Contacts of the helix formed by residues 861 - 870 (chain A) in PDB entry 1DQA
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 HIS 861 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A COA 4.6 17.0 + - - +
568A ARG* 5.1 4.6 + - - -
721A LEU 5.4 0.4 + - - -
722A LYS* 3.9 26.9 - - + +
856A ALA* 2.8 22.3 + - + +
859A ALA* 3.5 33.5 + - + +
860A GLY* 1.3 79.8 - - - +
862A LEU* 1.3 58.7 + - - +
863A VAL 3.6 1.1 - - - -
864A LYS* 3.9 12.7 - - + +
865A SER* 3.0 32.6 + - - -
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Residues in contact with LEU 862 (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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101A COA 3.6 16.8 - - + +
201A MAH 3.9 17.0 - - + -
853A LEU* 3.7 13.7 - - + -
856A ALA* 3.7 9.2 + - + +
857A LEU* 3.7 30.5 - - + -
860A GLY 3.6 2.4 - - - -
861A HIS* 1.3 75.9 - - - +
863A VAL* 1.3 66.2 + - + +
865A SER* 2.8 18.4 + - - -
866A HIS* 3.2 41.8 + - + -
2B NAP 4.0 17.0 - - - +
590B ARG* 4.2 6.1 - - - +
661B SER* 5.2 1.8 - - - +
683B VAL* 3.7 20.0 - - + -
684B SER* 5.2 0.7 - - - -
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A GLY 5.3 0.2 + - - -
862A LEU* 1.3 76.6 - - + +
864A LYS* 1.3 64.1 + - + +
866A HIS* 3.1 8.4 + - - +
867A MET* 2.9 41.8 + - + +
2B NAP 5.8 1.1 - - - -
658B ASN* 4.9 1.6 - - - +
661B SER* 3.8 37.0 - - - +
662B LYS* 4.0 25.6 - - + +
665B GLU* 3.8 33.2 + - + +
683B VAL* 4.7 13.7 - - + +
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Residues in contact with LYS 864 (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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860A GLY 4.1 19.3 - - - +
861A HIS* 3.9 11.9 - - + +
862A LEU 3.3 0.6 - - - -
863A VAL* 1.3 78.6 - - + +
865A SER* 1.3 61.9 + - - +
867A MET* 3.1 20.2 + - + +
868A ILE* 3.2 14.7 + - - +
665B GLU* 4.6 21.7 + - - +
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Residues in contact with SER 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A COA 3.3 51.6 + - - +
561A CYS* 3.2 9.1 - - - -
861A HIS* 3.0 13.9 + - - -
862A LEU* 2.8 19.9 + - - -
864A LYS* 1.3 75.3 - - - +
866A HIS* 1.3 63.4 + - - +
868A ILE* 2.8 27.5 - - - +
869A HIS* 3.0 11.6 + - - -
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Residues in contact with HIS 866 (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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101A COA 2.9 42.4 + - + +
559A GLU* 3.9 3.8 + - - -
560A GLY 3.5 12.3 + - - -
561A CYS* 3.7 12.1 - - + +
862A LEU* 3.2 22.5 + - + +
863A VAL* 3.1 10.7 + - - +
865A SER* 1.3 79.8 + - - +
867A MET* 1.3 66.2 + - + +
870A ASN* 2.9 66.5 + - + +
2B NAP 3.4 28.6 + + - +
658B ASN* 3.5 15.7 - - - +
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Residues in contact with MET 867 (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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863A VAL* 2.9 39.0 + - + +
864A LYS* 3.1 12.1 + - + +
866A HIS* 1.3 83.9 - - + +
868A ILE* 1.3 61.8 + - - +
870A ASN 4.7 3.4 + - - +
2B NAP 5.0 2.0 - - - +
524B GLY 5.4 0.5 - - - +
658B ASN* 3.9 32.8 - - + +
662B LYS* 4.4 27.6 - - + -
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Residues in contact with ILE 868 (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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101A COA 5.8 0.4 - - + -
864A LYS 3.2 13.7 + - - +
865A SER* 2.8 28.7 - - - +
867A MET* 1.3 80.6 - - - +
869A HIS* 1.3 88.3 + - + +
524B GLY* 3.7 15.0 - - - +
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Residues in contact with HIS 869 (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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101A COA 3.7 56.1 + - + +
560A GLY* 3.3 6.9 - - - -
561A CYS* 3.6 15.0 - - - -
564A ALA* 5.1 2.0 - - + -
865A SER 3.0 7.1 + - - -
868A ILE* 1.3 113.3 + - + +
870A ASN* 1.3 58.3 + - - +
524B GLY* 3.1 16.2 + - - -
525B ALA* 3.1 23.9 + - - -
528B GLU* 3.7 26.6 - - + +
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Residues in contact with ASN 870 (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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558A THR 4.3 0.2 + - - -
560A GLY 3.0 21.8 - - - +
866A HIS* 2.9 55.1 + - + +
867A MET* 5.1 2.7 - - - -
868A ILE 3.7 0.4 - - - -
869A HIS* 1.3 80.6 - - - +
2B NAP 3.1 43.5 + - - +
524B GLY 3.7 3.7 + - - -
525B ALA* 2.9 35.8 + - - +
658B ASN* 3.2 25.5 + - - -
807B GLY* 4.9 4.5 + - - -
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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