Contacts of the helix formed by residues 797 - 806 (chain D) in PDB entry 6CET
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 GLN 797 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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775D TYR* 2.3 36.8 + - + +
777D LEU* 5.5 8.1 - - + -
780D GLU* 5.2 12.1 + - - +
795D ALA* 4.2 14.8 - - - +
796D GLN* 1.3 93.2 - - - +
798D VAL* 1.3 60.7 + - - +
799D PHE 3.1 2.6 + - - -
800D GLU* 3.5 22.7 + - - +
1283D VAL 5.3 4.2 + - - -
1284D ASP* 5.4 3.8 - - - +
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Residues in contact with VAL 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775D TYR* 4.3 4.2 - - + -
795D ALA 5.1 4.8 - - - +
796D GLN 4.6 1.8 - - - +
797D GLN* 1.3 77.4 - - - +
799D PHE* 1.3 77.4 + - + +
801D GLU* 2.9 45.2 - - + +
802D PHE* 3.0 14.6 + - - +
979D GLU* 3.6 27.6 - - + +
986D PHE* 3.6 27.4 - - + -
1369D TRP* 4.4 21.8 - - + -
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Residues in contact with PHE 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796D GLN* 3.2 32.1 + - + +
797D GLN 3.1 1.4 - - - -
798D VAL* 1.3 84.5 - - + +
800D GLU* 1.3 59.4 + - - +
802D PHE* 3.4 24.5 - + + +
803D ILE* 2.8 31.4 + - - +
986D PHE* 6.4 2.7 - + - -
1284D ASP* 5.3 12.1 - - + -
1285D ASP 5.6 2.0 - - - +
1286D PHE* 3.5 41.7 - + + -
1369D TRP* 3.3 48.2 - + - -
1391D MET* 4.6 20.0 - - + -
1392D ALA* 4.7 6.3 - - + -
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Residues in contact with GLU 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775D TYR* 4.9 9.9 + - + +
797D GLN* 3.5 18.7 + - - +
798D VAL 3.3 1.0 - - - -
799D PHE* 1.3 74.7 - - - +
801D GLU* 1.3 60.5 + - - +
803D ILE* 3.2 10.9 - - + +
804D CYS* 2.9 30.0 + - - +
1284D ASP* 2.9 34.4 - - + +
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Residues in contact with GLU 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775D TYR* 3.6 42.4 - - + -
797D GLN 4.2 1.2 + - - -
798D VAL* 2.9 39.1 - - + +
800D GLU* 1.3 75.9 - - - +
802D PHE* 1.3 62.6 + - - +
804D CYS* 4.1 5.6 - - - -
805D GLN* 2.9 50.3 + - + +
856D MET* 5.4 2.3 - - - +
983D LEU* 3.4 36.9 - - + +
986D PHE* 3.8 6.9 - - - -
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Residues in contact with PHE 802 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798D VAL* 3.0 20.2 + - + +
799D PHE* 3.4 27.4 - + + +
801D GLU* 1.3 87.3 - - - +
803D ILE* 1.3 66.5 + - + +
805D GLN* 3.9 4.3 + - - +
806D ARG 4.3 0.2 + - - -
807D LEU 4.1 0.5 + - - -
808D MET* 3.3 67.1 - - + +
986D PHE* 3.4 46.9 - + + -
987D VAL* 6.4 0.2 - - + -
1286D PHE* 6.4 0.2 - + - -
1290D GLN* 5.0 4.7 - - + -
1391D MET* 4.1 39.9 - - + -
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Residues in contact with ILE 803 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799D PHE 2.8 19.7 + - - +
800D GLU* 3.2 20.2 - - + +
802D PHE* 1.3 80.3 - - + +
804D CYS* 1.3 62.3 + - + +
807D LEU* 3.4 38.9 + - + +
808D MET* 4.9 1.1 - - - -
1287D ALA* 5.6 1.3 - - + -
1290D GLN* 3.4 44.6 - - + +
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Residues in contact with CYS 804 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800D GLU 2.9 19.7 + - - +
801D GLU* 3.2 7.8 + - - +
803D ILE* 1.3 81.7 - - + +
805D GLN* 1.3 74.3 + - - +
807D LEU 4.7 0.6 + - - -
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Residues in contact with GLN 805 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771D THR* 5.5 7.3 - - - +
772D GLU 4.5 2.3 - - - -
773D GLY* 3.4 23.6 + - - +
801D GLU* 2.9 37.4 + - + +
802D PHE* 3.9 2.4 + - - +
803D ILE 3.5 0.4 - - - -
804D CYS* 1.3 88.5 - - - +
806D ARG* 1.3 66.7 + - + +
808D MET* 5.8 1.1 - - + -
811D TYR* 6.0 1.0 - - - -
852D TYR* 4.9 3.8 + - - -
854D LEU* 3.3 30.3 - - + +
855D SER 3.5 12.9 + - - -
856D MET* 3.4 30.0 - - + +
866D LYS* 5.5 6.7 - - - +
983D LEU* 6.0 1.6 - - + -
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Residues in contact with ARG 806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D PHE 4.3 2.4 + - - -
804D CYS 5.0 0.4 - - - -
805D GLN* 1.3 83.8 - - + +
807D LEU* 1.3 62.1 - - - +
808D MET* 3.0 35.4 - - + +
809D GLN* 3.9 10.7 + - - +
810D GLY* 3.0 22.7 + - - -
811D TYR* 4.7 6.0 + - - -
812D GLN* 3.9 15.7 + - - +
852D TYR* 5.7 4.3 - - + -
854D LEU* 4.1 8.5 - - + -
866D LYS* 3.6 33.3 - - + +
871D THR* 3.9 24.5 + - - +
986D PHE 3.8 6.3 + - - -
987D VAL* 3.1 46.7 + - - +
990D VAL* 5.2 10.1 - - - +
991D GLU* 4.5 4.4 + - - +
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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