Contacts of the helix formed by residues 424 - 438 (chain B) in PDB entry 3THY
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 SER 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B GLU* 2.9 20.1 + - - -
377B ILE* 4.6 5.2 - - - -
402B ARG* 3.2 19.9 + - - -
423B LEU* 1.3 74.1 - - - +
425B GLU* 1.3 66.7 + - - +
426B GLN* 4.0 6.1 - - - -
427B THR* 2.9 28.6 + - - -
428B GLU* 3.0 18.7 + - - +
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Residues in contact with GLU 425 (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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423B LEU 3.5 2.4 + - - +
424B SER* 1.3 72.2 - - - +
426B GLN* 1.3 79.0 + - - +
428B GLU* 3.9 6.6 - - - +
429B ALA* 3.3 23.0 + - - +
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Residues in contact with GLN 426 (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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376B ASN* 5.6 1.3 - - - +
400B ALA* 3.9 29.8 - - + +
402B ARG* 3.1 42.1 + - - +
424B SER* 3.1 4.4 - - - -
425B GLU* 1.3 99.5 + - - +
427B THR* 1.3 61.7 + - - +
429B ALA* 3.6 6.0 + - - +
430B LEU* 3.5 12.5 + - - +
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Residues in contact with THR 427 (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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362B ILE* 5.2 4.7 - - + -
364B GLU* 3.4 11.9 + - - +
379B ILE* 4.4 1.0 - - + +
402B ARG* 2.8 26.7 + - - +
405B LEU* 3.9 26.9 - - + -
423B LEU* 4.0 24.5 - - + -
424B SER* 2.9 18.9 + - - -
426B GLN* 1.3 73.4 - - - +
428B GLU* 1.3 66.5 + - - +
429B ALA 3.0 2.2 - - - -
430B LEU* 2.7 16.2 + - + +
431B ILE* 2.9 20.7 + - + +
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Residues in contact with GLU 428 (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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421B SER 4.6 2.9 - - - +
423B LEU* 3.4 38.1 + - - +
424B SER 3.0 13.7 + - - +
425B GLU* 3.5 8.5 + - - +
427B THR* 1.3 75.9 - - - +
429B ALA* 1.3 56.5 + - - +
431B ILE* 3.0 18.5 - - + +
432B HIS* 2.9 29.5 + - - +
448B ARG* 2.9 38.3 + - - +
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Residues in contact with ALA 429 (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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425B GLU 3.3 14.5 + - - +
426B GLN* 3.7 6.3 - - - +
427B THR 3.0 0.8 - - - -
428B GLU* 1.3 76.6 - - - +
430B LEU* 1.3 60.4 + - - +
432B HIS* 3.3 11.1 - - - +
433B ARG* 3.0 39.0 + - - +
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Residues in contact with LEU 430 (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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401B SER 5.3 2.2 - - - +
402B ARG* 3.7 27.6 - - + +
405B LEU* 3.6 36.6 - - + -
406B GLU* 3.9 29.4 - - + +
409B MET* 4.7 7.9 - - - -
426B GLN 3.5 8.3 + - - +
427B THR* 2.7 15.5 + - + +
429B ALA* 1.3 70.6 - - - +
431B ILE* 1.3 68.3 + - + +
432B HIS 3.0 1.1 - - - -
433B ARG* 2.8 43.6 + - + +
434B ALA* 2.9 14.5 + - + +
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Residues in contact with ILE 431 (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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362B ILE* 4.9 7.2 - - + -
405B LEU* 5.2 0.4 - - + -
409B MET* 4.8 11.7 - - - -
417B LEU* 4.4 24.3 - - + +
419B LEU* 4.4 15.5 - - + -
423B LEU* 5.2 0.2 - - + -
427B THR* 2.9 30.2 + - + +
428B GLU* 3.0 40.2 - - + +
430B LEU* 1.3 78.6 - - + +
432B HIS* 1.3 74.9 + - + +
434B ALA* 3.3 9.9 + - - +
435B THR* 2.8 36.8 + - - +
446B VAL* 5.4 4.7 - - + -
448B ARG* 4.0 11.9 - - - +
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Residues in contact with HIS 432 (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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428B GLU 2.9 20.6 + - - +
429B ALA* 3.3 12.6 - - - +
431B ILE* 1.3 83.8 - - + +
433B ARG* 1.3 66.7 + - + +
435B THR* 2.9 19.8 + - + +
436B SER* 3.1 27.2 + - - -
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Residues in contact with ARG 433 (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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401B SER 5.6 2.4 + - - -
406B GLU* 5.8 0.2 - - - +
429B ALA* 3.0 25.3 + - - +
430B LEU* 2.8 48.0 + - + +
432B HIS* 1.3 75.8 - - + +
434B ALA* 1.3 61.1 + - - +
436B SER* 3.3 21.5 + - - -
437B VAL* 3.6 15.4 + - + +
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Residues in contact with ALA 434 (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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409B MET* 4.3 24.9 - - + -
417B LEU* 6.1 0.7 - - + -
430B LEU* 2.9 15.0 + - + +
431B ILE* 3.7 9.9 - - - +
433B ARG* 1.3 76.9 - - - +
435B THR* 1.3 58.6 + - - +
436B SER 3.6 0.2 + - - -
437B VAL* 4.5 4.6 - - - +
438B SER* 3.1 20.8 + - - -
444B ILE* 4.0 17.7 - - + +
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Residues in contact with THR 435 (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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417B LEU* 5.7 1.4 - - - +
431B ILE* 2.8 18.7 + - - +
432B HIS* 2.9 17.0 + - + +
434B ALA* 1.3 76.8 - - - +
436B SER* 1.3 63.1 + - - +
438B SER* 3.5 15.2 + - - +
443B ARG* 4.0 19.0 + - + +
444B ILE* 4.5 19.2 + - - +
446B VAL* 4.4 17.5 - - + +
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Residues in contact with SER 436 (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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432B HIS* 3.1 30.3 + - - -
433B ARG* 3.3 11.7 + - - -
435B THR* 1.3 78.9 - - - +
437B VAL* 1.3 72.0 + - - +
438B SER 3.5 4.0 - - - +
439B VAL* 5.1 0.3 - - - -
443B ARG* 5.0 6.8 + - - +
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Residues in contact with VAL 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ARG* 3.6 17.4 + - + +
434B ALA* 4.3 5.4 + - - +
436B SER* 1.3 79.3 - - - +
438B SER* 1.3 71.1 + - - +
439B VAL* 2.9 13.3 + - - +
545B MET* 4.4 29.8 - - + -
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Residues in contact with SER 438 (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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434B ALA 3.1 19.8 + - - -
435B THR 3.5 8.7 + - - +
436B SER 3.5 6.4 - - - +
437B VAL* 1.3 79.3 - - - +
439B VAL* 1.3 67.5 + - - +
441B ASP* 4.9 0.7 - - - -
442B ASP* 3.1 28.3 - - - -
443B ARG* 3.3 15.4 + - - +
444B ILE* 3.6 17.1 + - - +
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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
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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