Contacts of the helix formed by residues 656 - 671 (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 PRO 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A VAL 4.6 1.1 - - - +
655A ASP* 1.4 87.9 - - + +
657A LEU* 1.3 61.8 + - - +
659A ARG* 3.7 6.2 + - + +
660A ARG* 3.1 23.8 + - - +
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Residues in contact with LEU 657 (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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655A ASP* 3.2 11.9 - - - +
656A PRO* 1.3 78.8 - - - +
658A MET* 1.3 66.1 + - + +
660A ARG* 3.0 33.4 + - - +
661A ALA* 3.0 25.4 + - + +
682A LEU* 4.4 15.0 - - + -
684A ILE* 5.2 7.6 - - + -
692A PHE* 6.1 3.6 - - + -
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Residues in contact with MET 658 (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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643A ALA* 3.9 4.2 - - + +
647A PHE* 3.5 56.4 - - + +
649A VAL* 3.9 29.2 - - + -
653A ALA 4.6 2.7 - - - +
654A VAL* 3.5 12.1 - - + -
655A ASP* 2.7 50.6 + - - +
657A LEU* 1.3 72.4 - - + +
659A ARG* 1.3 57.1 + - - +
660A ARG 3.2 0.2 + - - -
661A ALA* 3.2 5.0 + - - +
662A ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 659 (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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637A ASP* 2.7 41.7 + - - -
639A HIS* 3.5 38.9 + - + +
640A THR* 3.4 11.1 + - - +
643A ALA* 4.3 1.3 - - - -
654A VAL* 3.9 9.1 - - + +
655A ASP 3.1 9.5 + - - +
656A PRO* 4.2 7.0 - - + +
658A MET* 1.3 78.8 - - - +
660A ARG* 1.3 56.3 + - - +
662A ALA* 3.9 0.4 - - - +
663A LYS* 2.9 58.0 + - - +
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Residues in contact with ARG 660 (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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656A PRO 3.1 15.5 + - - +
657A LEU* 3.0 46.0 + - - +
659A ARG* 1.3 76.4 - - - +
661A ALA* 1.3 60.3 + - - +
663A LYS* 3.5 5.3 + - - +
664A THR* 2.7 38.8 + - + +
681A GLU 5.1 4.0 + - - -
682A LEU* 3.5 38.4 - - - +
683A ALA* 5.5 2.0 - - - +
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Residues in contact with ALA 661 (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* 5.4 0.2 - - - -
647A PHE* 4.2 11.7 - - + -
657A LEU* 3.0 14.5 + - + +
658A MET 3.2 6.7 + - - +
660A ARG* 1.3 73.8 - - - +
662A ALA* 1.3 60.4 + - - +
664A THR* 3.5 1.8 + - - -
665A ILE* 2.9 38.7 + - + +
678A LEU* 5.9 0.2 - - + -
682A LEU* 3.8 25.1 - - + -
692A PHE* 4.1 25.6 - - + -
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Residues in contact with ALA 662 (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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639A HIS* 3.1 30.1 - - - +
642A THR* 4.0 14.8 - - + +
643A ALA* 3.8 17.0 - - + +
646A MET* 4.7 8.5 - - - -
647A PHE* 5.1 0.8 - - - -
658A MET 3.0 14.5 + - - +
659A ARG 3.9 1.3 - - - +
661A ALA* 1.3 75.5 - - - +
663A LYS* 1.3 58.7 + - - +
665A ILE* 4.0 1.2 - - - +
666A ASN* 2.9 35.4 + - - +
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Residues in contact with LYS 663 (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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639A HIS* 3.2 35.3 + - + +
659A ARG* 2.9 48.6 + - - +
660A ARG* 3.8 7.0 - - - +
661A ALA 3.3 0.2 - - - -
662A ALA* 1.3 77.1 - - - +
664A THR* 1.3 62.8 + - + +
666A ASN* 3.7 2.6 - - - +
667A PHE* 3.1 24.2 + - + +
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Residues in contact with THR 664 (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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660A ARG* 2.7 41.0 + - + +
661A ALA* 3.9 3.4 + - - -
662A ALA 3.3 0.2 - - - -
