Contacts of the helix formed by residues 686 - 699 (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 TYR 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A ALA* 3.9 6.6 - - + +
676A HIS* 3.8 45.1 - + + -
679A SER* 3.2 19.4 + - - +
685A PRO* 1.3 71.0 - - - +
687A GLU* 1.3 86.9 + - - +
689A ALA* 3.1 5.7 + - - +
690A GLN* 3.1 60.5 + - + +
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Residues in contact with GLU 687 (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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685A PRO* 4.4 14.4 - - + +
686A TYR* 1.3 97.0 - - - +
688A GLU* 1.3 62.3 - - - +
690A GLN* 3.1 19.3 + - - +
691A ALA* 3.2 11.6 + - - +
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Residues in contact with GLU 688 (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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684A ILE* 3.2 32.9 - - + +
685A PRO* 3.0 16.3 + - + +
687A GLU* 1.3 78.7 - - - +
689A ALA* 1.3 57.7 + - - +
691A ALA* 3.2 9.3 + - + +
692A PHE* 2.9 66.5 + - + -
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Residues in contact with ALA 689 (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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675A ALA 3.7 5.8 - - - +
678A LEU* 3.4 23.2 - - + +
679A SER* 3.5 39.3 - - - +
684A ILE* 3.4 9.8 - - + +
685A PRO 3.2 2.2 + - - -
686A TYR 3.1 10.1 + - - +
688A GLU* 1.3 78.7 - - - +
690A GLN* 1.3 60.3 + - - +
692A PHE* 3.5 5.1 + - - +
693A ILE* 3.3 20.7 + - - +
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Residues in contact with GLN 690 (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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675A ALA* 3.7 19.3 - - + +
686A TYR* 3.1 51.1 + - + +
687A GLU* 3.1 13.6 + - - +
689A ALA* 1.3 77.2 - - - +
691A ALA* 1.3 63.4 + - - +
693A ILE* 3.5 6.0 + - - +
694A GLU* 3.2 24.5 + - - +
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Residues in contact with ALA 691 (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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687A GLU 3.2 7.8 + - - +
688A GLU* 3.2 13.2 + - + +
690A GLN* 1.3 75.1 - - - +
692A PHE* 1.3 69.3 + - + +
694A GLU* 3.2 9.1 + - - +
695A ARG* 3.0 33.6 + - - +
833A BGL 4.3 17.6 + - - +
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Residues in contact with PHE 692 (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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646A MET* 3.2 23.8 - - + +
647A PHE* 3.5 37.0 - + - -
657A LEU* 6.1 3.6 - - + -
661A ALA* 4.1 22.0 - - + -
665A ILE* 3.7 11.8 - - + +
678A LEU* 4.4 6.1 - - + -
682A LEU* 5.1 5.6 - - + -
684A ILE* 4.6 14.1 - - + -
688A GLU* 2.9 50.5 + - + -
689A ALA* 3.6 15.0 - - - +
690A GLN 3.3 0.2 - - - -
691A ALA* 1.3 81.4 - - + +
693A ILE* 1.3 56.9 + - - +
695A ARG* 3.6 11.8 + - - -
696A TYR* 3.1 22.9 + - - +
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Residues in contact with ILE 693 (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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665A ILE* 4.9 8.1 - - + -
674A SER 4.3 4.3 - - - +
675A ALA* 3.6 38.8 - - + +
678A LEU* 3.7 17.5 - - + -
689A ALA 3.3 12.9 + - - +
690A GLN* 3.7 7.6 - - - +
691A ALA 3.2 0.4 - - - -
692A PHE* 1.3 73.9 - - - +
694A GLU* 1.3 68.6 + - + +
696A TYR* 2.9 18.4 + - + +
697A PHE* 3.0 37.6 + - + -
704A ARG* 6.1 0.2 - - - +
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Residues in contact with GLU 694 (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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690A GLN 3.2 12.4 + - - +
691A ALA* 3.2 12.5 + - - +
693A ILE* 1.3 80.8 - - + +
695A ARG* 1.3 51.6 + - - +
697A PHE 3.1 3.3 + - - -
698A GLN* 2.8 58.5 + - - +
704A ARG* 3.2 26.5 + - - +
833A BGL 4.0 29.8 - - - +
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Residues in contact with ARG 695 (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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645A TRP 4.8 2.4 - - - +
646A MET* 2.7 52.5 + - + +
647A PHE* 3.9 22.4 - - - +
691A ALA* 3.0 22.2 + - - +
692A PHE* 3.7 17.8 - - - +
694A GLU* 1.3 74.5 - - - +
696A TYR* 1.3 54.5 + - - +
698A GLN* 3.1 11.6 + - - +
699A SER* 2.5 35.0 + - - -
833A BGL 3.1 52.1 + - + +
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Residues in contact with TYR 696 (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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616A LEU* 5.2 1.4 - - - +
619A LEU* 4.8 2.9 - - - +
628A LEU* 4.4 14.0 - - - +
642A THR* 3.7 19.7 - - + -
646A MET* 4.1 7.2 - - - +
665A ILE* 3.6 28.5 - - + -
666A ASN* 2.9 30.7 + - - -
669A VAL* 3.9 22.2 - - + +
692A PHE 3.1 14.3 + - - +
693A ILE* 2.9 12.9 + - + +
695A ARG* 1.3 76.5 - - - +
697A PHE* 1.3 87.7 + + - +
699A SER* 3.0 7.9 + - - -
700A PHE* 2.8 58.3 + + - +
703A VAL* 4.1 11.7 - - + +
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Residues in contact with PHE 697 (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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669A VAL* 4.2 8.5 - - + -
693A ILE* 3.0 35.9 + - + +
694A GLU 4.0 1.6 - - - +
696A TYR* 1.3 88.3 - + - +
698A GLN* 1.3 60.9 + - - +
699A SER 3.2 0.2 - - - -
700A PHE 3.2 17.7 - - - +
701A PRO* 3.0 28.9 - - - +
703A VAL* 3.3 27.1 - - + -
704A ARG* 3.5 60.7 + - + +
707A ILE* 3.9 20.6 - - + -
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Residues in contact with GLN 698 (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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645A TRP 6.2 0.2 - - - +
694A GLU* 2.8 40.6 + - - +
695A ARG* 3.1 10.5 + - - +
697A PHE* 1.3 78.5 - - - +
699A SER* 1.3 60.2 + - - +
701A PRO* 3.9 10.8 - - - +
704A ARG* 5.0 6.8 - - - +
833A BGL 3.7 40.5 + - - +
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Residues in contact with SER 699 (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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627A ASN* 3.3 24.1 - - - +
642A THR 5.3 0.4 + - - -
645A TRP* 3.9 37.1 + - - +
646A MET* 4.5 4.7 - - - +
695A ARG 2.5 19.6 + - - -
696A TYR* 3.0 9.3 + - - -
698A GLN* 1.3 77.2 - - - +
700A PHE* 1.3 79.8 + - - +
701A PRO* 3.6 3.1 - - - +
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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