Contacts of the helix formed by residues 565 - 581 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A GLN* 3.8 21.5 - - - +
560A PHE* 3.5 37.6 - - + -
564A VAL* 1.3 78.4 - - - +
566A MET* 1.3 59.4 + - - +
567A GLU* 3.1 20.2 - - + +
568A GLU* 2.8 68.8 + - + +
569A ILE 3.8 1.2 + - - -
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Residues in contact with MET 566 (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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504A TRP* 3.6 57.0 - - + +
543A ALA* 3.6 26.5 - - - +
546A ASP* 3.4 30.1 - - + +
547A THR* 4.1 8.7 - - - +
559A GLN 4.6 2.2 + - - -
561A VAL* 4.0 13.9 - - + +
564A VAL* 3.6 24.4 + - + +
565A ARG* 1.3 71.7 - - - +
567A GLU* 1.3 61.8 + - - +
568A GLU 3.2 0.4 - - - -
569A ILE* 3.3 16.9 + - + +
570A VAL* 3.1 30.1 + - - +
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Residues in contact with GLU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A THR* 3.6 34.7 + - + +
550A ARG* 5.9 1.9 - - - +
559A GLN 4.7 6.9 + - - +
565A ARG* 3.1 22.3 - - + +
566A MET* 1.3 88.9 + - - +
568A GLU* 1.3 58.4 + - + +
570A VAL* 3.5 6.9 + - - -
571A GLU* 3.2 26.5 + - - +
607A ILE* 3.7 31.4 - - + -
610A ILE* 3.7 11.3 - - + +
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Residues in contact with GLU 568 (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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508A LYS* 3.0 44.8 + - + +
560A PHE* 4.8 0.3 - - - -
563A GLY 4.6 2.3 - - - +
564A VAL* 3.7 11.4 - - + -
565A ARG* 2.8 73.8 + - + +
567A GLU* 1.3 77.6 - - + +
569A ILE* 1.3 59.9 + - - +
571A GLU* 3.9 9.2 - - - +
572A GLY* 3.0 24.9 + - - -
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Residues in contact with ILE 569 (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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504A TRP* 3.8 39.0 - - + -
507A ILE* 5.1 2.5 - - + -
508A LYS* 3.9 36.6 - - + +
511A VAL* 5.7 2.7 - - + -
539A LEU* 3.9 11.4 - - + +
540A LEU* 5.0 0.4 - - - -
543A ALA* 3.9 18.2 - - + -
564A VAL* 4.0 9.6 - - + -
565A ARG 4.2 6.5 - - - +
566A MET* 3.3 20.1 + - - +
568A GLU* 1.3 72.1 - - - +
570A VAL* 1.3 59.8 + - - +
572A GLY* 4.5 1.1 - - - +
573A CYS* 2.9 46.7 + - - +
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Residues in contact with VAL 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU* 3.8 21.9 - - + +
543A ALA* 3.8 6.3 - - + +
544A HIS* 3.8 32.1 - - - +
547A THR* 4.7 3.4 - - - +
566A MET 3.1 16.4 + - - +
567A GLU* 3.7 9.4 - - - +
568A GLU 3.3 0.4 - - - -
569A ILE* 1.3 76.4 - - - +
571A GLU* 1.3 61.7 + - - +
574A THR* 2.8 31.2 + - - -
602A LEU* 3.9 23.6 - - + -
610A ILE* 3.9 22.9 - - + -
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Residues in contact with GLU 571 (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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567A GLU 3.2 15.3 + - - +
568A GLU* 3.9 8.9 - - - +
570A VAL* 1.3 79.0 - - - +
572A GLY* 1.3 57.2 + - - +
575A GLY* 2.9 26.9 + - - -
607A ILE* 5.1 5.5 - - - +
609A ASN* 3.5 51.3 + - + +
610A ILE* 4.0 12.3 - - + +
613A VAL* 3.9 13.6 - - + +
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Residues in contact with GLY 572 (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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508A LYS* 6.4 1.1 - - - -
511A VAL* 3.3 22.0 - - - +
512A GLY* 6.0 1.5 - - - -
515A ARG* 5.3 4.2 - - - +
568A GLU 3.0 18.9 + - - -
569A ILE* 4.0 1.1 - - - -
571A GLU* 1.3 76.7 - - - +
573A CYS* 1.3 55.5 + - - +
575A GLY* 3.3 2.5 + - - -
576A ALA* 3.0 22.9 + - - +
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Residues in contact with CYS 573 (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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511A VAL* 3.9 16.8 - - - -
536A LEU* 3.7 32.3 - - + +
539A LEU* 3.7 29.2 - - - -
540A LEU* 4.0 11.4 - - + -
569A ILE* 2.9 36.1 + - - +
572A GLY* 1.3 68.9 - - - +
574A THR* 1.3 65.7 + - - +
576A ALA* 3.2 3.8 + - - +
577A LEU* 3.0 30.3 + - - +
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Residues in contact with THR 574 (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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540A LEU* 3.2 25.3 - - - +
