Contacts of the helix formed by residues 981 - 989 (chain A) in PDB entry 4QMH
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 GLU 981 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979A GLU 3.0 0.2 + - - -
980A SER* 1.3 79.1 - - - +
982A MET* 1.3 58.7 + - - +
983A ILE 3.3 2.7 - - - +
984A ALA* 3.9 10.5 - - + +
985A ASP* 2.9 42.2 + - - +
1017A GLU* 5.4 3.6 - - - +
1018A ASP* 2.9 20.3 + - - +
1021A SER* 3.6 32.2 - - - +
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Residues in contact with MET 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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939A VAL* 4.4 5.4 - - + -
940A ARG* 4.3 20.4 - - + +
943A PHE* 3.6 26.7 - - + -
944A PRO* 3.8 36.6 - - + -
947A LEU* 3.5 14.3 - - + +
976A GLU 3.4 24.7 - - - +
977A PHE 3.8 4.3 - - - +
979A GLU* 3.3 24.1 + - + +
980A SER* 3.2 10.7 - - - +
981A GLU* 1.3 77.6 - - - +
983A ILE* 1.3 62.7 + - - +
985A ASP* 3.8 5.4 - - - +
986A ALA* 3.2 17.3 + - - +
1018A ASP* 4.6 0.4 + - - -
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Residues in contact with ILE 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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943A PHE* 3.9 21.3 - - + -
947A LEU* 4.1 9.6 - - + -
977A PHE 3.7 16.7 + - - +
978A PHE* 3.7 34.1 - - + -
981A GLU 3.3 0.4 - - - -
982A MET* 1.3 75.5 - - - +
984A ALA* 1.3 65.2 + - - +
986A ALA* 3.1 5.2 + - - +
987A LEU* 2.9 31.0 + - + +
998A LEU* 4.1 7.9 - - + -
1001A TRP* 3.8 19.5 - - + -
1002A LEU* 3.9 21.3 - - + -
1018A ASP* 4.9 2.6 + - - +
1022A MET* 3.6 20.4 - - + -
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Residues in contact with ALA 984 (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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981A GLU* 3.5 14.8 + - + +
982A MET 3.5 0.2 - - - -
983A ILE* 1.3 79.9 - - - +
985A ASP* 1.3 59.8 + - - +
987A LEU* 3.2 6.3 + - - +
988A LYS* 2.9 30.7 + - - +
1018A ASP* 5.6 0.2 + - - -
1021A SER* 3.5 44.6 + - - +
1022A MET* 4.5 3.0 - - + +
1025A HIS* 3.5 16.9 + - + +
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Residues in contact with ASP 985 (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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980A SER 4.4 5.0 - - - +
981A GLU* 2.9 36.9 + - - +
982A MET* 3.8 6.7 - - - +
984A ALA* 1.3 76.8 - - - +
986A ALA* 1.3 62.9 + - - +
988A LYS* 3.6 25.5 + - - +
989A GLY* 3.8 4.9 + - - -
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Residues in contact with ALA 986 (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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947A LEU* 4.1 21.1 - - + -
948A HIS* 6.1 0.2 - - - -
982A MET 3.2 12.9 + - - +
983A ILE 3.1 8.6 + - - +
985A ASP* 1.3 76.6 - - - +
987A LEU* 1.3 64.6 + - - +
989A GLY 4.3 0.3 - - - -
990A GLY* 3.3 21.8 + - - -
994A LEU* 3.3 19.6 - - + +
998A LEU* 3.9 16.2 - - + -
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Residues in contact with LEU 987 (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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983A ILE* 2.9 35.9 + - + +
984A ALA* 3.2 7.8 + - - +
986A ALA* 1.3 75.5 - - - +
988A LYS* 1.3 68.2 + - - +
990A GLY* 3.2 9.9 + - - -
994A LEU* 4.4 2.7 - - + -
995A LYS* 4.0 11.1 - - - +
998A LEU* 3.8 29.4 - - + -
999A TRP* 3.7 52.5 - - + +
1002A LEU* 4.4 3.8 - - + -
1022A MET* 4.6 7.2 - - + -
1025A HIS* 4.1 17.3 - - + -
1029A HIS* 3.7 19.5 - - + +
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Residues in contact with LYS 988 (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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984A ALA 2.9 17.1 + - - +
985A ASP* 3.6 19.7 - - - +
986A ALA 3.3 0.2 - - - -
987A LEU* 1.3 80.2 - - - +
989A GLY* 1.3 62.3 + - - +
990A GLY 3.3 1.7 + - - -
995A LYS* 5.8 0.3 - - - +
1025A HIS* 3.6 24.5 - - + +
1029A HIS* 5.3 2.4 + - - -
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Residues in contact with GLY 989 (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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985A ASP 3.8 7.2 + - - -
986A ALA 4.3 0.4 - - - -
988A LYS* 1.3 82.1 - - - +
990A GLY* 1.3 63.0 + - - +
991A SER 3.7 0.7 + - - -
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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