Contacts of the helix formed by residues 983 - 993 (chain A) in PDB entry 4DQL
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 983 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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934A TYR* 2.6 38.6 + - - +
962A HIS* 3.5 17.1 + - - -
979A VAL* 3.0 17.9 + - - +
980A MET 3.1 4.4 + - - +
982A GLN* 1.3 83.2 - - - +
984A GLY* 1.3 64.1 + - - +
985A LYS* 3.1 3.6 + - - -
986A LYS* 3.2 12.6 + - + -
987A LEU* 3.0 22.8 + - + +
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Residues in contact with GLY 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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980A MET 3.0 12.3 + - - -
981A GLU 3.3 6.2 + - - -
982A GLN 3.3 5.3 + - - -
983A ASP* 1.3 77.4 - - - +
985A LYS* 1.3 60.9 + - - +
987A LEU* 3.9 4.7 - - - -
988A ILE* 3.0 32.1 + - - +
1017A SER* 3.9 20.0 - - - -
1021A VAL* 4.3 4.5 - - - -
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Residues in contact with LYS 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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982A GLN 5.1 0.4 + - - -
983A ASP 3.3 0.8 - - - -
984A GLY* 1.3 73.1 - - - +
986A LYS* 1.3 59.6 + - - +
988A ILE* 3.8 1.0 - - - +
989A GLU* 2.9 57.5 + - + +
1021A VAL* 4.0 23.3 - - + +
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Residues in contact with LYS 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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930A GLU* 2.6 37.7 + - - -
932A HIS* 3.9 13.8 + - + +
983A ASP* 3.2 13.9 + - + +
985A LYS* 1.3 79.5 - - - +
987A LEU* 1.3 66.6 + - + +
989A GLU* 3.5 16.2 + - + +
990A LEU* 3.0 38.2 + - + +
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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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900A ILE* 3.7 33.3 - - + +
932A HIS* 4.8 6.7 - - + -
934A TYR* 3.6 33.9 - - + +
980A MET* 3.9 44.4 - - + +
983A ASP* 3.0 18.4 + - + +
984A GLY* 3.2 4.2 + - - +
986A LYS* 1.3 81.2 - - + +
988A ILE* 1.3 59.8 + - + +
990A LEU* 3.3 11.0 + - + +
991A LEU* 3.0 33.4 + - - +
1014A LEU* 5.0 11.7 - - + -
1017A SER* 6.2 0.2 - - - -
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Residues in contact with ILE 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 GLY 3.0 17.3 + - - +
985A LYS 4.1 2.0 - - - +
987A LEU* 1.3 74.7 - - + +
989A GLU* 1.3 60.4 + - - +
991A LEU* 3.3 3.1 + - + +
992A ASP* 2.8 30.7 + - - +
1014A LEU* 3.9 17.3 - - + +
1017A SER* 3.8 11.0 - - - +
1018A TYR* 3.6 36.6 - - + +
1021A VAL* 3.8 14.6 - - + -
1022A HIS* 3.5 35.0 - - + +
1032A TRP* 3.9 27.1 - - + -
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Residues in contact with GLU 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 LYS* 2.9 47.6 + - + +
986A LYS* 3.6 21.6 - - + +
988A ILE* 1.3 73.2 - - - +
990A LEU* 1.3 62.0 + - + +
992A ASP* 3.3 9.7 + - - +
993A GLN* 3.1 34.8 + - - +
1021A VAL* 5.5 4.2 - - + +
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Residues in contact with LEU 990 (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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898A PRO* 4.1 21.9 - - + +
899A LEU 5.3 0.2 - - - +
900A ILE* 4.3 13.5 - - + -
930A GLU* 3.6 24.2 - - + +
932A HIS* 3.6 34.8 - - + +
986A LYS* 3.0 33.1 + - + +
987A LEU* 3.3 8.7 + - + +
989A GLU* 1.3 76.5 - - + +
991A LEU* 1.3 61.2 + - - +
993A GLN* 3.1 30.4 + - - +
994A GLY 3.2 1.0 + - - -
995A ALA* 2.9 29.9 + - + +
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Residues in contact with LEU 991 (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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900A ILE* 4.0 11.9 - - + -
987A LEU 3.0 21.4 + - - +
988A ILE* 3.8 7.2 - - + +
990A LEU* 1.3 78.7 - - - +
992A ASP* 1.3 63.0 + - - +
994A GLY* 3.0 12.8 + - - -
995A ALA* 3.5 29.2 + - + +
997A PHE* 4.0 17.0 - - + +
1014A LEU* 3.6 34.5 - - + -
1032A TRP* 3.8 26.2 - - + +
1036A LEU* 3.9 24.9 - - + +
1104A 1PE 3.9 15.2 + - - +
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Residues in contact with ASP 992 (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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988A ILE* 2.8 26.8 + - - +
989A GLU* 3.3 7.8 + - - +
991A LEU* 1.3 73.0 - - - +
993A GLN* 1.3 59.3 + - + +
994A GLY 3.3 0.9 + - - -
1018A TYR* 3.9 15.4 + - - -
1021A VAL* 5.3 0.2 - - - +
1022A HIS* 2.6 38.5 + - - -
1032A TRP* 4.5 5.7 + - - -
1104A 1PE 3.6 20.7 + - - -
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Residues in contact with GLN 993 (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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898A PRO* 4.7 13.2 - - + +
989A GLU* 3.3 18.3 + - - +
990A LEU* 3.1 33.1 + - - +
991A LEU 3.1 1.4 - - - -
992A ASP* 1.3 76.9 - - + +
994A GLY* 1.3 58.8 + - - +
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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