Contacts of the helix formed by residues 565 - 581 (chain B) in PDB entry 1TH1
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 ARG 565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B GLN* 3.8 18.6 - - - +
560B PHE* 4.3 25.0 - - + -
564B VAL* 1.3 90.6 - - - +
566B MET* 1.3 64.3 + - - +
567B GLU* 3.5 28.2 + - - +
568B GLU* 3.2 41.7 + - + +
569B ILE* 3.9 3.6 - - - +
607B ILE* 3.5 30.5 - - - +
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Residues in contact with MET 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B TRP* 3.8 44.4 - - + +
543B ALA* 3.7 30.7 - - - +
546B ASP* 4.0 29.4 - - + +
547B THR* 4.1 7.6 - - - +
559B GLN 4.9 1.2 + - - -
561B VAL* 4.0 37.4 - - + +
564B VAL* 3.9 10.5 + - + +
565B ARG* 1.3 71.4 - - - +
567B GLU* 1.3 67.6 + - - +
568B GLU 3.2 0.9 - - - -
569B ILE* 3.4 16.2 + - + +
570B VAL* 3.2 26.1 + - - +
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Residues in contact with GLU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B THR* 4.2 28.7 + - + +
565B ARG* 3.3 36.4 + - - +
566B MET* 1.3 84.5 + - - +
568B GLU* 1.3 59.7 + - - +
569B ILE 3.3 0.2 - - - -
570B VAL* 3.8 8.3 - - + -
571B GLU* 3.2 22.7 + - - +
607B ILE* 3.9 19.6 - - + +
610B ILE* 3.4 14.8 - - + +
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Residues in contact with GLU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LYS* 3.2 39.7 + - + +
560B PHE* 4.9 5.7 - - - -
564B VAL* 3.7 12.9 - - + +
565B ARG* 3.2 59.1 + - + +
566B MET 3.2 0.2 - - - -
567B GLU* 1.3 74.7 - - - +
569B ILE* 1.3 61.4 + - - +
571B GLU* 3.6 8.8 + - - +
572B GLY* 3.1 23.9 + - - -
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Residues in contact with ILE 569 (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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504B TRP* 3.8 42.4 - - + +
507B ILE* 4.8 4.5 - - + -
508B LYS* 3.9 37.5 - - + +
511B VAL* 5.6 3.1 - - + -
539B LEU* 4.0 9.6 - - + +
543B ALA* 3.8 16.4 - - + -
564B VAL* 4.3 5.8 - - + -
565B ARG 3.9 13.5 - - - +
566B MET* 3.6 16.2 - - + +
567B GLU 3.3 0.4 - - - -
568B GLU* 1.3 75.7 - - - +
570B VAL* 1.3 58.5 + - - +
572B GLY* 5.2 0.7 - - - -
573B CYS* 3.1 41.3 + - - +
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 3.7 19.3 - - + +
543B ALA* 3.7 28.3 - - + +
544B HIS* 4.0 9.4 - - - +
547B THR* 4.6 3.1 - - + +
566B MET 3.2 16.8 + - - +
567B GLU* 3.7 12.8 - - + +
568B GLU 3.3 0.4 - - - -
569B ILE* 1.3 77.0 - - - +
571B GLU* 1.3 60.3 + - - +
574B THR* 2.8 32.9 + - - +
602B LEU* 3.8 28.7 - - + -
610B ILE* 4.1 15.9 - - + -
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Residues in contact with GLU 571 (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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515B ARG* 3.1 31.7 + - - +
567B GLU 3.2 17.3 + - - +
568B GLU* 3.8 8.4 - - - +
570B VAL* 1.3 75.6 - - - +
572B GLY* 1.3 58.9 + - - +
575B GLY* 2.9 23.2 + - - -
607B ILE* 5.6 1.4 - - - +
609B ASN* 3.5 50.9 + - + +
610B ILE* 3.8 10.4 - - + +
613B VAL* 3.9 10.6 - - + +
1482D LEU* 5.8 0.9 - - - +
1484D ASP* 5.1 2.8 - - - +
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Residues in contact with GLY 572 (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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511B VAL* 3.3 23.8 - - - +
512B GLY* 5.6 2.5 - - - -
515B ARG* 3.6 14.7 + - - -
568B GLU 3.1 17.2 + - - -
569B ILE* 4.1 0.4 - - - -
570B VAL 3.5 0.2 - - - -
571B GLU* 1.3 78.4 - - - +
573B CYS* 1.3 51.0 + - - +
575B GLY* 3.3 1.0 + - - -
576B ALA* 2.8 29.5 + - - +
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Residues in contact with CYS 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B VAL* 3.9 22.9 - - - -
536B LEU* 3.6 32.0 - - + +
539B LEU* 3.8 21.5 - - - -
540B LEU* 4.0 13.2 - - + -
569B ILE* 3.1 32.7 + - - +
570B VAL 4.3 0.7 - - - +
572B GLY* 1.3 69.9 - - - +
574B THR* 1.3 60.6 + - - +
575B GLY 3.1 0.9 - - - -
576B ALA* 3.3 4.2 + - - +
577B LEU* 3.0 36.8 + - - +
