Contacts of the helix formed by residues 919 - 935 (chain B) 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 SER 919 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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884B ASP* 4.5 3.3 + - - +
917B PRO* 4.1 13.0 - - - +
918B SER* 1.3 81.9 + - - +
920B SER* 1.3 60.6 + - - +
921B ARG* 3.2 12.0 + - - +
922B SER* 2.7 46.2 + - - -
923B LEU* 3.6 7.4 + - - +
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Residues in contact with SER 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918B SER 3.8 3.8 + - - -
919B SER* 1.3 71.9 - - - +
921B ARG* 1.3 58.7 + - - +
923B LEU* 3.5 2.4 + - - +
924B LEU* 3.0 36.8 + - - +
997B PHE* 3.8 30.5 - - - -
1000B THR* 4.9 4.7 - - - -
1001B ALA* 4.3 17.2 - - - +
1004B GLU* 2.6 36.2 + - - +
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Residues in contact with ARG 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919B SER* 3.1 8.0 + - - +
920B SER* 1.3 80.0 + - - +
922B SER* 1.3 66.5 + - - +
924B LEU* 3.7 8.8 - - - +
925B ASP* 2.8 26.2 + - - +
1004B GLU* 6.1 0.4 - - - +
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Residues in contact with SER 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B CYS* 4.8 3.6 - - - -
884B ASP* 2.6 41.7 + - - +
885B PHE* 3.4 11.6 - - - -
908B PHE* 4.1 4.7 - - - -
919B SER* 2.7 26.4 + - - -
921B ARG* 1.3 72.7 - - - +
923B LEU* 1.3 59.6 + - - +
925B ASP* 3.2 3.0 + - - +
926B PHE* 2.8 29.8 + - - +
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Residues in contact with LEU 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B LEU* 5.0 0.4 - - + -
908B PHE* 3.6 36.3 - - + -
911B TRP* 3.6 38.1 - - + -
917B PRO* 4.7 0.9 - - + -
919B SER 3.6 7.0 + - - +
920B SER 3.5 7.5 + - - +
921B ARG 3.2 0.6 - - - -
922B SER* 1.3 78.4 - - - +
924B LEU* 1.3 61.0 + - + +
926B PHE* 3.3 14.1 + - + +
927B ARG* 2.8 28.4 + - + +
955B TYR* 4.4 15.3 - - + -
958B ILE* 4.1 15.9 - - + -
997B PHE* 3.8 26.0 - - + -
1001B ALA* 5.5 1.8 - - + -
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Residues in contact with LEU 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920B SER* 3.0 37.6 + - - +
921B ARG* 3.8 6.7 - - - +
923B LEU* 1.3 80.0 - - + +
925B ASP* 1.3 61.7 + - - +
927B ARG* 3.1 12.6 + - - +
928B ARG* 3.0 22.3 + - - +
958B ILE* 4.5 6.7 - - + -
962B LEU* 4.0 24.0 - - + -
1001B ALA* 3.4 39.5 - - + +
1004B GLU* 4.4 4.9 - - + +
1005B GLU* 3.8 34.0 - - + +
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Residues in contact with ASP 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885B PHE* 3.6 17.5 - - + -
921B ARG 2.8 21.8 + - - +
922B SER* 3.5 5.2 - - - +
924B LEU* 1.3 72.0 - - - +
926B PHE* 1.3 64.0 + - - +
928B ARG* 3.1 19.0 + - - +
929B LYS* 3.1 24.7 + - - +
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Residues in contact with PHE 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843B VAL* 4.1 11.9 - - + -
845B LEU* 4.1 7.2 - - + -
885B PHE* 3.3 47.8 - + + -
886B LEU 5.0 0.4 - - - -
906B PHE* 3.8 32.3 - + + -
907B HIS 3.9 0.2 - - - -
908B PHE* 3.6 36.8 - + + -
922B SER 2.8 20.5 + - - +
923B LEU* 3.4 17.7 - - + +
925B ASP* 1.3 72.5 - - - +
927B ARG* 1.3 59.2 + - - +
929B LYS* 3.5 3.7 + - - +
930B VAL* 3.1 43.3 + - + +
955B TYR* 3.8 19.1 - + - -
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Residues in contact with ARG 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923B LEU* 2.8 19.4 + - + +