663A LYS* 1.3 74.4 - - + +
665A ILE* 1.3 56.5 + - - +
667A PHE* 3.0 16.4 + - - +
668A GLY* 2.5 34.0 + - - -
673A MET* 4.1 8.9 - - - +
678A LEU* 3.5 23.6 - - - +
681A GLU* 5.0 12.6 - - + +
682A LEU* 4.6 6.4 - - + +
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Residues in contact with ILE 665 (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* 3.5 35.0 - - + -
661A ALA 2.9 22.5 + - - +
662A ALA* 4.0 2.9 - - - +
664A THR* 1.3 71.4 + - - +
666A ASN* 1.3 58.6 + - - +
667A PHE 2.9 4.7 - - - -
668A GLY* 4.1 1.8 - - - +
669A VAL* 2.8 37.6 + - + +
673A MET* 5.6 2.0 - - - -
678A LEU* 4.1 23.8 - - + -
692A PHE* 3.7 24.9 - - + +
693A ILE* 5.1 8.7 - - + -
696A TYR* 3.6 32.5 - - + -
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Residues in contact with ASN 666 (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* 3.5 25.7 - - + +
628A LEU* 5.4 0.2 - - - +
638A ILE* 3.4 20.5 + - - +
639A HIS* 3.4 29.2 - - + +
642A THR* 3.1 23.4 + - - -
662A ALA 2.9 18.6 + - - +
663A LYS 3.7 5.2 - - - +
665A ILE* 1.3 77.5 - - - +
667A PHE* 1.3 57.0 + - - +
669A VAL* 3.3 16.6 - - - +
670A LEU* 3.8 5.5 - - - +
696A TYR* 2.9 33.1 + - - -
700A PHE* 4.9 0.2 - - - -
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Residues in contact with PHE 667 (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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663A LYS* 3.1 14.5 + - + +
664A THR* 3.2 20.4 - - - +
665A ILE 2.9 0.2 - - - -
666A ASN* 1.3 77.9 - - - +
668A GLY* 1.3 61.7 + - - +
669A VAL 3.4 0.2 - - - -
670A LEU* 3.2 29.8 - - + +
671A TYR* 3.8 32.2 - + - -
673A MET* 4.1 9.6 - - + -
681A GLU* 5.6 5.2 - - + -
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Residues in contact with GLY 668 (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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664A THR 2.5 19.4 + - - -
665A ILE* 3.1 1.5 + - - -
667A PHE* 1.3 70.6 - - - +
669A VAL* 1.3 66.3 + - - +
670A LEU 3.0 2.7 + - - -
671A TYR* 3.1 9.0 + - - -
672A GLY 3.0 22.6 + - - -
673A MET* 3.2 36.4 + - - -
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Residues in contact with VAL 669 (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* 5.0 0.2 - - + -
619A LEU* 4.3 16.4 - - + -
665A ILE* 2.8 27.8 + - + +
666A ASN* 3.3 19.3 - - - +
668A GLY* 1.3 70.5 - - - +
670A LEU* 1.3 59.1 + - - +
672A GLY* 2.9 26.3 + - - +
696A TYR* 3.9 20.6 - - + +
697A PHE* 4.2 10.3 - - + -
703A VAL* 3.8 28.5 - - + -
706A TRP* 5.9 1.7 - - - -
707A ILE* 4.2 17.2 - - + +
749A PHE* 4.4 3.6 - - - -
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Residues in contact with LEU 670 (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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615A GLU* 3.8 41.1 - - + +
616A LEU* 4.0 16.6 - - + -
619A LEU* 3.9 27.1 - - + -
666A ASN 3.8 11.2 - - - +
667A PHE* 3.2 28.0 + - + +
668A GLY 3.0 0.2 - - - -
669A VAL* 1.3 81.3 - - - +
671A TYR* 1.3 60.8 + - + +
672A GLY 3.6 0.2 - - - -
706A TRP* 5.8 0.5 - - - -
749A PHE* 3.8 15.1 - - - +
750A ASN* 4.0 14.0 - - - +
753A VAL* 4.4 25.1 - - + +
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Residues in contact with TYR 671 (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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667A PHE* 3.8 42.9 - + - -
668A GLY* 3.1 1.7 + - - -
670A LEU* 1.3 79.0 - - + +
672A GLY* 1.3 51.1 + - - +
673A MET* 2.7 67.2 + - + +
677A ARG* 3.1 36.5 + - - -
681A GLU* 4.3 1.7 + - - -
746A ARG* 3.5 28.2 - - + +
749A PHE* 3.2 16.4 - - - -
750A ASN* 3.6 22.0 - - + +
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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