Contacts of the helix formed by residues 668 - 684 (chain B) in PDB entry 1T9D
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B LEU* 5.0 0.4 - - - +
666B ASN 3.8 4.2 + - - +
667B PHE* 1.3 84.2 - - - +
669B PRO* 1.3 74.1 - - - +
670B GLU* 3.0 22.6 + - - +
671B VAL* 3.1 30.9 + - + +
672B GLU* 3.1 20.4 + - - +
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Residues in contact with PRO 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B MET* 4.5 13.0 - - + +
667B PHE* 3.6 31.3 - - + -
668B ASP* 1.3 89.0 - - - +
670B GLU* 1.3 63.4 + - + +
672B GLU* 3.4 4.5 + - + +
673B ARG* 3.2 49.9 + - - +
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Residues in contact with GLU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ASP* 3.0 10.7 + - - +
669B PRO* 1.3 78.1 - - + +
671B VAL* 1.3 67.8 + - + +
673B ARG* 3.2 28.5 + - - +
674B GLN* 3.0 48.8 + - - +
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Residues in contact with VAL 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ASP* 3.1 34.2 + - + +
670B GLU* 1.3 78.8 - - + +
672B GLU* 1.3 57.3 + - - +
674B GLN* 3.1 18.2 + - + +
675B GLN* 2.8 40.8 + - + +
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Residues in contact with GLU 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B MET* 3.4 40.1 + - - +
472B LYS* 5.2 1.0 + - - -
648B LYS 5.8 2.5 - - - +
649B VAL* 5.1 11.9 - - - +
650B PRO* 4.9 21.1 - - + +
667B PHE* 3.4 15.0 - - + -
668B ASP 3.1 12.6 + - - +
669B PRO* 3.7 10.8 - - + +
670B GLU 3.3 0.2 - - - -
671B VAL* 1.3 77.1 - - - +
673B ARG* 1.3 57.9 + - + +
675B GLN* 3.1 10.0 + - + +
676B THR* 2.8 39.3 + - - +
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Residues in contact with ARG 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B MET* 3.8 26.1 - - - +
669B PRO* 3.2 38.7 + - - +
670B GLU* 3.5 32.9 + - - +
672B GLU* 1.3 81.0 - - + +
674B GLN* 1.3 61.1 + - - +
676B THR* 3.4 8.6 + - - -
677B GLU* 3.2 21.5 + - - +
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Residues in contact with GLN 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B GLU* 3.0 36.5 + - - +
671B VAL* 3.6 21.2 - - + +
673B ARG* 1.3 76.5 - - - +
675B GLN* 1.3 63.6 + - + +
677B GLU* 3.5 6.6 + - - +
678B LEU* 3.1 24.1 + - - +
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Residues in contact with GLN 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B SER* 4.8 7.6 - - - +
589B LEU* 5.9 0.7 - - - -
593B HIS* 3.0 26.0 + - - -
671B VAL* 2.8 28.5 + - + +
672B GLU* 3.1 13.7 + - + +
674B GLN* 1.3 75.7 - - - +
676B THR* 1.3 59.4 + - - +
678B LEU* 3.4 19.7 + - - +
679B ARG* 2.8 38.5 + - - +
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Residues in contact with THR 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B GLU* 2.8 23.9 + - - +
673B ARG* 3.6 12.1 - - - -
674B GLN 3.3 0.2 - - - -
675B GLN* 1.3 77.0 - - - +
677B GLU* 1.3 57.9 + - - +
679B ARG* 3.3 25.5 + - - +
680B HIS* 2.9 61.9 + - + +
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Residues in contact with GLU 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673B ARG 3.2 13.7 + - - +
674B GLN* 3.8 6.5 - - - +
675B GLN 3.3 0.2 - - - -
676B THR* 1.3 79.9 - - - +
678B LEU* 1.3 63.9 + - - +
680B HIS* 3.3 10.5 + - - +
681B LYS* 3.0 28.2 + - - +
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Residues in contact with LEU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B HIS* 3.7 21.3 - - + -
674B GLN 3.1 18.4 + - - +
675B GLN* 3.6 17.7 - - - +
677B GLU* 1.3 76.5 - - - +
679B ARG* 1.3 62.2 + - - +
681B LYS* 3.2 14.4 + - + +
682B ARG* 2.9 63.1 + - + +
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Residues in contact with ARG 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B SER* 4.8 1.4 + - - -
593B HIS* 3.8 19.6 + - + -
595B TYR* 3.1 35.0 - - + +
647B LYS 4.6 3.6 + - - -
648B LYS* 3.3 43.1 + - - +
675B GLN* 2.8 19.1 + - - +
676B THR* 3.4 44.5 + - - +
678B LEU* 1.3 76.5 - - - +
680B HIS* 1.3 56.6 + - - +
682B ARG* 3.3 0.7 + - - -
683B THR* 2.8 33.3 + - + +
687B HIS* 2.8 32.7 + - - +
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Residues in contact with HIS 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B THR* 2.9 43.7 + - + +
677B GLU* 3.5 10.1 - - - +
679B ARG* 1.3 78.1 - - - +
681B LYS* 1.3 56.9 + - - +
683B THR* 3.8 0.7 - - - -
684B GLY 2.9 10.0 + - - -
685B GLY* 2.6 38.4 + - - +
687B HIS* 2.7 43.4 + - - -
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Residues in contact with LYS 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B GLU* 3.0 16.6 + - - +
678B LEU* 3.2 17.2 + - + +
680B HIS* 1.3 78.2 - - - +
682B ARG* 1.3 63.8 + - + +
684B GLY* 3.5 8.2 + - - -
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Residues in contact with ARG 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B GLU* 3.4 49.6 + - - +
593B HIS* 3.0 44.9 + - + +
678B LEU* 2.9 45.2 + - + +
679B ARG 4.0 2.9 - - - +
681B LYS* 1.3 78.7 - - + +
683B THR* 1.3 59.9 + - + +
684B GLY 3.4 1.3 + - - -
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Residues in contact with THR 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B HIS* 3.9 10.1 - - + +
595B TYR* 3.6 37.0 - - + -
679B ARG* 2.8 23.2 + - + +
680B HIS 3.5 1.4 + - - -
682B ARG* 1.3 78.8 - - - +
684B GLY* 1.3 60.9 + - - +
686B LYS* 3.1 27.4 + - - +
687B HIS* 3.0 34.6 + - + -
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Residues in contact with GLY 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B HIS 2.9 4.6 + - - -
681B LYS* 3.5 7.1 + - - -
682B ARG 3.4 3.8 + - - -
683B THR* 1.3 81.0 - - - +
685B GLY* 1.3 61.2 + - - +
686B LYS* 4.5 4.2 - - - +
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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