Contacts of the helix formed by residues 679 - 695 (chain A) in PDB entry 1TBF
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 SER 679 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ASN* 4.1 4.2 - - - +
677A ASP 4.0 2.2 + - - -
678A GLU* 1.3 70.7 - - - +
680A VAL* 1.3 65.1 + - - +
682A GLU* 3.2 17.9 + - - -
683A HIS* 3.0 31.2 + - - -
721A LEU* 4.0 15.5 - - - -
724A ASP* 2.7 27.1 + - - -
727A LEU* 3.7 21.0 - - - +
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Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ASN* 3.4 15.0 + - + +
665A LEU* 4.0 15.5 - - + -
666A ILE* 4.6 7.9 - - + -
672A LEU* 3.6 40.6 - - + +
673A ALA* 3.6 17.3 - - + +
676A TYR* 3.8 7.3 - - + -
677A ASP* 3.6 36.6 - - - +
678A GLU 3.7 4.7 - - - +
679A SER* 1.3 75.6 - - - +
681A LEU* 1.3 65.5 + - - +
683A HIS* 3.4 3.5 + - - +
684A HIS* 3.1 20.1 + - - +
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A HIS* 3.7 21.3 - - + +
658A PRO* 3.5 31.6 - - + -
660A VAL 3.6 13.5 - - - +
661A SER* 3.9 2.0 - - - -
662A ASN* 2.8 47.8 + - - +
665A LEU* 3.6 19.7 - - + -
672A LEU* 5.6 2.5 - - + -
680A VAL* 1.3 74.1 - - - +
682A GLU* 1.3 67.6 + - - +
684A HIS* 3.0 8.7 + - + +
685A HIS* 2.8 45.5 + - + +
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Residues in contact with GLU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MG 4.0 12.3 - - - -
662A ASN* 3.0 27.8 + - - -
679A SER* 3.2 16.2 + - - +
681A LEU* 1.3 83.2 - - - +
683A HIS* 1.3 65.0 + - - +
685A HIS* 3.3 12.0 + - + -
686A PHE* 3.0 21.3 + - - +
720A ILE* 3.5 29.4 - - - +
721A LEU* 3.8 20.3 - - + +
723A THR* 4.0 5.7 - - - +
724A ASP* 3.5 32.0 - - + +
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Residues in contact with HIS 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A TYR* 3.5 43.6 + + + +
678A GLU* 3.1 22.7 + - + -
679A SER* 3.0 28.6 + - - +
682A GLU* 1.3 74.0 - - - +
684A HIS* 1.3 58.4 + - - +
686A PHE* 3.3 10.7 + + + +
687A ASP* 2.9 28.1 + - - +
717A LYS* 4.4 18.2 + - - -
721A LEU* 3.9 29.5 - - + +
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Residues in contact with HIS 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ARG* 5.4 0.2 + - - -
655A LEU 4.1 9.0 - - - -
656A ASP* 2.7 44.6 + - - +
658A PRO* 5.6 2.2 - - + -
672A LEU* 3.6 44.1 - - + +
675A MET* 6.0 0.2 - - - +
676A TYR* 3.8 10.0 + - + -
680A VAL 3.1 11.5 + - - +
681A LEU* 3.0 11.7 + - + +
683A HIS* 1.3 77.6 - - - +
685A HIS* 1.4 66.3 + + - +
687A ASP* 3.2 11.7 + - - +
688A GLN* 3.0 42.5 + - + +
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Residues in contact with HIS 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MG 4.1 4.1 - - - -
652A SER 3.8 6.0 - - - +
653A HIS 2.8 32.5 - - - +
654A ASP* 3.3 24.1 + - - -
655A LEU 2.8 36.0 + - - +
656A ASP 4.8 0.2 - - - -
657A HIS* 3.5 29.2 + - - -
681A LEU* 2.8 44.6 + - + +
682A GLU* 3.3 12.1 + - + +
684A HIS* 1.4 75.5 - + - +
686A PHE* 1.4 57.0 + - - +
688A GLN* 3.3 4.4 + - - +
689A CYS* 2.9 26.9 + - - +
720A ILE* 4.1 4.0 - - + -
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Residues in contact with PHE 686 (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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682A GLU 3.0 17.8 + - - +
683A HIS* 3.6 9.6 - + - +
685A HIS* 1.4 74.2 - - - +
687A ASP* 1.3 67.8 + - - +
689A CYS* 3.1 7.3 + - + +
690A LEU* 3.0 61.7 + - + +
713A LEU* 3.8 12.6 - - + -
716A ILE* 4.2 15.7 - - + -
717A LYS* 3.6 63.9 - - + +
720A ILE* 4.1 13.6 - - + +
721A LEU* 6.0 2.2 - - + -
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Residues in contact with ASP 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A MET* 5.3 4.4 - - - +