570A VAL* 2.8 23.1 + - - -
573A CYS* 1.3 75.0 - - - +
575A GLY* 1.3 58.2 + - - +
577A LEU* 3.4 5.2 + - - +
578A HIS* 2.9 27.9 + - - +
599A PHE* 4.0 19.7 - - + -
602A LEU* 3.5 10.8 - - + +
610A ILE* 6.0 0.2 - - - -
613A VAL* 3.6 37.0 - - + +
614A ALA* 3.9 9.9 - - - +
617A VAL* 4.1 2.3 - - + +
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Residues in contact with GLY 575 (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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515A ARG* 3.7 10.7 - - - +
571A GLU 2.9 18.0 + - - -
572A GLY 3.6 2.0 - - - -
573A CYS 3.2 0.2 - - - -
574A THR* 1.3 77.2 - - - +
576A ALA* 1.3 61.3 + - - +
578A HIS* 3.5 4.7 - - - +
579A ILE* 3.4 28.1 + - - +
613A VAL* 3.8 19.3 - - - +
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Residues in contact with ALA 576 (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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511A VAL* 4.1 22.7 - - + +
514A ILE* 4.6 1.3 - - + -
515A ARG* 4.1 18.1 - - + +
518A ALA* 4.6 1.0 - - - +
536A LEU* 3.9 19.5 - - + -
572A GLY 3.0 15.7 + - - +
573A CYS 3.2 5.6 + - - +
575A GLY* 1.3 75.7 - - - +
577A LEU* 1.3 58.9 + - - +
579A ILE* 3.4 4.3 + - - +
580A LEU* 3.0 36.1 + - + +
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Residues in contact with LEU 577 (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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533A ILE* 3.8 32.5 - - + -
536A LEU* 4.2 28.0 - - + -
537A VAL* 4.0 18.4 - - + -
540A LEU* 4.0 25.1 - - + -
573A CYS 3.0 21.9 + - - +
574A THR* 3.8 4.9 - - - +
576A ALA* 1.3 75.1 - - - +
578A HIS* 1.3 54.0 + - - +
580A LEU* 3.6 4.2 - - + +
581A ALA* 2.8 36.4 + - - +
590A ILE* 3.7 18.0 - - + +
599A PHE* 4.3 10.1 - - + -
617A VAL* 4.1 9.9 - - + -
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Residues in contact with HIS 578 (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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574A THR 2.9 17.6 + - - +
575A GLY* 3.5 9.4 - - - +
576A ALA 3.3 0.2 - - - -
577A LEU* 1.3 78.5 - - - +
579A ILE* 1.3 77.9 + - + +
581A ALA* 3.6 11.3 - - - +
582A ARG* 4.3 4.8 + - - +
613A VAL* 4.1 23.1 - - + +
616A GLY* 3.1 38.1 + - - -
617A VAL* 4.0 10.7 - - + +
620A GLU* 3.8 18.6 - - + +
654A TYR* 3.3 30.0 + + - -
1477C GLN* 4.4 6.5 - - - -
1482C LEU* 5.3 6.7 - - + -
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Residues in contact with ILE 579 (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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515A ARG* 3.9 19.3 - - + +
518A ALA* 3.4 38.4 - - + +
519A LEU* 3.7 22.4 - - + +
524A HIS* 4.1 1.2 + - - -
575A GLY 3.4 13.9 - - - +
576A ALA 3.4 5.5 + - - +
577A LEU 3.3 0.2 - - - -
578A HIS* 1.3 93.7 - - + +
580A LEU* 1.3 67.1 + - - +
581A ALA 3.1 2.3 + - - -
582A ARG* 3.3 49.2 + - - +
1482C LEU* 4.8 14.6 - - + -
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Residues in contact with LEU 580 (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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514A ILE* 4.2 13.0 - - + -
518A ALA* 3.6 21.8 - - + -
524A HIS* 4.8 8.4 - - + +
527A LEU* 4.4 22.4 - - + -
532A ALA* 5.4 2.7 - - + -
533A ILE* 4.3 19.3 - - + -
536A LEU* 3.9 22.7 - - + -
576A ALA 3.0 30.6 + - - +
577A LEU* 3.3 7.8 + - - +
579A ILE* 1.3 76.1 - - - +
581A ALA* 1.3 57.1 + - - +
582A ARG* 2.9 7.8 + - - +
583A ASP* 3.3 4.3 + - - +
586A ASN* 2.9 43.5 + - - +
590A ILE* 4.6 6.5 - - + -
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Residues in contact with ALA 581 (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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577A LEU 2.8 18.7 + - - +
578A HIS 3.6 9.9 - - - +
579A ILE 3.1 0.4 - - - -
580A LEU* 1.3 75.0 - - - +
582A ARG* 1.3 57.2 + - - +
583A ASP 3.3 1.6 - - - +
586A ASN* 4.7 0.4 - - - -
587A ARG* 3.0 38.0 + - + +
590A ILE* 3.9 16.1 - - + +
617A VAL* 4.2 12.1 - - + +
620A GLU* 3.4 22.3 - - + +
621A LEU* 5.0 2.7 - - + -
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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