Contacts of the helix formed by residues 973 - 985 (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 ASP 973 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734B TYR* 4.0 9.1 + - - -
748B GLU* 5.4 1.9 - - - +
972B ILE* 1.3 76.8 - - - +
974B ILE* 1.3 59.2 + - - +
975B ALA* 3.4 10.2 + - - +
976B ALA* 2.7 44.6 + - + +
977B THR* 2.9 27.8 + - - -
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Residues in contact with ILE 974 (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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734B TYR* 3.3 14.0 + - + +
735B MET* 4.1 17.7 - - + -
957B LEU* 3.6 31.6 - - + -
961B VAL* 3.8 33.0 - - + -
972B ILE* 4.1 12.8 - - + -
973B ASP* 1.3 71.9 - - - +
975B ALA* 1.3 57.2 + - - +
977B THR* 3.0 8.1 + - - -
978B LEU* 2.8 27.2 + - - +
995B PHE* 4.6 4.5 - - + -
998B ALA* 5.7 2.5 - - + -
999B LEU* 3.2 37.2 - - + +
1002B VAL* 4.7 6.3 - - + -
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Residues in contact with ALA 975 (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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734B TYR* 3.7 3.4 + - - +
748B GLU* 3.7 30.7 - - + +
752B LEU* 3.6 18.1 - - + +
973B ASP* 3.2 7.8 + - - +
974B ILE* 1.3 74.6 - - - +
976B ALA* 1.3 59.7 + - - +
978B LEU* 3.4 5.3 + - - +
979B GLU* 3.0 33.7 + - - +
995B PHE* 4.3 15.9 - - + -
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Residues in contact with ALA 976 (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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973B ASP* 2.7 39.9 + - + +
975B ALA* 1.3 73.9 - - - +
977B THR* 1.3 57.7 + - - +
979B GLU* 3.2 16.5 + - - +
980B HIS* 2.9 27.6 + - - +
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Residues in contact with THR 977 (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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957B LEU* 3.8 17.3 - - + -
960B MET* 3.5 40.6 - - + -
961B VAL* 4.4 9.4 - - + +
973B ASP 2.9 14.6 + - - -
974B ILE* 3.0 13.5 + - - -
976B ALA* 1.3 74.1 - - - +
978B LEU* 1.3 59.0 + - - +
980B HIS* 3.2 9.7 + - + +
981B LEU* 2.9 27.0 + - + +
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Residues in contact with LEU 978 (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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749B TRP* 4.5 0.7 - - + -
752B LEU* 3.7 27.1 - - + -
957B LEU* 3.8 10.7 - - + +
974B ILE 2.8 13.2 + - - +
975B ALA* 3.6 10.3 - - - +
977B THR* 1.3 74.8 - - - +
979B GLU* 1.3 52.3 + - - +
981B LEU* 3.2 16.3 + - + -
982B ARG* 2.7 51.8 + - - +
988B MET* 3.5 15.0 - - + +
989B VAL* 3.5 41.1 - - + -
995B PHE* 4.0 15.9 - - + -
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Residues in contact with GLU 979 (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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751B ALA* 5.2 5.4 - - - +
752B LEU* 3.7 20.4 - - + +
755B TYR* 3.5 47.9 - - + +
975B ALA* 3.0 19.3 + - - +
976B ALA* 3.3 17.5 - - - +
977B THR 3.2 0.2 - - - -
978B LEU* 1.3 75.3 - - - +
980B HIS* 1.3 52.5 + - - +
982B ARG* 2.9 6.7 + - - +
983B ASP* 2.8 39.5 + - - +
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Residues in contact with HIS 980 (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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807B MET* 3.2 16.9 + - + -
808B ASP 3.7 15.2 + - - -
960B MET* 4.1 24.0 - - + -
976B ALA 2.9 13.1 + - - +
977B THR* 3.4 10.5 - - - +
979B GLU* 1.3 74.3 - - - +
981B LEU* 1.3 61.3 + - - +
983B ASP* 3.5 18.9 + - - +
984B GLN* 3.1 54.7 + - + +
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Residues in contact with LEU 981 (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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806B ILE* 3.7 23.8 - - + +
953B GLY 3.9 9.9 - - - +
956B VAL* 3.8 9.0 - - + -
957B LEU* 3.7 41.3 - - + +
960B MET* 3.4 29.4 - - + -
977B THR 2.9 16.4 + - - +
978B LEU* 3.4 15.9 - - + +
979B GLU 3.1 0.2 - - - -
980B HIS* 1.3 77.9 - - + +
982B ARG* 1.3 58.1 + - - +
984B GLN* 2.8 25.1 + - - +
985B ARG* 3.1 12.0 + - - +
988B MET* 3.9 22.1 - - + +
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Residues in contact with ARG 982 (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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749B TRP* 3.6 22.0 - - - -
752B LEU* 3.1 41.8 + - - +
753B CYS* 4.0 4.2 - - - +
755B TYR* 4.2 22.2 + - + -
757B ALA* 3.7 5.2 - - + +
782B TYR* 3.3 25.1 + - - +
978B LEU* 2.7 36.8 + - - +
979B GLU* 2.9 4.7 + - - +
981B LEU* 1.3 69.1 - - - +
983B ASP* 1.3 63.2 + - - +
984B GLN 3.3 0.2 + - - -
985B ARG 3.5 9.6 - - - +
986B PRO* 5.6 0.2 - - + -
987B GLY* 4.7 10.1 - - - +
988B MET* 3.1 28.8 + - + +
989B VAL 2.8 27.7 + - - -
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Residues in contact with ASP 983 (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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755B TYR* 2.6 33.7 + - - -
757B ALA* 4.1 12.6 - - - +
758B GLU 5.2 1.6 + - - -
782B TYR* 3.5 5.4 - - - -
784B HIS* 2.9 28.4 + - - -
979B GLU 2.8 16.6 + - - -
980B HIS* 3.5 25.1 + - - +
981B LEU 3.2 0.2 - - - -
982B ARG* 1.3 73.6 - - - +
984B GLN* 1.3 62.7 + - + +
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Residues in contact with GLN 984 (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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782B TYR* 3.8 5.5 + - - +
785B SER* 3.1 29.9 + - - +
804B SER* 3.7 6.8 - - - -
805B PRO 4.0 6.2 - - - +
806B ILE* 3.4 26.3 - - + +
807B MET* 2.7 55.0 + - - +
980B HIS* 3.1 42.4 + - + +
981B LEU* 2.8 7.8 + - - +
983B ASP* 1.3 85.5 - - + +
985B ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 985 (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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779B VAL* 3.3 14.2 - - - +
781B THR* 3.9 11.5 - - - +
782B TYR* 3.7 5.4 - - - +
802B ASN* 3.7 28.3 + - - +
803B ALA 4.0 4.8 - - - +
804B SER* 2.9 36.1 + - - +
806B ILE* 4.2 4.5 - - + -
818B ALA* 3.5 33.2 + - - -
819B THR* 4.6 0.2 - - - -
820B GLN 3.9 10.3 - - - +
947B ASP 3.0 25.9 + - - -
948B GLY 3.0 18.9 + - - -
949B ALA* 4.8 0.2 - - - +
981B LEU 3.1 3.6 + - - -
982B ARG* 3.5 11.0 - - - -
983B ASP 3.6 1.2 - - - -
984B GLN* 1.3 80.5 - - - +
986B PRO* 1.3 81.5 - - + +
988B MET* 3.2 27.3 - - + +
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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