Contacts of the strand formed by residues 790 - 800 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711C VAL* 4.1 16.5 - - + +
712C ILE 3.6 8.5 - - - +
713C PRO* 3.5 7.7 - - - +
714C ALA* 3.0 25.1 + - - +
725C THR* 3.4 9.8 - - - +
783C ALA* 3.6 0.5 - - - -
784C SER* 2.8 35.5 + - - +
785C GLY* 3.5 18.7 - - - -
786C PRO* 4.0 8.5 - - - +
787C THR* 5.6 3.4 - - - +
789C GLU* 1.3 81.4 - - - +
791C LEU* 1.3 59.5 + - - +
792C TYR 4.0 0.2 - - - -
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Residues in contact with LEU 791 (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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710C ALA 3.6 1.2 - - - +
711C VAL* 3.2 4.7 - - - -
712C ILE* 2.6 51.2 + - + +
717C VAL* 4.0 10.3 - - + -
721C LEU* 5.0 0.9 - - + -
725C THR* 3.7 26.1 + - + +
728C MET* 3.6 43.3 - - + -
729C ILE* 4.0 18.6 - - + -
781C MET* 4.1 12.8 - - + -
782C GLU 4.1 1.1 - - - +
790C ASP* 1.3 70.5 - - - +
792C TYR* 1.3 73.6 + - - +
793C ILE 3.8 1.0 + - - +
851C LEU* 3.7 19.7 - - + -
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Residues in contact with TYR 792 (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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597B PRO 5.1 5.2 - - - -
598B ARG* 5.7 1.3 - - + -
599B ALA* 3.9 2.6 + - - +
641B ARG* 3.8 30.6 + - + +
709C GLU* 2.8 38.7 + - + +
710C ALA 3.6 9.0 - - - -
711C VAL* 4.0 15.5 - - + +
780C LEU* 5.0 4.5 - - + -
781C MET* 3.2 7.9 - - - +
782C GLU* 2.9 72.6 + - + +
784C SER* 4.0 15.8 - - - +
790C ASP 3.8 1.6 + - - -
791C LEU* 1.3 73.5 - - - +
793C ILE* 1.3 62.5 + - - +
794C SER* 3.5 32.9 - - - -
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Residues in contact with ILE 793 (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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709C GLU* 3.2 5.2 - - - +
710C ALA* 3.0 42.2 + - + +
712C ILE* 4.8 4.5 - - + -
779C THR* 4.1 9.9 - - + -
780C LEU 3.3 11.9 - - - +
781C MET* 3.9 24.2 - - + -
791C LEU* 5.0 1.8 - - + -
792C TYR* 1.3 78.8 - - - +
794C SER* 1.3 68.0 + - - +
847C MET* 3.8 36.3 - - + +
850C GLU* 4.4 1.3 - - + -
851C LEU* 3.6 42.8 - - + +
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Residues in contact with SER 794 (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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640B GLY* 3.3 27.2 + - - -
708C CYS 3.3 12.1 - - - -
709C GLU* 4.3 0.7 - - - +
778C ILE 3.8 0.7 + - - +
779C THR* 3.4 3.1 - - - -
780C LEU* 2.9 50.7 + - - +
792C TYR* 3.5 25.9 - - - -
793C ILE* 1.3 77.3 - - - +
795C CYS* 1.3 64.1 + - - +
796C THR* 4.3 0.7 + - - -
847C MET* 4.4 0.9 - - - -
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Residues in contact with CYS 795 (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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707C VAL* 3.4 3.3 - - - +
708C CYS* 3.0 42.6 + - - +
777C CYS* 4.0 12.3 - - - -
778C ILE 3.5 4.3 - - - -
779C THR* 3.6 25.4 - - - -
793C ILE* 4.7 0.2 - - - -
794C SER* 1.3 76.7 - - - +
796C THR* 1.3 61.3 + - - +
797C MET 4.2 0.2 - - - -
843C CYS* 3.5 11.9 - - - +
846C VAL* 4.4 1.3 - - + -
847C MET* 3.6 33.6 - - + -
850C GLU* 4.0 9.9 - - - -
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Residues in contact with THR 796 (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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742A MET* 5.4 1.6 - - + -
638B ILE* 3.3 33.7 - - + +
639B ALA* 3.6 1.2 - - - -
640B GLY* 2.9 27.2 + - - -
584C LEU* 4.5 6.1 - - + -
706C VAL 3.5 9.9 - - - +
707C VAL* 3.5 7.1 - - + +
777C CYS* 3.3 4.7 - - - -
778C ILE* 3.1 44.1 + - + +
794C SER* 4.8 0.7 + - - -
795C CYS* 1.3 73.6 + - - +
797C MET* 1.3 68.0 + - - +
798C PRO* 3.6 11.4 - - + +
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Residues in contact with MET 797 (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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704C LYS 3.5 3.1 - - - +
705C SER* 3.3 2.6 - - - -
706C VAL* 2.7 40.4 + - - +
753C ALA* 4.7 0.7 - - + -
757C VAL* 3.8 21.8 - - + -
774C SER 3.2 27.6 - - - +
775C SER* 4.4 4.3 - - - +
776C ASN 3.5 14.6 - - - +
777C CYS* 3.7 12.8 - - + -
796C THR* 1.3 77.9 - - - +
798C PRO* 1.3 60.1 - - - +
799C SER 3.4 2.7 + - - -
800C ILE* 3.8 22.6 - - + +
842C VAL* 4.4 0.7 - - + -
843C CYS* 3.8 27.8 - - - -
846C VAL* 3.8 30.1 - - + -
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Residues in contact with PRO 798 (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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742A MET* 6.2 3.1 - - + -
697C ASN 4.4 2.0 - - - +
698C TRP* 3.5 57.7 - - + +
701C GLY* 3.2 16.7 - - - +
702C ARG 3.3 2.3 + - - +
704C LYS 3.6 2.5 - - - +
705C SER* 2.7 32.2 + - - +
776C ASN 3.9 5.4 - - - +
796C THR* 3.6 15.2 - - + +
797C MET* 1.3 86.3 - - - +
799C SER* 1.3 60.3 + - - +
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Residues in contact with SER 799 (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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697C ASN* 3.8 21.2 + - - +
702C ARG* 3.0 28.2 - - - +
773C GLY 2.9 25.1 + - - +
774C SER* 3.1 22.7 + - - -
776C ASN* 3.0 19.3 + - - +
797C MET* 3.4 1.6 - - - +
798C PRO* 1.3 82.2 - - - +
800C ILE* 1.3 59.8 + - - +
801C GLU* 3.4 6.3 + - - +
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Residues in contact with ILE 800 (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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702C ARG 3.5 0.2 + - - -
703C GLY* 3.6 0.9 - - - -
704C LYS* 2.8 46.8 + - + +
706C VAL* 4.2 12.6 - - + -
757C VAL* 5.9 0.2 - - + -
761C TYR* 3.6 16.2 - - - +
774C SER* 3.9 18.4 - - - +
797C MET* 3.8 38.4 - - + -
799C SER* 1.3 69.7 - - - +
801C GLU* 1.3 60.0 + - - +
802C ILE* 3.5 22.4 + - + -
839C ALA* 3.7 33.2 - - + +
842C VAL* 4.0 11.7 - - + -
843C CYS* 4.3 2.2 - - + -
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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