Contacts of the helix formed by residues 861 - 870 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C COA 4.6 18.2 - - - +
568C ARG* 5.2 4.3 - - - -
721C LEU 5.5 0.4 - - - -
722C LYS* 4.1 25.5 + - + +
855C ALA 5.4 0.2 - - - -
856C ALA* 2.8 27.9 + - + +
859C ALA* 3.4 34.4 + - + +
860C GLY* 1.3 77.2 + - - +
862C LEU* 1.3 62.7 + - - +
863C VAL 3.6 1.6 - - - -
864C LYS* 3.5 21.7 + - + +
865C SER* 3.0 24.6 + - - -
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Residues in contact with LEU 862 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C COA 3.7 23.1 - - + +
853C LEU* 3.5 29.2 - - + -
856C ALA* 3.9 8.4 + - + +
857C LEU* 3.9 18.6 - - + -
860C GLY 3.7 2.2 - - - -
861C HIS* 1.3 75.9 - - - +
863C VAL* 1.3 64.0 + - - +
865C SER* 2.8 19.6 + - - -
866C HIS* 3.2 23.3 + - + -
4D NAP 3.9 11.7 - - - +
203D MAH 4.0 5.8 - - + -
590D ARG* 3.9 22.7 - - - +
661D SER* 4.8 4.3 - - - +
683D VAL* 3.6 28.3 - - + -
684D SER* 5.3 0.4 - - - -
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Residues in contact with VAL 863 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLY 5.3 0.2 + - - -
862C LEU* 1.3 76.9 - - + +
864C LYS* 1.3 66.0 + - + +
866C HIS* 3.2 7.0 + - - +
867C MET* 3.0 37.6 + - + +
4D NAP 5.9 1.3 - - - -
658D ASN* 4.8 1.1 - - - +
661D SER* 3.7 37.2 - - - +
662D LYS* 3.9 31.0 - - + +
665D GLU* 3.8 31.9 + - + +
683D VAL* 4.8 8.5 - - + -
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Residues in contact with LYS 864 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859C ALA 5.1 1.4 + - - -
860C GLY* 3.3 28.8 + - - +
861C HIS* 3.5 21.2 + - + +
862C LEU 3.3 0.6 - - - -
863C VAL* 1.3 77.4 - - + +
865C SER* 1.3 62.6 + - - +
867C MET* 3.2 18.1 + - - +
868C ILE* 3.2 24.5 + - + +
665D GLU* 4.6 14.1 + - - +
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Residues in contact with SER 865 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C COA 3.1 56.8 - - - -
561C CYS* 3.2 11.7 - - - -
861C HIS* 3.0 12.6 + - - -
862C LEU 2.8 19.8 + - - -
864C LYS* 1.3 74.9 - - - +
866C HIS* 1.3 58.0 + - - +
868C ILE* 3.3 9.6 + - - -
869C HIS* 2.9 29.2 + - - -
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Residues in contact with HIS 866 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C COA 3.0 39.6 - - - -
559C GLU* 3.6 13.3 + - - -
560C GLY 3.5 12.8 + - - -
561C CYS* 3.7 8.7 - - + +
862C LEU* 3.2 22.9 + - + +
863C VAL* 3.8 5.2 - - - +
865C SER* 1.3 80.0 + - - +
867C MET* 1.3 63.7 + - + +
870C ASN* 2.7 70.6 + - + +
871C ARG* 4.1 0.7 - - - +
4D NAP 3.2 27.2 + + - +
658D ASN* 3.3 15.5 - - - +
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Residues in contact with MET 867 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863C VAL* 3.0 38.4 + - + +
864C LYS* 3.2 10.3 + - - +
866C HIS* 1.3 80.5 - - + +
868C ILE* 1.3 64.1 + - + +
871C ARG* 3.5 66.1 + - - +
658D ASN* 3.9 22.9 - - + +
662D LYS* 3.9 21.1 - - + +
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Residues in contact with ILE 868 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864C LYS* 3.3 21.8 - - + +
865C SER* 3.5 9.9 - - - +
866C HIS 3.1 0.4 - - - -
867C MET* 1.3 82.3 - - + +
869C HIS* 1.3 85.7 + - + +
870C ASN 3.7 0.2 - - - -
524D GLY* 3.4 14.8 - - - +
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Residues in contact with HIS 869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C COA 3.7 53.4 + - + +
560C GLY* 3.3 7.4 - - - -
561C CYS* 3.7 17.0 - - - +
564C ALA* 5.4 0.9 - - + -
865C SER* 2.9 26.5 + - - -
868C ILE* 1.3 94.3 + - + +
870C ASN* 1.3 58.3 - - - +
524D GLY* 3.0 24.9 - - - +
525D ALA* 3.1 14.9 + - - -
526D CYS 3.9 0.2 + - - -
528D GLU* 3.8 26.3 - - + +
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Residues in contact with ASN 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C GLU* 4.3 0.4 - - - +
560C GLY 3.1 17.0 + - - +
866C HIS* 2.7 54.9 + - + +
869C HIS* 1.3 75.0 - - - +
871C ARG* 1.3 58.2 + - - +
4D NAP 3.0 47.9 + - - +
525D ALA 3.0 18.6 - - - +
658D ASN* 3.0 25.3 + - - +
807D GLY* 4.6 4.7 + - - -
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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