924B LEU* 3.1 12.6 + - - +
926B PHE* 1.3 70.4 - - - +
928B ARG* 1.3 66.7 + - - +
929B LYS 3.1 1.6 - - - -
930B VAL* 3.6 1.1 - - - +
931B ASN* 2.8 39.8 + - - +
955B TYR* 3.8 29.6 - - + +
958B ILE* 4.6 7.4 - - - -
959B ASP* 2.9 29.6 + - - +
962B LEU* 3.5 42.0 - - - +
963B ASN* 3.0 27.5 + - - +
1005B GLU* 3.9 16.4 + - - -
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Residues in contact with ARG 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924B LEU 3.0 11.6 + - - +
925B ASP* 3.1 16.8 + - - +
927B ARG* 1.3 82.9 - - - +
929B LYS* 1.3 59.5 + - + +
931B ASN* 3.8 4.1 - - - +
932B LYS* 3.0 30.5 + - - +
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Residues in contact with LYS 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881B TRP* 3.3 53.4 - - + +
885B PHE* 3.5 29.8 - - + -
887B VAL* 5.8 0.2 - - + -
906B PHE* 3.7 17.0 - - + -
925B ASP* 3.1 25.4 + - - +
926B PHE* 3.9 5.4 - - - +
927B ARG 3.1 0.4 - - - -
928B ARG* 1.3 75.8 - - + +
930B VAL* 1.3 68.8 + - - +
932B LYS* 3.4 4.8 + - - +
933B CYS* 3.1 23.6 + - - +
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Residues in contact with VAL 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B VAL* 4.3 11.9 - - + +
843B VAL* 3.7 20.2 - - + -
906B PHE* 3.5 38.3 - - + -
926B PHE* 3.1 34.0 + - + +
927B ARG 3.6 1.1 - - - +
929B LYS* 1.3 79.7 - - - +
931B ASN* 1.3 64.5 + - - +
933B CYS* 3.4 3.6 + - - +
934B TYR* 3.1 23.6 + - - +
941B ILE* 5.0 8.7 - - + -
955B TYR* 3.4 21.1 - - - +
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Residues in contact with ASN 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B ARG* 2.8 42.7 + - - +
928B ARG* 4.1 4.5 - - - +
930B VAL* 1.3 81.1 - - - +
932B LYS* 1.3 62.5 + - - +
933B CYS 3.2 1.6 - - - -
934B TYR* 3.7 10.0 - - - +
935B ARG* 3.3 19.2 + - - -
941B ILE* 4.6 8.7 - - - +
955B TYR* 4.6 0.2 + - - -
959B ASP* 3.1 34.9 + - - +
963B ASN* 3.9 8.0 + - - +
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Residues in contact with LYS 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928B ARG 3.0 19.1 + - - +
929B LYS* 3.4 5.1 + - - +
931B ASN* 1.3 74.0 - - - +
933B CYS* 1.3 60.4 + - - +
935B ARG* 4.2 9.9 + - - +
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Residues in contact with CYS 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840B VAL 5.5 0.2 - - - -
841B VAL* 4.3 12.6 - - - +
904B THR* 4.3 15.9 - - - -
906B PHE* 3.5 30.3 - - + -
929B LYS 3.1 16.5 + - - +
930B VAL 3.6 1.8 - - - +
932B LYS* 1.3 78.4 - - - +
934B TYR* 1.3 62.6 + - - +
935B ARG* 3.4 2.0 + - - +
937B ARG* 4.1 16.6 + - - -
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Residues in contact with TYR 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B ALA* 4.4 9.4 + - - -
841B VAL* 4.0 19.5 - - + -
930B VAL 3.1 16.7 + - - +
931B ASN* 3.5 13.2 + - - +
933B CYS* 1.3 77.9 - - - +
935B ARG* 1.3 67.5 + - - +
936B GLY* 3.0 29.3 + - - -
937B ARG* 3.1 47.0 + - + +
938B SER 3.7 11.6 + - - -
939B CYS* 2.5 34.6 + - - -
940B PRO 4.7 0.7 - - - -
941B ILE* 3.8 42.0 - - + -
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Residues in contact with ARG 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931B ASN 3.3 11.9 + - - -
932B LYS* 4.2 8.0 + - - +
933B CYS 3.4 5.1 - - - +
934B TYR* 1.3 77.7 - - - +
936B GLY* 1.3 64.7 + - - +
937B ARG* 3.4 12.7 + - - +
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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