Contacts of the helix formed by residues 973 - 983 (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 ASP 973 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734A TYR* 3.5 12.2 + - - -
748A GLU* 4.6 2.9 - - - +
972A ILE* 1.3 74.5 - - - +
974A ILE* 1.3 58.5 + - - +
975A ALA* 3.2 12.0 + - - +
976A ALA* 3.1 33.2 + - + +
977A THR* 2.9 32.6 + - - -
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Residues in contact with ILE 974 (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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731A ILE* 5.4 2.2 - - + -
734A TYR* 3.1 27.2 + - + +
735A MET* 3.5 22.4 - - + -
957A LEU* 4.0 18.1 - - + +
961A VAL* 4.2 29.6 - - + -
972A ILE* 5.5 3.6 - - + -
973A ASP* 1.3 71.6 - - - +
975A ALA* 1.3 59.7 + - - +
977A THR* 3.1 8.4 + - - -
978A LEU* 2.9 28.4 + - - +
995A PHE* 4.0 14.8 - - + -
998A ALA* 5.9 0.9 - - + -
999A LEU* 3.0 37.0 - - + -
1002A VAL* 4.8 3.4 - - + -
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Residues in contact with ALA 975 (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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734A TYR* 3.3 2.8 + - - -
748A GLU* 3.6 32.3 - - + +
752A LEU* 3.9 17.4 - - + +
973A ASP* 3.2 9.3 + - - +
974A ILE* 1.3 77.1 - - - +
976A ALA* 1.3 57.7 + - - +
978A LEU* 3.3 6.9 + - - +
979A GLU* 3.1 32.9 + - - +
995A PHE* 4.3 10.4 - - + -
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Residues in contact with ALA 976 (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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973A ASP* 3.1 35.2 + - + +
975A ALA* 1.3 73.6 - - - +
977A THR* 1.3 66.1 + - - +
979A GLU* 3.2 18.4 + - - +
980A HIS* 3.1 20.8 + - - +
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Residues in contact with THR 977 (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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957A LEU* 3.7 18.2 - - + -
960A MET* 4.6 26.0 - - + -
961A VAL* 4.2 13.4 - - + +
973A ASP 2.9 21.8 + - - -
974A ILE* 3.1 9.1 + - - -
976A ALA* 1.3 75.5 - - - +
978A LEU* 1.3 60.5 + - - +
980A HIS* 3.3 11.2 - - + +
981A LEU* 3.2 21.3 + - + +
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Residues in contact with LEU 978 (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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749A TRP* 4.6 0.4 - - + -
752A LEU* 3.6 31.0 - - + -
957A LEU* 4.0 14.1 - - + +
974A ILE 2.9 11.3 + - - +
975A ALA* 3.5 9.6 - - - +
976A ALA 3.2 0.2 - - - -
977A THR* 1.3 74.7 - - - +
979A GLU* 1.3 64.1 + - - +
981A LEU* 3.1 21.4 + - + +
982A ARG* 3.0 30.1 + - - +
988A MET* 3.5 22.7 - - + +
989A VAL* 3.6 24.0 - - + -
995A PHE* 3.7 24.0 - - + -
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Residues in contact with GLU 979 (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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751A ALA* 5.6 4.5 - - - +
752A LEU* 3.9 18.6 - - + +
755A TYR* 3.6 47.8 + - + +
975A ALA* 3.1 17.5 + - - +
976A ALA* 3.2 18.2 + - - +
978A LEU* 1.3 72.6 - - - +
980A HIS* 1.3 66.0 + - - +
982A ARG* 2.8 5.5 + - - +
983A ASP* 2.8 30.1 + - - +
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Residues in contact with HIS 980 (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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807A MET* 3.5 26.4 + - + +
808A ASP 3.9 12.8 + - - -
960A MET* 4.3 17.3 - - + -
976A ALA 3.1 11.8 + - - +
977A THR* 3.3 14.6 - - + +
979A GLU* 1.3 75.2 - - - +
981A LEU* 1.3 62.1 + - + +
983A ASP* 3.4 24.7 + - - +
984A GLN* 3.3 30.6 + - + +
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Residues in contact with LEU 981 (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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806A ILE* 3.6 32.3 - - + +
953A GLY 4.1 5.8 - - - +
956A VAL* 3.7 14.1 - - + -
957A LEU* 3.9 40.4 - - + +
960A MET* 4.0 13.0 - - - -
977A THR* 3.2 12.3 + - + +
978A LEU* 3.1 18.7 + - + +
979A GLU 3.0 1.0 - - - -
980A HIS* 1.3 80.4 - - + +
982A ARG* 1.3 56.1 + - - +
983A ASP 3.1 0.2 - - - -
984A GLN* 2.9 22.3 + - - +
985A ARG 3.0 13.4 + - - +
988A MET* 4.1 23.8 - - + +
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Residues in contact with ARG 982 (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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749A TRP* 3.7 22.8 - - - -
752A LEU* 3.0 43.4 + - - +
753A CYS* 4.1 5.7 + - - +
755A TYR* 4.3 23.0 + - + -
757A ALA* 3.6 5.6 - - + +
782A TYR* 3.1 28.3 + - - +
978A LEU* 3.0 22.4 + - - +
979A GLU 2.8 11.4 + - - +
981A LEU* 1.3 69.1 - - - +
983A ASP* 1.3 64.2 + - - +
984A GLN 3.1 1.8 - - - -
985A ARG 3.6 8.8 - - - +
986A PRO* 5.4 1.1 - - + -
987A GLY* 4.6 7.3 + - - +
988A MET* 3.2 30.6 + - + +
989A VAL* 2.9 27.9 + - - +
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Residues in contact with ASP 983 (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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755A TYR* 2.7 29.1 + - - -
757A ALA* 3.9 15.0 - - - +
758A GLU 4.8 3.6 + - - -
759A PRO 4.8 0.2 - - - +
782A TYR* 3.7 1.7 - - - -
784A HIS* 2.7 36.4 + - - -
979A GLU* 2.8 14.8 + - - +
980A HIS* 3.4 22.5 + - - +
982A ARG* 1.3 79.1 - - - +
984A GLN* 1.3 55.8 + - + +
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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