Contacts of the helix formed by residues 829 - 837 (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 ASP 829 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C LEU* 5.5 13.4 - - - +
43C CYS 5.6 1.3 - - - +
269C LYS* 3.8 27.1 + - - -
270C PHE* 6.6 0.4 - - + -
607C ARG* 3.4 28.7 + - - -
680C GLN* 5.1 1.0 + - - -
747C THR* 4.8 0.7 - - - -
827C MET 3.8 2.8 + - - +
828C LEU* 1.4 75.6 - - - +
830C ARG* 1.4 66.5 + - - +
831C ASP* 4.1 14.8 - - - +
832C GLU* 3.1 29.9 + - + +
833C ASP* 3.2 9.8 + - - +
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Residues in contact with ARG 830 (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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41C LEU* 6.2 0.6 - - - +
42C GLY* 2.9 40.9 + - - +
43C CYS* 4.0 20.7 + - + +
45C GLU* 6.1 0.4 - - - +
741C GLU* 5.2 1.2 + - - -
743C PHE* 3.3 52.0 - - - +
744C TYR* 2.8 49.3 + - - +
745C LEU* 3.5 15.7 + - - +
747C THR* 4.0 18.9 - - - +
829C ASP* 1.4 70.6 - - - +
831C ASP* 1.4 57.5 + - - +
833C ASP* 3.3 10.1 + - - +
834C MET* 3.0 38.5 + - - +
1223C ARG 4.3 11.2 - - - +
1225C PRO* 4.4 7.4 - - + -
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Residues in contact with ASP 831 (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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43C CYS 5.5 0.2 + - - -
270C PHE* 4.5 31.6 - - + -
829C ASP* 3.2 17.5 - - - +
830C ARG* 1.4 75.0 - - - +
832C GLU* 1.3 74.3 + - - +
834C MET* 3.8 1.9 + - - +
835C LEU* 3.7 15.4 + - - +
1223C ARG* 3.8 51.3 + - + +
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Residues in contact with GLU 832 (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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607C ARG* 3.0 47.3 + - - +
608C LEU* 4.2 13.0 + - + +
826C CYS* 5.4 1.7 - - - -
827C MET 5.0 0.7 - - - +
828C LEU* 3.4 30.4 - - + +
829C ASP* 3.1 32.8 + - + +
831C ASP* 1.3 80.7 + - - +
833C ASP* 1.3 68.2 + - - +
835C LEU* 3.1 23.9 + - - +
836C ILE* 3.2 19.2 + - + +
1223C ARG* 5.7 0.4 - - - +
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Residues in contact with ASP 833 (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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741C GLU* 4.0 10.4 - - - +
744C TYR* 3.0 28.8 + - - -
747C THR* 4.3 11.7 - - - -
748C HIS* 2.7 36.9 + - - -
828C LEU* 3.9 20.5 - - + +
829C ASP 3.2 13.2 + - - +
830C ARG* 3.7 10.6 + - - +
832C GLU* 1.3 78.3 - - - +
834C MET* 1.3 67.3 + - - +
835C LEU 3.0 1.2 + - - -
837C THR* 3.2 28.7 + - - +
838C GLY 4.6 0.2 + - - -
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Residues in contact with MET 834 (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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741C GLU* 3.7 45.0 - - + +
743C PHE* 4.1 13.0 - - + -
830C ARG* 3.0 25.5 + - + +
831C ASP 4.4 3.1 - - - +
833C ASP* 1.3 78.5 - - - +
835C LEU* 1.3 61.5 + - - +
837C THR 5.0 0.2 - - - -
838C GLY* 4.6 6.9 + - - +
1212C LEU* 5.5 1.1 - - + -
1220C LEU* 3.2 21.3 - - + +
1222C THR 4.2 4.7 - - - +
1223C ARG* 3.4 37.0 - - + +
1224C GLY* 3.8 3.4 - - - +
1228C TYR* 3.6 42.4 - - + -
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Residues in contact with LEU 835 (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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610C THR* 4.4 13.0 - - - +
611C SER 5.5 2.2 - - - +
664C VAL* 3.7 26.7 - - + +
665C GLY 4.2 10.5 - - - +
831C ASP 3.7 10.0 + - - +
832C GLU* 3.1 11.4 + - - +
833C ASP 3.0 0.6 + - - -
834C MET* 1.3 82.5 - - - +
836C ILE* 1.3 69.4 + - + +
838C GLY* 3.6 8.5 + - - -
907C PRO* 4.0 21.2 - - + +
1220C LEU* 3.9 25.3 - - + +
1223C ARG* 3.3 40.4 - - - +
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Residues in contact with ILE 836 (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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608C LEU* 4.3 21.3 - - + -
610C THR* 4.0 25.6 - - + +
665C GLY 4.9 7.6 - - - +
666C HIS 5.7 2.9 + - - +
667C ILE* 4.4 22.2 - - + -
805C ARG* 4.5 9.2 + - - -
808C VAL* 4.6 13.5 - - + -
809C VAL* 6.3 0.9 - - + -
828C LEU* 5.1 9.9 - - + -
832C GLU* 3.2 22.4 + - + +
833C ASP* 4.2 0.9 - - - +
835C LEU* 1.3 92.7 - - + +
837C THR* 1.4 68.2 + - + +
907C PRO* 4.4 11.4 - - - +
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Residues in contact with THR 837 (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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741C GLU* 5.8 0.3 + - - -
742C HIS* 5.3 2.3 + - - -
744C TYR* 3.9 6.9 + - - -
748C HIS* 3.4 24.5 + - + +
801C GLY 5.0 2.6 + - - -
805C ARG* 3.9 32.9 + - + +
808C VAL* 5.6 7.6 - - + -
828C LEU* 4.6 5.6 - - + -
833C ASP* 3.2 39.0 + - - +
836C ILE* 1.4 79.2 - - + +
838C GLY* 1.3 69.0 + - - +
907C PRO* 5.8 0.9 - - - -
908C SER 3.7 11.1 - - - +
910C THR* 5.4 1.0 - - - -
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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