676A TYR* 3.8 18.0 + - - +
683A HIS 2.9 13.8 + - - +
684A HIS* 3.4 18.6 + - - +
686A PHE* 1.3 78.5 - - - +
688A GLN* 1.3 65.0 + - - +
690A LEU* 3.3 9.3 + - - +
691A MET* 3.0 27.9 + - - +
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Residues in contact with GLN 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ASN* 4.0 19.9 - - - +
655A LEU* 3.7 20.2 - - + +
656A ASP* 3.5 27.5 + - + +
684A HIS* 3.0 43.0 + - - +
685A HIS 3.6 7.4 - - - +
687A ASP* 1.3 81.6 + - - +
689A CYS* 1.3 61.9 + - - +
691A MET* 3.2 16.2 + - - +
692A ILE* 3.0 30.1 + - + +
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Residues in contact with CYS 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TRP* 5.3 0.6 + - - -
648A ILE* 4.2 5.2 - - - -
652A SER* 3.6 30.3 - - - -
655A LEU* 3.6 9.1 - - - +
685A HIS 2.9 13.5 + - - +
686A PHE* 3.1 17.0 + - + +
688A GLN* 1.3 76.9 - - - +
690A LEU* 1.3 57.6 + - - +
692A ILE* 3.4 4.3 + - - +
693A LEU* 3.0 50.5 + - - +
716A ILE* 3.9 23.6 - - - -
720A ILE* 4.1 2.2 - - + -
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Residues in contact with LEU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PHE* 3.0 53.1 + - + +
687A ASP* 3.7 11.4 - - - +
689A CYS* 1.3 73.6 - - - +
691A MET* 1.3 66.5 + - - +
693A LEU* 3.3 8.4 + - + +
694A ASN* 2.9 43.4 + - - +
709A TYR* 5.7 0.4 - - - +
713A LEU* 3.9 37.5 - - + -
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Residues in contact with MET 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ASN* 5.3 9.0 - - - +
687A ASP* 3.0 15.6 + - - +
688A GLN* 3.2 21.1 + - - +
690A LEU* 1.3 78.6 - - - +
692A ILE* 1.3 68.7 + - - +
694A ASN* 3.5 5.1 + - - +
695A SER* 2.7 52.8 + - - +
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Residues in contact with ILE 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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598A TRP* 3.7 22.7 - - + +
601A SER* 3.6 33.7 - - - +
602A VAL* 4.0 9.4 - - + -
605A ASN* 3.8 26.7 - - + +
655A LEU* 3.9 28.5 - - + -
688A GLN* 3.0 19.4 + - + +
689A CYS* 3.9 3.8 - - - +
691A MET* 1.3 86.5 - - - +
693A LEU* 1.3 63.8 + - - +
694A ASN 3.0 3.3 + - - -
695A SER* 3.2 15.3 + - - +
698A ASN* 3.3 16.5 - - - +
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TRP* 3.5 23.6 - - + +
648A ILE* 4.4 5.4 - - + -
689A CYS* 3.0 40.6 + - - +
690A LEU* 3.3 8.9 + - + +
692A ILE* 1.3 76.0 - - - +
694A ASN* 1.3 61.0 + - - +
695A SER 3.6 0.2 - - - -
698A ASN 4.3 3.4 - - - -
699A GLN* 3.2 30.1 + - - +
700A ILE* 3.7 26.0 - - + +
701A LEU* 4.2 20.0 - - + -
709A TYR* 5.6 3.6 - - + +
713A LEU* 4.1 25.6 - - + -
716A ILE* 4.3 8.1 - - + -
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Residues in contact with ASN 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 LEU* 2.9 35.1 + - - +
691A MET* 3.8 5.7 - - - +
693A LEU* 1.3 80.1 - - - +
695A SER* 1.3 63.9 + - - +
696A PRO* 3.6 3.8 - - - +
699A GLN* 4.2 21.0 + - - +
709A TYR* 3.6 20.0 + - - -
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Residues in contact with SER 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A SER* 5.8 0.2 - - - -
691A MET* 2.7 43.9 + - - +
692A ILE* 3.2 13.1 + - - -
694A ASN* 1.3 79.1 - - - +
696A PRO* 1.3 74.4 - - - +
697A GLY 3.2 0.3 + - - -
698A ASN* 3.1 30.0 + - - +
699A GLN* 3.7 6.2 - - - +
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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
------------------------------------------------------------
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