MET* 1.3 65.7 + - - +
880C GLU 3.0 2.7 + - - -
881C ARG 3.2 9.0 + - - -
882C ALA* 3.2 10.9 + - - +
910C THR 4.2 7.6 - - - +
911C ALA 4.5 0.4 - - - +
915C PHE* 3.3 51.5 - - + +
916C GLY* 3.7 6.7 - - - -
3007C GOL 3.5 33.2 - - - +
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Residues in contact with MET 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C LEU* 4.8 15.3 - - + -
843C PHE* 3.8 26.0 - - + -
864C HIS* 3.3 33.0 - - + +
866C SER* 3.9 5.2 - - - +
875C SER 3.2 8.2 + - - +
876C GLN* 3.0 11.9 + - - +
878C ILE* 1.3 77.3 - - - +
880C GLU* 1.3 63.9 + - - +
882C ALA* 3.1 20.0 - - - +
883C LEU* 3.1 15.6 + - + +
898C THR 5.0 0.7 - - - +
899C GLY* 3.3 36.6 - - - +
900C ARG 3.6 13.2 - - - +
901C LEU* 3.7 20.2 - - + -
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Residues in contact with GLU 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C LEU* 3.9 18.5 - - + +
876C GLN* 3.0 37.2 + - - +
877C SER* 3.3 12.9 - - - +
878C ILE 3.0 0.2 - - - -
879C MET* 1.3 75.2 - - - +
881C ARG* 1.3 66.6 + - - +
882C ALA 2.8 3.4 - - - -
883C LEU* 2.7 23.2 + - - +
884C PHE* 2.9 27.7 + - + -
1011C THR* 4.2 18.9 + - + -
1143C PHE* 4.0 27.2 - - + -
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Residues in contact with ARG 881 (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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877C SER 3.1 9.5 + - - +
878C ILE* 3.2 2.0 + - - +
880C GLU* 1.3 79.1 - - - +
882C ALA* 1.3 59.3 + - - +
884C PHE* 3.9 11.2 - - + -
885C HIS* 2.7 49.7 + - + +
914C GLY 3.6 16.6 - - - -
915C PHE* 3.5 43.6 - - + +
916C GLY 4.6 0.2 - - - -
917C GLY* 4.2 6.1 - - - +
1006C PHE* 3.6 18.2 - - - -
1007C GLY 3.2 21.6 + - - -
1009C SER 3.4 24.2 + - - +
1010C PHE* 5.4 0.2 - - - +
1011C THR* 4.6 13.9 - - + +
1080C ALA* 5.3 7.5 - - - +
1151C PHE* 3.7 14.9 - - - -
1262C GLU* 5.8 1.1 - - - -
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Residues in contact with ALA 882 (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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843C PHE* 4.4 17.5 - - + -
864C HIS* 5.5 8.5 + - + +
878C ILE 3.2 9.7 + - - +
879C MET* 3.1 19.3 - - - +
880C GLU 2.7 0.4 + - - -
881C ARG* 1.3 77.2 - - - +
883C LEU* 1.3 67.9 + - + +
885C HIS* 3.1 13.0 + - - +
886C MET* 3.3 10.6 + - - +
916C GLY 3.4 23.5 + - - +
919C GLN 4.7 4.0 - - - +
920C GLY 4.4 6.1 - - - +
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Residues in contact with LEU 883 (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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713C LEU* 4.1 35.2 - - + -
714C LYS* 4.6 7.9 - - - +
715C ILE* 4.2 17.3 - - + -
864C HIS* 3.6 18.4 - - + +
879C MET* 3.1 21.4 + - - +
880C GLU* 2.7 14.5 + - - +
882C ALA* 1.3 71.1 - - - +
884C PHE* 1.4 52.0 + - - +
885C HIS 2.6 15.9 + - - -
886C MET* 3.0 23.9 + - - +
897C GLY* 3.8 17.3 - - - +
898C THR 3.1 32.3 - - - +
899C GLY 4.8 0.2 - - - +
955C HIS* 3.2 12.4 + - - -
1143C PHE* 5.0 6.1 - - + -
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Residues in contact with PHE 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C ILE* 4.2 10.3 - - + -
880C GLU* 2.9 40.6 + - + -
881C ARG* 3.8 6.3 - - - +
883C LEU* 1.4 72.8 - - - +
885C HIS* 1.3 78.8 + - + +
886C MET 3.8 0.4 - - - -
887C ASP* 3.7 2.4 - - - +
955C HIS* 3.8 8.5 - - - -
956C PHE* 3.4 44.0 - + + -
1005C LYS* 3.5 11.3 + - - -
1011C THR* 4.3 17.7 - - + -
1141C TYR* 4.1 34.3 - + + -
1143C PHE* 4.0 21.3 - + - -
1150C PRO* 4.4 10.5 - - + -
1151C PHE* 4.2 16.6 - + + -
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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