Contacts of the strand formed by residues 604 - 612 (chain A) in PDB entry 1TAQ
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 TRP 604 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A ALA* 3.6 6.2 - - - +
601A GLU* 2.9 40.0 + - + +
602A GLU 4.7 1.9 - - - +
603A GLY* 1.3 92.1 - - - +
605A LEU* 1.3 72.6 + - - +
776A GLY 3.3 26.5 - - - -
778A ARG* 3.5 46.2 - - + -
790A GLU* 3.4 42.2 - - + -
791A ALA* 3.3 18.6 - - - +
792A PRO* 3.8 17.1 - - + +
793A LYS* 3.8 1.5 - - - +
825A GLU* 5.0 3.8 - - - +
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Residues in contact with LEU 605 (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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600A ALA* 3.8 6.7 - - - -
604A TRP* 1.3 78.4 - - - +
606A LEU* 1.3 60.1 + - - +
607A VAL* 4.5 2.1 - - - +
790A GLU* 3.4 3.3 - - - +
791A ALA* 2.8 31.0 + - - +
793A LYS* 3.8 33.7 - - + +
796A ALA* 4.0 25.4 - - + -
823A ILE* 4.0 10.8 - - + -
824A GLY* 3.3 32.8 - - - +
825A GLU* 3.6 20.0 - - + +
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Residues in contact with LEU 606 (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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449A VAL* 5.2 3.1 - - + -
598A PHE* 3.9 12.8 - - + +
599A ILE 4.2 6.5 - - - +
600A ALA* 3.8 20.3 - - + +
605A LEU* 1.3 72.5 - - - +
607A VAL* 1.3 61.8 + - - +
608A ALA* 4.0 1.4 + - + -
780A LEU* 3.6 25.1 - - + -
781A LEU* 6.4 0.2 - - + -
788A VAL* 4.2 13.7 - - + -
789A LEU 3.5 14.1 - - - +
790A GLU* 4.2 8.1 - - + +
822A GLY 3.9 0.2 - - - +
823A ILE* 3.2 4.7 - - - +
824A GLY 2.6 39.2 + - - +
825A GLU 4.2 0.7 - - - +
826A ASP* 3.7 5.2 - - - +
827A TRP* 3.2 40.2 - - + +
830A ALA* 4.1 4.4 - - + +
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Residues in contact with VAL 607 (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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605A LEU 4.5 4.9 - - - +
606A LEU* 1.3 75.2 - - - +
608A ALA* 1.3 59.4 + - - +
609A LEU* 4.0 18.2 - - + -
787A LEU 3.6 1.7 - - - +
788A VAL* 3.6 2.1 - - - -
789A LEU* 2.8 49.4 + - + +
791A ALA* 4.7 9.6 - - + -
796A ALA* 4.0 30.3 - - + +
799A VAL* 4.9 2.2 - - + -
800A ALA* 3.7 30.5 - - + +
821A VAL* 5.3 0.2 - - + -
822A GLY 3.2 13.9 - - - +
823A ILE* 4.2 8.7 - - + -
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Residues in contact with ALA 608 (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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606A LEU* 4.0 0.6 - - + -
607A VAL* 1.3 73.4 - - - +
609A LEU* 1.3 59.7 + - - +
786A GLU* 3.3 24.9 - - - +
787A LEU 3.5 5.8 - - - +
788A VAL* 4.3 6.3 - - + +
821A VAL* 3.5 0.7 - - - -
822A GLY 2.9 31.0 + - - -
827A TRP* 4.4 12.6 - - + +
830A ALA* 3.7 21.0 - - + +
832A GLU 3.5 11.2 - - - +
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Residues in contact with LEU 609 (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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607A VAL* 4.0 13.2 - - + +
608A ALA* 1.3 76.0 - - - +
610A ASP* 1.3 62.8 + - - +
785A ASP 4.3 0.2 - - - +
786A GLU* 3.3 3.4 - - - +
787A LEU* 2.9 37.2 + - + +
789A LEU* 3.4 40.8 - - + -
800A ALA 3.7 18.8 - - - +
803A ALA* 3.6 14.1 - - + -
804A LYS 3.8 6.7 - - - +
807A MET* 3.5 24.0 - - - +
819A VAL* 3.8 4.7 - - + -
820A GLU 3.5 4.9 - - - -
821A VAL* 3.5 29.4 - - + +
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Residues in contact with ASP 610 (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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609A LEU* 1.3 76.5 - - - +
611A TYR* 1.3 67.6 + - - +
612A SER* 3.4 3.3 + - - -
785A ASP* 2.9 29.4 + - - +
786A GLU* 3.8 8.2 - - + +
807A MET* 5.4 0.9 - - - -
819A VAL* 3.0 7.2 - - - +
820A GLU* 2.6 60.8 + - - +
832A GLU* 3.9 25.6 - - - +
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Residues in contact with TYR 611 (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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610A ASP* 1.3 72.9 + - - +
612A SER* 1.3 64.6 + - - +
613A GLN 3.3 3.1 + - - -
614A ILE* 3.7 42.5 + - + +
760A LEU 4.0 1.1 + - - -
761A MET* 3.6 46.4 - - + -
764A ALA* 3.5 18.7 - - - +
785A ASP* 3.0 27.4 + - + +
807A MET* 2.9 37.1 + - + -
808A GLU* 4.7 0.2 - - - -
810A VAL* 3.5 8.7 - - + +
817A LEU* 4.1 22.0 - - + -
818A GLU 3.4 5.8 - - - -
819A VAL* 3.4 24.9 - - + -
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Residues in contact with SER 612 (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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610A ASP* 3.4 4.2 + - - -
611A TYR* 1.3 67.8 - - - +
613A GLN* 1.3 81.4 + - - +
614A ILE* 3.0 2.1 + - - -
617A ARG* 3.2 25.5 + - - -
818A GLU* 2.9 25.7 + - - +
820A GLU* 3.7 28.9 + - - +
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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