Contacts of the helix formed by residues 431 - 441 (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 ASN 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A THR 2.6 30.5 + - - +
394A LYS* 4.2 7.3 - - - +
395A GLN 4.3 8.1 + - - -
396A GLU* 5.1 3.4 + - - -
427A LEU 4.0 4.9 - - - +
428A THR 4.1 2.1 + - - +
429A CYS 2.9 6.5 + - - +
430A ASN* 1.3 77.7 - - - +
432A TYR* 1.3 62.2 + - - +
433A LYS* 3.3 20.6 + - - +
434A ASN* 2.9 50.4 + - - +
435A LYS* 3.1 25.9 + - - +
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Residues in contact with TYR 432 (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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430A ASN 3.8 4.3 + - - -
431A ASN* 1.3 72.6 + - - +
433A LYS* 1.3 98.5 + - + +
435A LYS* 3.3 14.1 + - - +
436A MET* 3.0 51.6 + - - +
474A ARG 4.1 8.1 - - - +
475A HIS* 4.1 17.2 - - + +
476A GLN* 6.0 4.0 - - + -
275B LEU* 4.7 7.2 - - + +
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Residues in contact with LYS 433 (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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396A GLU* 3.5 34.4 + - - +
431A ASN* 3.3 18.9 + - - +
432A TYR* 1.3 122.4 - - + +
434A ASN* 1.3 60.0 + - - +
436A MET* 3.5 4.3 + - - +
437A MET* 3.1 33.0 + - + +
275B LEU* 4.0 30.6 - - + +
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Residues in contact with ASN 434 (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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392A ALA 5.1 3.6 + - - -
393A THR 4.5 2.4 + - - -
395A GLN 4.6 7.3 + - - +
398A MET* 3.8 16.9 - - - +
402A LEU* 3.3 28.3 - - + +
427A LEU* 2.8 37.1 + - - +
428A THR* 4.7 1.6 - - - -
431A ASN* 2.9 36.0 + - - +
433A LYS* 1.3 75.4 - - - +
435A LYS* 1.3 60.1 + - - +
437A MET* 3.3 1.4 + - - +
438A VAL* 3.0 37.4 + - - +
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Residues in contact with LYS 435 (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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428A THR* 3.1 37.0 - - + +
430A ASN* 4.2 7.4 - - - +
431A ASN 3.1 18.2 + - - +
432A TYR* 3.4 13.0 - - - +
434A ASN* 1.3 78.1 - - - +
436A MET* 1.3 61.2 - - - +
438A VAL 3.3 0.3 + - - -
439A CYS* 3.2 21.7 + - - -
470A HIS 3.0 26.2 + - - +
471A LEU* 3.5 16.9 - - + +
473A SER* 3.0 14.5 + - - -
474A ARG* 4.4 12.4 + - - +
475A HIS* 3.6 32.8 - - + +
1486C ASP* 2.8 26.4 + - - -
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Residues in contact with MET 436 (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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432A TYR* 3.0 42.4 + - - +
433A LYS 3.8 4.9 - - - +
435A LYS* 1.3 77.3 - - - +
437A MET* 1.3 60.8 + - - +
439A CYS* 3.5 2.8 + - - +
440A GLN* 3.2 29.2 + - - +
475A HIS* 3.8 18.8 - - + +
476A GLN* 3.3 36.6 - - + +
477A GLU* 4.1 16.0 - - + +
271B MET* 3.5 39.0 - - + -
275B LEU* 4.4 17.7 - - + -
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Residues in contact with MET 437 (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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399A GLU* 4.0 23.1 - - + +
402A LEU* 4.0 17.5 - - + -
433A LYS 3.1 20.1 + - - +
434A ASN* 3.8 4.3 - - - +
436A MET* 1.3 75.0 - - - +
438A VAL* 1.3 64.0 + - - +
440A GLN* 3.2 12.4 + - - +
441A VAL* 3.2 24.7 + - + +
232B PHE* 3.4 33.9 - - + -
268B GLY* 3.7 25.8 - - - +
271B MET* 4.0 9.6 - - - -
272B ALA* 4.0 19.1 - - - -
275B LEU* 4.4 10.1 - - + -
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Residues in contact with VAL 438 (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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402A LEU* 3.8 31.2 - - + -
406A VAL* 4.1 11.4 - - + -
424A LEU* 4.2 14.1 - - + -
428A THR* 4.2 9.4 - - - +
434A ASN 3.0 22.3 + - - +
435A LYS 3.3 0.2 + - - -
437A MET* 1.3 75.5 - - - +
439A CYS* 1.3 58.8 + - - +
440A GLN 3.4 0.7 + - - -
441A VAL* 3.4 11.6 + - - +
443A GLY* 2.9 43.5 + - - -
447A LEU* 5.0 4.3 - - + -
471A LEU* 3.9 27.6 - - + -
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Residues in contact with CYS 439 (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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435A LYS 3.2 17.7 + - - -
436A MET 3.7 8.3 - - - +
438A VAL* 1.3 75.4 - - - +
440A GLN* 1.3 62.9 + - - +
441A VAL 3.6 0.3 + - - -
442A GLY* 3.8 9.4 + - - -
443A GLY 4.4 0.7 + - - +
444A ILE* 4.2 15.7 - - - +
471A LEU* 4.0 12.3 - - - -
475A HIS* 3.9 20.4 - - - -
477A GLU* 4.3 11.0 - - + +
480A MET* 3.9 29.3 - - - +
481A ALA* 3.9 22.7 - - - -
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Residues in contact with GLN 440 (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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436A MET 3.2 17.2 + - - +
437A MET* 3.2 8.1 + - - +
439A CYS* 1.3 79.7 + - - +
441A VAL* 1.3 56.8 + - - +
442A GLY 3.4 2.0 + - - -
477A GLU* 3.0 27.3 + - - +
480A MET* 5.1 4.8 - - - +
267B GLU* 3.9 8.7 - - - +
268B GLY* 3.7 30.5 + - - -
270B LYS* 5.1 8.5 - - - +
271B MET* 3.9 39.1 + - + +
274B ARG* 5.2 0.7 + - - -
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Residues in contact with VAL 441 (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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399A GLU 5.5 0.2 - - - +
402A LEU* 4.7 1.6 - - + +
403A GLY* 4.1 21.3 - - - +
406A VAL* 3.6 25.7 - - + +
437A MET* 3.3 21.3 - - + +
438A VAL* 3.4 15.4 + - - +
440A GLN* 1.3 79.4 - - - +
442A GLY* 1.3 59.5 + - - +
232B PHE* 4.3 17.7 - - + -
267B GLU* 3.4 43.9 - - - +
268B GLY* 4.1 7.6 - - - -
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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