Contacts of the helix formed by residues 826 - 837 (chain A) in PDB entry 2QEP
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 THR 826 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773A LYS* 3.7 46.2 - - + +
801A ILE* 5.8 6.1 - - + -
820A GLN* 4.6 3.8 + - - +
822A PRO* 3.5 6.2 - - - +
823A LEU* 2.7 46.2 + - + +
825A ALA* 1.3 82.4 - - + +
827A VAL* 1.3 56.1 + - - +
828A ALA* 3.4 2.5 - - - -
829A ASP* 3.1 18.9 + - - +
830A PHE* 2.8 27.0 + - - +
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Residues in contact with VAL 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A PRO* 4.5 2.9 - - + -
823A LEU 3.2 17.3 - - - +
824A PRO* 3.3 13.8 + - + +
825A ALA 3.8 1.2 - - - -
826A THR* 1.3 68.9 - - - +
828A ALA* 1.3 68.0 + - - +
830A PHE* 3.0 16.2 + - + +
831A TRP* 3.0 26.1 + - - +
857A TYR* 3.2 26.9 - - + -
859A TYR* 3.4 32.1 - - + -
868A TYR* 3.7 29.8 - - + -
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Residues in contact with ALA 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A HIS* 3.6 37.0 - - + +
825A ALA 6.1 0.4 - - - +
826A THR 5.2 0.2 - - - -
827A VAL* 1.3 77.7 - - - +
829A ASP* 1.3 57.4 + - - +
831A TRP* 3.3 3.2 + - - +
832A GLN* 3.0 29.0 + - - +
868A TYR* 4.2 18.2 - - + +
869A HIS* 3.7 22.3 - - + +
871A TYR* 4.0 4.7 - - - -
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Residues in contact with ASP 829 (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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773A LYS* 4.8 10.9 - - - +
789A LEU* 3.8 27.4 - - + +
794A SER* 4.2 5.8 + - - -
795A HIS* 4.1 16.6 - - - +
796A SER* 4.8 7.7 + - - -
800A TYR 4.5 8.1 - - - +
801A ILE* 4.2 10.1 - - + -
825A ALA 4.5 4.4 - - - +
826A THR* 3.1 28.6 + - - +
827A VAL 3.0 0.4 - - - -
828A ALA* 1.3 77.2 - - - +
830A PHE* 1.3 66.1 + - - +
832A GLN* 3.1 14.7 + - - +
833A MET* 3.0 22.9 + - - +
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Residues in contact with PHE 830 (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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801A ILE* 4.1 12.0 - - + +
819A THR* 4.3 11.0 - - + -
822A PRO* 3.3 31.9 - - + -
826A THR 2.8 13.4 + - - +
827A VAL 3.0 7.6 + - - +
829A ASP* 1.3 74.3 - - - +
831A TRP* 1.3 70.1 + + - +
833A MET* 3.3 14.8 + - + +
834A VAL* 3.0 49.5 + - + +
842A ILE* 4.0 14.1 - - + -
859A TYR* 3.3 48.0 - + + -
942A ILE* 4.1 22.7 - - + -
944A HIS* 4.5 6.1 - - - -
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Residues in contact with TRP 831 (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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827A VAL* 3.0 28.0 + - + +
828A ALA* 3.8 5.6 - - - +
830A PHE* 1.3 76.4 - + - +
832A GLN* 1.3 56.0 + - - +
834A VAL* 3.0 30.9 + - + +
835A TRP* 2.8 35.5 + - - +
842A ILE* 4.4 10.8 - - + -
859A TYR* 3.2 53.6 + + - -
860A TRP* 4.7 2.2 - - + -
868A TYR* 3.7 27.3 - + + -
871A TYR* 3.9 22.1 - - + -
873A VAL* 3.7 29.6 - - + -
890A PHE* 4.8 13.5 - + + -
892A LEU* 3.7 25.4 - - + +
903A VAL* 4.8 6.5 - - + -
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Residues in contact with GLN 832 (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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789A LEU* 3.8 22.8 - - + +
790A LYS 2.9 31.3 + - - +
793A ASN 3.7 5.5 - - - -
794A SER* 3.4 28.2 + - - +
795A HIS 4.3 0.9 + - - -
828A ALA 3.0 13.5 + - - +
829A ASP* 3.1 13.3 + - - +
831A TRP* 1.3 75.1 - - - +
833A MET* 1.3 58.1 + - - +
835A TRP* 3.3 0.7 + - - +
836A GLU* 2.9 61.7 + - - +
869A HIS* 6.0 0.6 - - + -
871A TYR* 3.4 23.7 - - + +
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Residues in contact with MET 833 (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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787A VAL* 4.0 19.1 - - + -
789A LEU* 3.9 14.6 - - + +
801A ILE* 3.7 18.2 - - + -
803A ALA* 3.2 26.2 - - + -
817A ILE* 3.8 14.8 - - + -
819A THR* 3.7 33.4 - - + +
829A ASP 3.0 12.0 + - - +
830A PHE* 3.5 15.9 - - + +
832A GLN* 1.3 74.0 - - - +
834A VAL* 1.3 55.9 + - - +
836A GLU* 4.6 2.7 - - - +
837A SER* 2.4 40.2 + - - +
942A ILE* 4.0 22.4 - - + -
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Residues in contact with VAL 834 (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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830A PHE* 3.0 42.1 + - + +
831A TRP* 3.0 18.6 + - + +
833A MET* 1.3 77.8 - - - +
835A TRP* 1.3 63.5 + - - +
837A SER* 3.2 12.7 + - - -
838A GLY 4.0 0.3 - - - -
839A CYS* 3.3 37.1 + - + +
842A ILE* 4.6 3.6 - - + -
892A LEU* 4.0 16.6 - - + +
901A ARG* 5.6 0.2 + - - -
903A VAL* 4.1 15.5 - - + -
942A ILE* 3.7 18.4 - - + -
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Residues in contact with TRP 835 (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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831A TRP 2.8 19.2 + - - +
832A GLN 3.7 3.4 - - - +
834A VAL* 1.3 74.0 - - - +
836A GLU* 1.3 74.8 + - + +
838A GLY* 3.2 14.6 + - - -
871A TYR* 3.7 19.7 - + + -
892A LEU* 3.4 45.9 - - + +
894A ASN* 3.3 39.7 - - + +
897A THR* 5.6 0.4 - - - +
899A GLU* 3.2 50.6 + - + -
901A ARG* 3.4 52.8 + - + +
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Residues in contact with GLU 836 (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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788A LEU 4.7 1.6 - - - +
789A LEU* 4.0 5.2 - - - +
790A LYS* 3.2 44.6 + - - +
793A ASN* 3.1 28.0 + - - +
832A GLN* 2.9 42.0 + - + +
833A MET* 4.7 2.5 - - - +
835A TRP* 1.3 90.5 - - + +
837A SER* 1.3 59.9 + - - +
838A GLY 3.2 1.1 + - - -
871A TYR* 4.1 3.5 + - - +
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Residues in contact with SER 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A VAL* 6.1 1.6 - - - -
817A ILE* 3.8 24.9 - - - -
833A MET* 2.4 27.0 + - - -
834A VAL* 3.2 8.3 + - - -
836A GLU* 1.3 76.8 - - - +
838A GLY* 1.3 57.9 + - - +
839A CYS* 3.1 14.9 + - - +
939A CYS* 3.7 3.3 - - - +
940A PRO* 3.4 25.6 - - - +
942A ILE* 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