Contacts of the strand formed by residues 790 - 800 (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 ASP 790 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711B VAL* 4.1 16.2 - - + +
712B ILE 3.7 9.0 - - - +
713B PRO* 3.4 8.4 - - - +
714B ALA* 2.7 32.1 + - - +
725B THR* 3.5 7.8 - - - +
783B ALA* 3.7 0.3 - - - -
784B SER* 2.9 34.3 + - - +
785B GLY* 3.6 18.8 - - - +
786B PRO* 4.4 5.7 - - - +
787B THR* 5.3 3.6 + - - -
789B GLU* 1.3 82.7 + - - +
791B LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 791 (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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710B ALA 3.6 1.4 - - - +
711B VAL* 3.2 4.9 - - - -
712B ILE* 2.7 47.8 + - + +
717B VAL* 4.0 11.2 - - + -
721B LEU* 5.0 0.7 - - + -
725B THR* 3.7 25.5 + - + +
728B MET* 3.5 46.4 - - + -
729B ILE* 3.9 20.9 - - + -
781B MET* 4.1 9.9 - - + -
782B GLU 4.4 0.4 - - - +
790B ASP* 1.3 72.0 - - - +
792B TYR* 1.3 72.8 + - - +
793B ILE* 3.8 0.6 + - + -
851B LEU* 3.6 18.8 - - + -
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Residues in contact with TYR 792 (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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709B GLU* 2.8 38.4 + - + +
710B ALA 3.6 9.2 - - - -
711B VAL* 4.1 15.5 - - + +
780B LEU* 5.0 4.5 - - + -
781B MET* 3.2 7.4 - - - +
782B GLU* 2.9 72.9 + - + +
784B SER* 4.1 15.1 - - - -
790B ASP 3.8 1.4 + - - -
791B LEU* 1.3 74.2 - - - +
793B ILE* 1.3 60.8 + - - +
794B SER* 3.7 27.9 - - - -
597C PRO 4.9 4.5 - - - -
598C ARG* 5.2 1.3 - - + -
599C ALA* 3.8 0.7 + - - +
641C ARG* 3.7 36.9 + - + +
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Residues in contact with ILE 793 (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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709B GLU* 3.1 5.9 - - - +
710B ALA* 3.0 48.2 + - + +
712B ILE* 4.7 3.8 - - + -
779B THR* 4.4 8.3 - - + -
780B LEU 3.3 11.4 - - - +
781B MET* 3.9 24.7 - - + -
791B LEU* 5.0 1.8 - - + -
792B TYR* 1.3 79.7 - - - +
794B SER* 1.3 68.8 + - - +
847B MET* 3.8 41.5 - - + +
850B GLU* 4.5 1.1 - - + -
851B LEU* 3.7 39.5 - - + +
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Residues in contact with SER 794 (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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708B CYS 3.1 14.6 - - - -
709B GLU* 4.2 0.9 - - - +
778B ILE 3.8 0.6 + - - +
779B THR* 3.3 5.2 - - - +
780B LEU* 2.9 50.0 + - - +
792B TYR* 3.7 19.0 - - - -
793B ILE* 1.3 73.7 - - - +
795B CYS* 1.3 64.1 - - - +
796B THR* 4.8 0.3 + - - -
847B MET* 4.5 0.9 - - - -
640C GLY* 3.3 32.3 + - - -
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Residues in contact with CYS 795 (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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707B VAL* 3.4 1.9 - - - -
708B CYS* 2.9 31.8 + - + +
777B CYS* 4.1 11.7 - - - -
778B ILE 3.4 4.5 - - - -
779B THR* 3.6 24.7 - - - -
793B ILE* 4.8 0.7 - - - -
794B SER* 1.3 75.5 - - - +
796B THR* 1.3 60.9 + - - +
797B MET 4.1 0.4 - - - -
843B CYS* 3.5 16.4 - - - +
846B VAL* 4.3 1.3 - - + -
847B MET* 3.6 41.9 - - + -
850B GLU* 4.0 10.5 - - - -
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Residues in contact with THR 796 (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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584B LEU* 4.6 5.8 - - + -
706B VAL 3.5 9.6 - - - +
707B VAL* 3.5 7.0 - - + +
777B CYS* 3.2 4.7 - - - -
778B ILE* 2.9 46.9 + - + +
794B SER* 4.8 0.3 + - - -
795B CYS* 1.3 73.6 + - - +
797B MET* 1.3 64.5 + - - +
798B PRO* 3.5 11.5 - - + +
638C ILE* 3.2 35.0 - - + +
639C ALA* 3.6 0.5 - - - -
640C GLY* 2.8 27.7 + - - -
742D MET* 5.3 1.8 - - + -
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Residues in contact with MET 797 (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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704B LYS 3.6 3.6 - - - +
705B SER* 3.4 1.2 - - - -
706B VAL* 2.8 38.1 + - - +
753B ALA* 4.8 0.7 - - + -
757B VAL* 3.8 21.3 - - + -
774B SER 3.2 27.4 - - - +
775B SER* 4.5 4.5 - - - +
776B ASN 3.5 13.5 - - - +
777B CYS* 3.8 11.7 - - + -
796B THR* 1.3 76.8 - - - +
798B PRO* 1.3 62.3 - - - +
799B SER 3.4 2.9 + - - +
800B ILE* 3.7 23.2 - - + +
842B VAL* 4.6 1.1 - - + -
843B CYS* 3.8 28.3 - - - -
846B VAL* 3.7 29.2 - - + -
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Residues in contact with PRO 798 (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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697B ASN 4.4 2.9 - - - +
698B TRP* 3.4 55.2 - - + +
701B GLY* 3.2 14.2 - - - +
702B ARG 3.4 1.9 + - - +
704B LYS 3.7 2.1 - - - +
705B SER* 2.6 33.6 + - - +
776B ASN* 3.9 4.9 - - + +
796B THR* 3.5 16.6 - - + +
797B MET* 1.3 84.5 - - - +
799B SER* 1.3 63.9 + - - +
742D MET* 6.3 2.0 - - + -
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Residues in contact with SER 799 (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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697B ASN* 3.9 14.9 + - - +
702B ARG* 3.0 32.2 - - - +
773B GLY 3.1 18.3 + - - +
774B SER* 3.2 21.4 + - - -
776B ASN* 3.3 20.6 + - - +
797B MET 3.4 2.4 - - - -
798B PRO* 1.3 82.2 - - - +
800B ILE* 1.3 63.9 + - - +
801B GLU* 3.4 6.2 + - - +
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Residues in contact with ILE 800 (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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703B GLY* 3.6 1.7 - - - -
704B LYS* 2.8 46.1 + - + +
706B VAL* 3.7 22.0 - - + -
761B TYR* 3.4 17.3 - - - +
774B SER* 3.9 6.7 - - - +
797B MET* 3.7 50.9 - - + -
799B SER* 1.3 71.2 - - - +
801B GLU* 1.3 57.9 + - - +
802B ILE* 3.6 27.9 + - + -
839B ALA* 3.8 20.2 - - + +
842B VAL* 4.3 9.4 - - + -
843B CYS* 4.4 1.8 - - + -
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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