Contacts of the strand formed by residues 777 - 784 (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 CYS 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A TRP* 3.8 5.0 - - - -
747A GLY 3.0 8.5 + - - +
749A TYR* 3.1 16.5 + - - +
750A ASN* 3.1 26.1 + - - +
753A ALA* 3.9 5.6 - - + -
775A SER 3.1 10.4 + - - +
776A ASN* 1.3 77.8 - - - +
778A ILE* 1.3 63.6 + - - +
779A THR* 3.7 20.0 - - - -
795A CYS* 3.9 18.2 - - - -
796A THR 3.4 7.0 - - - -
797A MET* 3.8 20.4 - - + -
846A VAL* 4.1 12.1 - - - -
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Residues in contact with ILE 778 (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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698A TRP* 3.8 19.7 - - + -
737A LEU* 4.0 18.8 - - + -
749A TYR* 3.3 20.2 - - + +
777A CYS* 1.3 76.1 - - - +
779A THR* 1.3 63.6 + - - +
780A LEU* 3.9 16.9 + - + +
794A SER* 3.8 1.4 + - - +
795A CYS* 3.4 2.1 - - - -
796A THR* 3.0 48.2 + - - +
738C VAL* 3.9 27.1 - - + -
741C ALA* 4.6 7.6 - - + -
742C MET* 4.3 12.6 - - + -
639D ALA* 4.2 13.9 - - + -
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Residues in contact with THR 779 (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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732A ASN* 3.0 30.5 + - - +
736A ASN* 4.0 10.4 - - - +
737A LEU* 4.8 1.4 - - - +
749A TYR 2.9 10.9 + - - +
750A ASN* 3.6 6.9 - - - +
777A CYS* 3.7 2.6 - - - -
778A ILE* 1.3 71.8 - - - +
780A LEU* 1.3 68.4 + - - +
781A MET* 4.2 4.7 - - + -
793A ILE* 4.2 13.5 - - + -
794A SER 3.4 8.7 - - - +
795A CYS* 3.6 10.6 - - - +
850A GLU* 2.7 49.7 + - + +
854A MET* 5.5 0.2 - - + -
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Residues in contact with LEU 780 (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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732A ASN* 3.7 2.2 - - - +
737A LEU* 4.1 13.5 - - + -
778A ILE* 3.9 19.1 - - + +
779A THR* 1.3 81.5 - - - +
781A MET* 1.3 67.1 + - - +
792A TYR* 4.9 4.3 - - + -
793A ILE* 3.2 4.7 - - - +
794A SER* 2.8 43.2 + - - +
734C ASN* 5.4 1.3 - - - +
738C VAL* 3.8 30.1 - - + -
639D ALA* 3.5 42.8 - - + +
642D ASN* 4.8 7.2 - - - +
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Residues in contact with MET 781 (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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728A MET* 3.9 28.7 - - + +
729A ILE* 4.0 17.2 - - + +
732A ASN* 3.6 41.5 + - + +
733A ILE* 5.2 5.5 - - - +
779A THR* 4.2 4.3 - - + -
780A LEU* 1.3 82.9 - - - +
782A GLU* 1.3 65.8 + - - +
791A LEU* 4.0 18.8 - - + -
792A TYR* 3.2 9.0 - - - +
793A ILE* 3.9 27.8 - - + -
850A GLU 4.6 1.3 - - - +
854A MET* 3.7 31.2 - - + -
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Residues in contact with GLU 782 (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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729A ILE* 3.4 14.8 - - + +
781A MET* 1.3 76.4 - - - +
783A ALA* 1.3 69.2 + - - +
791A LEU* 3.7 3.6 - - - +
792A TYR* 2.8 57.6 + - + +
730C GLU* 4.5 6.0 - - - +
595D ARG* 4.3 8.0 + - - -
641D ARG* 2.7 50.4 + - - +
642D ASN* 5.6 0.3 - - - +
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Residues in contact with ALA 783 (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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725A THR* 4.4 2.5 - - + -
729A ILE* 3.2 16.7 - - + +
782A GLU* 1.3 88.8 - - - +
784A SER* 1.3 60.5 + - - +
788A ASN* 3.6 43.3 + - + +
790A ASP 3.4 6.1 - - - +
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Residues in contact with SER 784 (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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711A VAL* 4.2 21.2 - - - +
783A ALA* 1.3 77.5 - - - +
785A GLY* 1.3 68.0 + - - +
788A ASN* 3.1 15.6 - - - +
789A GLU 3.2 0.7 + - - -
790A ASP* 2.8 37.5 + - - -
792A TYR* 4.0 22.8 - - - +
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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