Contacts of the strand formed by residues 777 - 784 (chain B) in PDB entry 1DQ8
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698B TRP* 3.7 5.6 - - - -
747B GLY 3.0 9.2 + - - +
749B TYR* 3.1 16.2 + - - +
750B ASN* 3.1 26.8 + - - +
753B ALA* 4.0 5.8 - - + -
775B SER 3.1 10.4 + - - +
776B ASN* 1.3 76.6 - - - +
778B ILE* 1.3 67.7 + - - +
779B THR* 3.8 20.0 - - - -
795B CYS* 4.1 7.4 - - - -
796B THR 3.2 8.1 - - - -
797B MET* 3.8 19.7 - - + -
846B VAL* 4.1 17.3 - - - -
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Residues in contact with ILE 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B TRP* 3.8 16.4 - - + -
737B LEU* 3.9 21.5 - - + -
749B TYR* 3.3 21.1 - - + +
777B CYS* 1.3 74.4 - - - +
779B THR* 1.3 61.8 + - - +
780B LEU* 4.0 16.1 - - + +
794B SER* 3.8 1.0 + - - +
795B CYS* 3.4 3.1 - - - -
796B THR* 2.9 52.1 + - - +
639C ALA* 4.5 7.2 - - + -
738D VAL* 4.1 24.5 - - + -
741D ALA* 4.3 8.3 - - + -
742D MET* 4.2 19.5 - - + -
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Residues in contact with THR 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B ASN* 3.0 33.1 + - - +
736B ASN* 4.1 5.2 - - - +
737B LEU* 4.7 1.4 - - - +
749B TYR 3.0 13.4 + - - +
750B ASN* 3.5 7.4 - - - +
777B CYS* 3.8 1.4 - - - -
778B ILE* 1.3 74.0 - - - +
780B LEU* 1.3 69.1 + - - +
781B MET* 4.0 17.7 - - + -
793B ILE* 4.4 4.5 - - + -
794B SER 3.3 9.2 - - - +
795B CYS* 3.6 13.7 - - - -
850B GLU* 2.7 40.0 + - + +
854B MET* 5.4 0.2 - - + -
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Residues in contact with LEU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B ASN* 3.7 1.8 - - - +
737B LEU* 4.1 15.5 - - + -
778B ILE* 4.0 17.9 - - + +
779B THR* 1.3 81.2 - - - +
781B MET* 1.3 66.9 - - - +
792B TYR* 5.0 4.2 - - + -
793B ILE* 3.3 5.0 - - - +
794B SER* 2.9 43.6 + - - +
639C ALA* 3.7 39.5 - - + +
641C ARG 5.8 0.2 - - - +
642C ASN* 4.5 7.4 - - - +
733D ILE* 6.2 0.2 - - + -
734D ASN* 5.2 1.1 - - - +
738D VAL* 3.8 31.2 - - + -
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Residues in contact with MET 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728B MET* 3.9 34.8 - - + +
729B ILE* 3.9 25.8 - - + +
732B ASN* 3.7 37.4 + - + +
733B ILE* 5.3 4.3 - - - +
779B THR* 4.0 5.4 - - + -
780B LEU* 1.3 81.9 - - - +
782B GLU* 1.3 64.5 + - - +
791B LEU* 4.1 6.3 - - + -
792B TYR* 3.2 9.4 - - - +
793B ILE* 3.9 29.4 - - + -
850B GLU 4.5 2.5 - - - +
854B MET* 3.6 34.1 - - + -
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Residues in contact with GLU 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B ILE* 3.6 12.9 - - - +
781B MET* 1.3 76.7 - - - +
783B ALA* 1.3 72.4 + - - +
784B SER* 5.7 0.2 - - - -
790B ASP 3.9 0.9 - - - +
791B LEU* 3.9 1.9 - - - +
792B TYR* 2.9 54.3 + - + -
595C ARG* 4.1 4.4 + - - -
641C ARG* 2.6 50.5 + - - +
730D GLU* 4.1 14.3 - - - +
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Residues in contact with ALA 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B THR* 4.5 2.5 - - + -
729B ILE* 3.4 16.5 - - + +
782B GLU* 1.3 85.8 - - - +
784B SER* 1.3 60.0 + - - +
788B ASN* 3.3 44.0 + - - +
790B ASP 3.7 6.1 - - - -
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Residues in contact with SER 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B VAL* 4.6 15.2 - - - +
783B ALA* 1.3 75.8 - - - +
785B GLY* 1.3 68.5 + - - +
788B ASN* 3.1 14.5 - - - +
790B ASP* 2.9 40.0 + - - -
792B TYR* 4.1 22.3 - - - +
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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