Contacts of the helix formed by residues 668 - 683 (chain A) in PDB entry 1T9A
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 668 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A LEU* 5.0 0.8 - - - +
666A ASN 3.6 5.9 + - - +
667A PHE* 1.3 81.6 - - - +
669A PRO* 1.3 72.3 - - - +
670A GLU* 2.9 26.4 + - - +
671A VAL* 3.0 28.4 + - + +
672A GLU* 2.9 21.5 + - - +
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Residues in contact with PRO 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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463A MET* 3.6 34.7 - - + +
667A PHE* 3.6 28.1 - - + +
668A ASP* 1.3 86.5 - - - +
670A GLU* 1.3 64.7 + - + +
672A GLU* 3.5 0.6 + - + -
673A ARG* 3.2 22.0 + - - +
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Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASP* 2.9 11.9 + - - +
669A PRO* 1.3 80.7 - - + +
671A VAL* 1.3 65.1 + - + +
673A ARG* 3.2 27.9 + - - +
674A GLN* 3.0 44.1 + - - +
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Residues in contact with VAL 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASP* 3.0 34.4 + - + +
670A GLU* 1.3 75.4 - - + +
672A GLU* 1.3 59.1 + - - +
674A GLN* 3.2 16.5 + - - +
675A GLN* 2.8 47.6 + - + +
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Residues in contact with GLU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A MET* 3.4 36.1 + - + +
472A LYS* 5.1 2.9 + - - -
646A ASP* 5.5 1.4 - - - +
648A LYS 6.0 0.7 - - - +
649A VAL* 4.8 13.5 - - - +
650A PRO* 4.6 23.1 - - + +
667A PHE* 3.4 21.7 - - + -
668A ASP 2.9 12.6 + - - +
669A PRO* 3.8 8.5 - - + +
671A VAL* 1.3 77.5 - - - +
673A ARG* 1.3 53.8 + - - +
675A GLN* 3.4 7.3 + - - +
676A THR* 2.6 44.2 + - - +
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Residues in contact with ARG 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A MET* 5.2 3.8 - - + +
669A PRO 3.2 10.5 + - - +
670A GLU* 3.4 30.9 + - - +
671A VAL 3.2 0.2 - - - -
672A GLU* 1.3 78.3 - - - +
674A GLN* 1.3 82.3 + - - +
676A THR* 3.3 8.8 + - - -
677A GLU* 3.2 56.7 + - + +
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Residues in contact with GLN 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLU* 3.0 37.6 + - - +
671A VAL* 3.6 21.4 - - - +
673A ARG* 1.3 93.8 - - - +
675A GLN* 1.3 69.8 + - - +
677A GLU* 3.1 15.4 + - - +
678A LEU* 3.0 23.5 + - - +
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Residues in contact with GLN 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER 5.2 0.5 - - - +
589A LEU* 5.9 3.7 - - + +
593A HIS* 3.7 30.0 + - - +
671A VAL* 2.8 40.7 + - + +
672A GLU* 3.7 7.0 - - - +
674A GLN* 1.3 77.5 + - - +
676A THR* 1.3 57.9 + - - +
678A LEU* 3.4 18.6 + - - +
679A ARG* 2.9 31.7 + - - +
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Residues in contact with THR 676 (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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672A GLU* 2.6 30.4 + - - +
673A ARG* 3.5 8.9 - - - -
675A GLN* 1.3 75.3 - - - +
677A GLU* 1.3 66.9 + - + +
679A ARG* 3.1 31.5 + - - +
680A HIS* 3.1 51.9 + - + +
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Residues in contact with GLU 677 (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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673A ARG* 3.2 44.3 + - + +
674A GLN* 3.1 16.7 + - - +
676A THR* 1.3 77.1 - - + +
678A LEU* 1.3 62.1 + - - +
679A ARG 3.2 0.7 + - - -
680A HIS* 3.3 20.7 + - + +
681A LYS* 3.3 31.4 + - - +
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Residues in contact with LEU 678 (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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593A HIS* 3.9 10.1 - - + -
674A GLN 3.0 15.5 + - - +
675A GLN* 3.6 22.9 - - - +
677A GLU* 1.3 76.4 - - - +
679A ARG* 1.3 57.0 + - - +
681A LYS* 3.5 12.2 + - + +
682A ARG* 3.1 76.9 + - + +
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Residues in contact with ARG 679 (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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588A SER* 5.1 0.2 - - - -
593A HIS* 3.5 19.1 + - + -
595A TYR* 3.2 26.7 - - - +
647A LYS 4.5 5.5 + - - -
648A LYS* 3.4 42.9 + - - +
675A GLN* 2.9 20.9 + - - +
676A THR* 3.1 49.3 + - - +
678A LEU* 1.3 75.2 - - - +
680A HIS* 1.3 71.5 + - - +
682A ARG 3.4 0.2 + - - -
683A THR* 2.9 37.5 + - + +
687A HIS* 2.9 30.1 + - - +
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Residues in contact with HIS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A THR* 3.1 36.7 + - + +
677A GLU* 3.3 11.2 + - + +
679A ARG* 1.3 87.6 - - - +
681A LYS* 1.3 60.2 + - + +
684A GLY 3.5 0.7 + - - -
685A GLY* 2.6 36.9 + - - +
687A HIS* 3.0 38.3 + - - -
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Residues in contact with LYS 681 (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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677A GLU* 3.3 25.8 + - - +
678A LEU* 3.8 15.2 - - + +
679A ARG 3.1 0.6 - - - -
680A HIS* 1.3 76.5 - - + +
682A ARG* 1.3 69.1 + - + +
684A GLY* 3.0 15.1 + - - -
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Residues in contact with ARG 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER 5.0 0.2 + - - -
592A GLU* 3.4 52.7 + - - +
593A HIS* 3.0 43.8 + - + -
678A LEU* 3.1 45.5 + - + +
679A ARG 4.0 1.8 - - - +
681A LYS* 1.3 81.2 - - + +
683A THR* 1.3 59.5 + - - +
684A GLY 3.2 0.9 + - - -
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Residues in contact with THR 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A HIS* 3.4 26.2 - - + +
595A TYR* 3.5 23.3 - - + -
679A ARG* 2.9 27.1 + - + +
682A ARG* 1.3 75.7 - - - +
684A GLY* 1.3 61.0 + - - +
685A GLY 3.6 2.1 + - - -
686A LYS* 3.0 26.0 + - - +
687A HIS* 2.9 32.2 + - + -
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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