Contacts of the helix formed by residues 836 - 847 (chain A) in PDB entry 2XT6
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 836 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A VAL* 1.3 79.5 - - - +
837A LYS* 1.3 66.2 + - - +
838A ALA* 3.6 16.7 - - - +
839A MET* 3.0 43.8 + - - +
840A LEU* 3.3 5.5 + - - +
1086A THR* 4.1 4.0 - - - -
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Residues in contact with LYS 837 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836A ASP* 1.3 71.6 - - - +
838A ALA* 1.4 53.1 + - - +
840A LEU* 3.1 9.1 + - - +
841A GLN* 2.9 58.8 + - - +
871A ALA 6.1 0.2 - - - +
1082A ILE* 4.0 28.0 - - + -
1086A THR* 4.0 11.3 - - + +
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Residues in contact with ALA 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A ASP* 3.6 18.8 - - - +
837A LYS* 1.4 76.2 - - - +
839A MET* 1.4 51.9 + - - +
841A GLN* 3.7 10.1 - - - +
842A ARG* 2.8 36.0 + - - +
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Residues in contact with MET 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A VAL* 3.9 19.7 - - + -
836A ASP* 3.0 26.1 + - - +
838A ALA* 1.4 71.8 - - - +
840A LEU* 1.4 65.2 + - - +
842A ARG* 3.3 11.4 + - - +
843A ILE* 3.1 40.5 + - + +
888A SER* 3.8 30.5 - - - +
891A ALA* 3.8 26.2 - - + -
892A GLU* 5.0 10.5 - - + +
930A LEU* 4.6 4.9 - - - -
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Residues in contact with LEU 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A VAL* 3.7 21.5 - - + -
836A ASP 3.3 8.9 + - - +
837A LYS* 3.1 8.1 + - - +
839A MET* 1.4 75.9 - - + +
841A GLN* 1.3 56.9 + - - +
843A ILE* 3.2 5.5 + - + +
844A GLY 3.0 23.7 + - - -
871A ALA* 3.3 21.4 - - - +
876A ILE* 4.3 9.2 - - + -
884A LEU* 3.8 36.6 - - + +
1049A PHE* 4.9 0.9 - - + -
1082A ILE* 3.8 38.8 - - + -
1085A PHE* 4.0 23.8 - - + -
1086A THR* 4.1 4.7 - - + -
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Residues in contact with GLN 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A LYS* 2.9 48.8 + - - +
838A ALA* 3.7 8.1 - - - +
840A LEU* 1.3 73.5 - - - +
842A ARG* 1.3 56.6 + - - +
844A GLY* 3.3 0.9 + - - -
845A ASP* 2.9 37.5 + - - -
871A ALA* 3.6 19.2 + - - +
872A TYR* 3.6 52.8 + - + +
1082A ILE* 6.1 0.6 - - - +
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Residues in contact with ARG 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A ALA 2.8 22.4 + - - +
839A MET* 3.5 13.1 - - - +
841A GLN* 1.3 74.7 - - - +
843A ILE* 1.4 55.5 + - - +
845A ASP* 3.4 7.1 + - - +
846A ALA* 3.0 27.5 + - - +
891A ALA* 4.5 8.3 - - - +
929A LEU 4.0 6.2 + - - -
930A LEU* 3.7 37.9 + - + +
932A THR 2.6 30.5 + - - -
933A ASN* 3.5 15.2 + - - +
934A PRO* 3.5 29.9 - - - +
939A THR* 5.4 0.4 - - - +
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Residues in contact with ILE 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A MET* 3.1 30.4 + - + +
840A LEU* 3.7 6.1 - - + +
842A ARG* 1.4 74.3 - - - +
844A GLY* 1.3 54.2 + - - +
846A ALA* 3.4 8.7 - - - +
847A HIS* 2.7 30.5 + - + -
880A PHE* 4.1 9.4 - - + -
883A LEU 4.0 7.0 - - - +
884A LEU* 3.4 48.0 - - + +
887A GLY 3.9 0.4 - - - -
888A SER 3.6 13.9 - - - +
927A LEU* 3.8 22.9 - - + -
930A LEU* 3.6 28.7 - - + -
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Residues in contact with GLY 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A LEU 3.0 10.1 + - - -
841A GLN 3.3 3.6 + - - -
842A ARG 3.3 0.2 - - - -
843A ILE* 1.3 74.7 - - - +
845A ASP* 1.4 62.5 + - - +
847A HIS* 3.2 22.4 + - - +
848A LEU 4.2 1.2 + - - -
867A ARG 4.1 4.7 - - - -
868A ARG* 3.9 18.1 - - - +
871A ALA* 3.8 20.6 - - - +
880A PHE* 4.0 10.5 - - - -
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Residues in contact with ASP 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A GLN* 2.9 23.0 + - - +
842A ARG* 3.4 7.1 + - - +
844A GLY* 1.4 69.2 - - - +
846A ALA* 1.3 63.9 + - - +
848A LEU* 3.1 16.6 + - - +
849A ALA* 3.2 13.5 + - - +
868A ARG* 3.6 16.5 + - - +
872A TYR* 2.6 36.8 + - - -
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Residues in contact with ALA 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A ARG 3.0 13.9 + - - +
843A ILE* 3.4 17.0 - - - +
845A ASP* 1.3 76.1 - - - +
847A HIS* 1.3 59.4 + - + +
848A LEU 3.1 1.9 + - - -
849A ALA* 3.3 11.2 + - - -
924A PHE* 3.8 3.8 - - - -
926A PRO* 3.8 28.6 - - - +
929A LEU* 3.5 30.5 - - + +
930A LEU* 4.7 7.9 - - + -
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Residues in contact with HIS 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A ILE* 2.7 36.0 + - + -
844A GLY* 3.2 12.8 + - - +
845A ASP 3.2 0.8 - - - -
846A ALA* 1.3 74.9 - - - +
848A LEU* 1.3 57.7 + - - +
850A LEU* 4.4 5.7 - - - +
864A LEU* 3.4 53.2 - - + +
867A ARG* 3.5 44.4 + - + -
880A PHE* 4.2 11.7 - + - -
883A LEU* 4.3 8.2 - - + +
912A HIS 5.2 2.6 + - - -
924A PHE* 4.8 3.5 - - - -
926A PRO* 4.0 24.8 - - + +
927A LEU* 4.3 14.5 - - + +
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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