Contacts of the strand formed by residues 790 - 800 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711D VAL* 3.9 18.6 - - + -
712D ILE 3.6 9.9 - - - +
713D PRO* 3.4 8.4 - - + +
714D ALA* 2.8 28.3 + - - +
725D THR* 3.5 8.7 - - - +
783D ALA* 3.6 0.3 - - - -
784D SER* 2.8 32.5 + - - +
785D GLY* 3.5 21.1 - - - -
786D PRO* 4.0 8.3 - - - +
787D THR* 5.4 2.2 + - - -
789D GLU* 1.3 84.0 + - - +
791D LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710D ALA 3.6 0.9 - - - +
711D VAL* 3.2 5.6 - - - -
712D ILE* 2.7 49.7 + - + +
717D VAL* 4.1 13.0 - - + -
721D LEU* 5.0 0.9 - - + -
725D THR* 3.7 14.3 + - + +
728D MET* 3.8 44.2 - - + -
729D ILE* 4.1 13.7 - - + -
781D MET* 3.9 21.5 - - + -
782D GLU 3.8 5.8 - - - +
790D ASP* 1.3 71.1 - - - +
792D TYR* 1.3 73.7 + - - +
793D ILE* 3.7 1.6 + - + +
851D LEU* 3.8 18.4 - - + -
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Residues in contact with TYR 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ARG* 4.3 21.3 - - - -
599A ALA* 3.9 0.9 + - - +
641A ARG* 3.8 37.4 + - + +
709D GLU* 2.9 37.7 + - + +
710D ALA 3.6 9.4 - - - -
711D VAL* 4.1 14.6 - - + +
780D LEU* 5.1 4.0 - - + -
781D MET* 3.2 6.9 - - - +
782D GLU* 2.8 64.6 + - + +
784D SER* 3.9 17.2 - - - -
790D ASP 3.9 1.6 + - - -
791D LEU* 1.3 73.6 - - - +
793D ILE* 1.3 58.9 + - - +
794D SER* 3.6 33.5 - - - -
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Residues in contact with ILE 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709D GLU* 3.3 4.9 - - - +
710D ALA* 3.1 41.5 + - + +
712D ILE* 4.8 1.8 - - + -
779D THR* 4.4 7.9 - - + -
780D LEU 3.2 10.5 - - - +
781D MET* 3.7 24.5 - - + -
791D LEU* 4.8 5.2 - - + +
792D TYR* 1.3 77.6 - - - +
794D SER* 1.3 70.4 + - - +
795D CYS* 4.7 0.4 - - - -
847D MET* 3.8 40.2 - - + +
850D GLU* 4.4 1.8 - - + -
851D LEU* 3.7 42.2 - - + +
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Residues in contact with SER 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A GLY* 3.4 25.1 + - - -
641A ARG 4.8 0.2 + - - -
708D CYS 3.2 14.1 - - - -
709D GLU* 4.2 0.4 - - - +
778D ILE 3.7 1.1 + - - +
779D THR* 3.4 4.3 - - - +
780D LEU* 2.8 51.2 + - - +
792D TYR* 3.6 25.1 - - - -
793D ILE* 1.3 75.5 - - - +
795D CYS* 1.3 65.5 + - - +
796D THR* 4.8 0.3 + - - -
847D MET* 4.4 0.7 - - - -
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Residues in contact with CYS 795 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707D VAL* 3.4 2.1 - - - +
708D CYS* 2.9 31.8 + - + +
777D CYS* 4.0 12.3 - - - -
778D ILE 3.4 4.5 - - - -
779D THR* 3.7 25.1 - - - -
793D ILE* 4.7 0.9 - - - -
794D SER* 1.3 76.9 - - - +
796D THR* 1.3 62.9 + - - +
797D MET 4.2 0.4 - - - -
843D CYS* 3.8 14.7 - - - +
846D VAL* 4.4 2.0 - - + -
847D MET* 3.6 40.8 - - + -
850D GLU* 4.0 9.9 - - - -
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Residues in contact with THR 796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A ILE* 3.3 34.1 - - + +
639A ALA* 3.6 0.5 - - - -
640A GLY 2.9 26.2 + - - -
742B MET* 5.3 0.2 - - + -
584D LEU* 4.5 6.5 - - + -
706D VAL 3.5 10.5 - - - +
707D VAL* 3.3 7.3 - - + +
777D CYS* 3.3 4.7 - - - -
778D ILE* 3.0 45.4 + - + +
794D SER* 4.8 0.5 + - - -
795D CYS* 1.3 76.0 + - - +
797D MET* 1.3 66.5 + - - +
798D PRO* 3.7 12.6 - - + +
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Residues in contact with MET 797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704D LYS 3.4 4.2 - - - +
705D SER* 3.4 1.2 - - - -
706D VAL* 2.8 37.1 + - - +
753D ALA* 4.4 1.1 - - + -
757D VAL* 3.8 22.4 - - + -
774D SER 3.2 28.3 - - - +
775D SER* 4.3 6.1 - - - +
776D ASN 3.5 14.4 - - - +
777D CYS* 3.8 12.1 - - + -
796D THR* 1.3 76.7 - - - +
798D PRO* 1.3 65.1 - - - +
799D SER 3.4 3.2 + - - -
800D ILE* 3.8 21.0 - - + +
842D VAL* 4.7 0.9 - - + -
843D CYS* 3.8 28.9 - - - -
846D VAL* 3.8 27.8 - - + -
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Residues in contact with PRO 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742B MET* 5.2 6.1 - - + -
697D ASN 4.3 5.4 - - - +
698D TRP* 3.7 54.7 - - + +
701D GLY* 3.2 14.5 - - - -
702D ARG 3.3 2.3 + - - +
704D LYS 3.7 0.5 - - - +
705D SER* 2.6 35.0 + - - +
776D ASN* 3.9 7.6 - - + +
796D THR* 3.7 15.9 - - + +
797D MET* 1.3 85.8 - - - +
799D SER* 1.3 58.4 + - - +
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Residues in contact with SER 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697D ASN* 4.1 15.6 + - - +
702D ARG* 3.0 31.1 - - - +
773D GLY* 2.9 25.4 + - - +
774D SER* 3.1 20.7 + - - -
776D ASN* 3.3 18.1 + - - +
797D MET* 3.4 1.8 - - - +
798D PRO* 1.3 80.9 - - - +
800D ILE* 1.3 63.3 + - - +
801D GLU* 3.4 6.9 + - - +
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Residues in contact with ILE 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703D GLY* 3.5 0.7 - - - -
704D LYS* 2.7 45.0 + - + +
706D VAL* 4.0 16.2 - - + -
761D TYR* 3.4 17.0 - - - +
774D SER* 3.8 19.5 - - - +
797D MET* 3.8 37.9 - - + +
799D SER* 1.3 71.3 - - - +
801D GLU* 1.3 58.2 + - - +
802D ILE* 3.6 27.8 + - + -
839D ALA* 3.7 29.2 - - + +
842D VAL* 4.3 10.5 - - + -
843D CYS* 4.4 1.1 - - + -
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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