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Residues in contact with THR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 3.2 19.6 - - - +
570B VAL* 2.8 23.0 + - - +
573B CYS* 1.3 75.7 - - - +
575B GLY* 1.3 57.3 + - - +
577B LEU* 3.5 10.2 + - - +
578B HIS* 2.9 27.2 + - - +
599B PHE* 3.8 20.6 - - + -
602B LEU* 3.6 12.5 - - + +
610B ILE* 5.1 0.9 - - - +
613B VAL* 3.5 37.0 - - + +
614B ALA* 3.9 8.3 - - + +
617B VAL* 4.1 1.9 - - + +
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Residues in contact with GLY 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ARG* 3.6 15.1 - - - +
571B GLU 2.9 19.8 + - - -
572B GLY 3.5 2.5 - - - -
574B THR* 1.3 77.0 - - - +
576B ALA* 1.3 61.9 + - - +
578B HIS* 3.4 4.9 - - - +
579B ILE* 3.3 28.8 + - - +
613B VAL* 3.9 19.5 - - - +
1482D LEU* 6.0 0.2 - - - -
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B VAL 4.1 16.4 - - - +
514B ILE* 4.2 10.1 - - + -
515B ARG* 4.1 12.5 - - - +
518B ALA* 4.6 1.6 - - - +
536B LEU* 4.0 24.5 - - + -
572B GLY 2.8 16.1 + - - +
573B CYS 3.7 4.7 - - - +
575B GLY* 1.3 75.8 - - - +
577B LEU* 1.3 59.3 + - - +
579B ILE* 3.6 3.0 + - - +
580B LEU* 3.1 33.8 + - - +
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Residues in contact with LEU 577 (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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533B ILE* 4.1 23.8 - - + -
536B LEU* 4.3 19.7 - - + -
537B VAL* 3.8 28.5 - - + +
540B LEU* 4.1 14.4 - - + -
573B CYS 3.0 21.6 + - - +
574B THR* 3.8 4.9 - - - +
576B ALA* 1.3 74.1 - - - +
578B HIS* 1.3 60.0 + - - +
580B LEU* 4.1 2.7 - - + -
581B ALA* 2.9 31.5 + - - +
590B ILE* 3.7 23.8 - - + +
599B PHE* 4.0 26.9 - - + -
617B VAL* 3.9 4.0 - - + +
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Residues in contact with HIS 578 (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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574B THR 2.9 17.6 + - - +
575B GLY* 3.4 7.9 - - - +
577B LEU* 1.3 75.6 - - - +
579B ILE* 1.3 80.8 + - + +
581B ALA* 3.3 16.1 + - - +
582B ARG* 4.0 5.6 + - - +
613B VAL* 4.0 15.9 - - + +
616B GLY* 3.1 34.9 + - - -
617B VAL* 3.9 11.0 - - + +
620B GLU* 3.8 18.6 - - + +
654B TYR* 3.2 32.4 + + - -
1482D LEU* 3.7 27.0 - - + +
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Residues in contact with ILE 579 (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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515B ARG* 3.8 22.4 - - + +
518B ALA* 3.5 33.0 - - + +
519B LEU* 3.7 24.0 - - + +
524B HIS* 3.7 6.4 + - - -
575B GLY 3.3 16.7 + - - +
576B ALA 4.2 1.1 - - - +
578B HIS* 1.3 96.7 - - + +
580B LEU* 1.3 60.8 + - - +
582B ARG* 3.4 49.1 - - - +
1482D LEU* 5.2 11.7 - - + +
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Residues in contact with LEU 580 (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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514B ILE* 4.5 11.7 - - + -
518B ALA* 3.7 18.8 - - + +
524B HIS* 4.3 12.5 - - + +
527B LEU* 4.0 22.9 - - + -
528B ARG 5.7 0.4 - - - +
532B ALA* 4.9 4.7 - - + -
533B ILE* 4.4 19.5 - - + -
536B LEU* 4.0 24.2 - - + -
576B ALA 3.1 21.8 + - - +
577B LEU* 3.8 8.1 - - + +
578B HIS 3.3 0.2 - - - -
579B ILE* 1.3 71.6 - - - +
581B ALA* 1.3 57.6 + - - +
582B ARG 3.0 10.8 + - - -
583B ASP* 3.4 4.5 + - - +
586B ASN* 3.0 44.9 + - - +
590B ILE* 4.7 5.6 - - + -
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Residues in contact with ALA 581 (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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577B LEU 2.9 18.1 + - - +
578B HIS 3.3 10.4 + - - +
580B LEU* 1.3 73.8 - - - +
582B ARG* 1.3 57.7 + - - +
583B ASP 3.2 3.6 - - - -
586B ASN* 4.8 0.4 - - - -
587B ARG* 2.9 38.0 + - + +
590B ILE* 4.0 16.6 - - + +
617B VAL* 4.3 11.7 - - + +
620B GLU* 3.5 18.7 - - + +
621B LEU* 5.1 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
------------------------------------------------------------
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