Contacts of the helix formed by residues 393 - 409 (chain A) in PDB entry 5NTI
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 CYS 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A TRP* 4.3 8.1 - - + -
388A PHE 5.2 0.6 + - - -
389A ARG* 6.1 0.2 - - - +
391A LEU* 3.8 23.0 - - - +
392A GLY* 1.3 80.4 - - - +
394A SER* 1.3 64.5 + - - +
395A GLU* 3.3 3.4 - - - -
396A LEU* 3.2 22.3 + - + -
397A ILE* 3.1 25.7 + - - +
482A ARG* 3.5 36.3 - - + +
601A C3S 4.2 13.0 - - - -
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A MET* 5.4 9.4 - - - +
388A PHE 6.0 0.4 - - - -
389A ARG* 5.8 13.0 - - - +
392A GLY* 3.9 0.8 - - - -
393A CYS* 1.3 74.0 - - - +
395A GLU* 1.3 60.7 + - - +
397A ILE* 3.8 8.0 - - - +
398A SER* 2.9 32.4 + - - -
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Residues in contact with GLU 395 (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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393A CYS 3.3 0.6 - - - -
394A SER* 1.3 81.1 + - - +
396A LEU* 1.3 56.4 + - - +
398A SER* 3.3 9.4 + - - -
399A SER* 2.8 40.8 + - - -
478A GLN* 3.4 14.9 - - - +
482A ARG* 6.0 4.0 - - - +
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A CYS* 3.2 23.7 + - - +
395A GLU* 1.3 76.1 - - - +
397A ILE* 1.3 58.8 + - - +
399A SER* 3.3 2.6 + - - -
400A ILE* 2.9 48.9 + - + +
475A LEU* 3.8 15.0 - - + +
478A GLN* 3.3 38.9 + - + +
479A HIS* 3.9 18.6 - - + +
482A ARG* 3.9 30.9 - - + +
601A C3S 4.3 18.6 - - + -
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Residues in contact with ILE 397 (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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385A MET* 3.6 35.9 - - + +
388A PHE* 3.9 20.9 - - + +
391A LEU* 3.7 24.0 - - + -
393A CYS* 3.1 25.5 + - - +
394A SER* 4.0 7.0 - - - +
396A LEU* 1.3 76.0 - - + +
398A SER* 1.3 57.5 + - - +
400A ILE* 3.2 6.7 + - + +
401A PHE* 2.9 40.4 + - + -
601A C3S 3.9 32.8 - - + -
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A MET* 3.8 28.2 - - - -
394A SER 2.9 19.5 + - - -
395A GLU* 3.3 15.1 + - - -
397A ILE* 1.3 73.5 - - - +
399A SER* 1.3 62.2 + - - +
401A PHE* 3.7 3.9 - - - +
402A ASP* 2.9 37.4 + - - +
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLU* 2.8 31.9 + - - -
396A LEU* 3.3 9.2 + - - -
398A SER* 1.3 78.0 + - - +
400A ILE* 1.3 57.4 + - - +
402A ASP* 3.3 9.8 + - - +
403A PHE* 3.0 28.2 + - - +
471A LYS* 5.4 6.1 + - - +
475A LEU* 3.7 21.7 - - - +
478A GLN* 3.7 13.4 + - - -
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Residues in contact with ILE 400 (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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358A MET* 5.1 5.4 - - + -
362A LEU* 3.8 29.4 - - + +
365A MET* 3.5 31.9 - - + -
396A LEU* 2.9 45.4 + - + +
397A ILE* 3.2 9.2 + - - +
399A SER* 1.3 73.5 - - - +
401A PHE* 1.3 59.7 + - + +
403A PHE* 3.2 9.5 + - + +
404A SER* 3.0 27.4 + - - -
475A LEU* 4.5 10.5 - - + +
601A C3S 4.1 30.5 - - + -
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Residues in contact with PHE 401 (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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365A MET* 4.3 10.5 - - + -
369A TYR* 3.7 27.3 + + - +
374A ARG* 3.5 22.9 - - + -
376A VAL* 3.5 39.3 - - + -
384A GLY 3.9 2.7 - - - -
385A MET* 3.6 44.6 - - + -
388A PHE* 3.9 14.8 - + - -
397A ILE* 2.9 29.2 + - + +
398A SER* 3.8 8.1 - - - +
399A SER 3.4 0.2 - - - -
400A ILE* 1.3 75.8 - - + +
402A ASP* 1.3 60.8 + - - +
404A SER* 4.6 4.3 - - - +
405A HIS* 3.1 27.5 + - - +
601A C3S 5.3 4.5 - - + -
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Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 5.8 1.9 + - - -
398A SER* 2.9 24.4 + - - +
399A SER* 3.4 9.0 - - - +
401A PHE* 1.3 74.1 - - - +
403A PHE* 1.3 60.7 + - - +
405A HIS* 3.3 7.9 + - - +
406A SER* 3.0 28.8 + - - -
471A LYS* 6.1 3.1 - - - +
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Residues in contact with PHE 403 (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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362A LEU* 3.6 34.1 - - + -
363A VAL* 4.2 4.5 - - + -
399A SER 3.0 14.1 + - - +
400A ILE* 3.5 8.5 - - + +
402A ASP* 1.3 74.5 - - - +
404A SER* 1.3 64.1 + - - +
406A SER* 2.7 25.5 + - - -
407A LEU* 3.1 32.9 + - + +
420A TYR* 5.1 0.4 - - - -
467A PRO* 3.7 31.0 - - + -
471A LYS* 4.2 19.7 - - + +
472A LEU* 3.6 32.5 - - + -
475A LEU* 3.6 24.2 - - + -
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU 4.8 1.0 + - - -
365A MET* 3.7 17.0 - - - +
366A CYS* 3.4 32.1 + - - +
369A TYR* 3.5 27.7 - - - +
400A ILE 3.0 15.9 + - - -
401A PHE 4.1 1.6 - - - -
403A PHE* 1.3 81.4 - - - +
405A HIS* 1.3 56.5 + - - +
407A LEU* 3.3 8.6 + - - +
408A SER* 3.0 28.1 + - - -
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Residues in contact with HIS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A TYR* 2.8 26.0 + - - +
371A ALA* 3.6 31.4 - - + +
374A ARG* 3.9 15.3 + - + +
401A PHE 3.1 20.2 + - - +
402A ASP* 3.5 9.9 - - - +
404A SER* 1.3 78.5 - - - +
406A SER* 1.3 58.9 + - - +
408A SER* 2.7 19.7 + - - -
409A ALA* 3.5 8.4 + - + +
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ASP 3.0 11.9 + - - -
403A PHE* 2.7 30.3 + - - -
405A HIS* 1.3 78.7 - - - +
407A LEU* 1.3 63.9 + - - +
409A ALA* 3.5 18.3 + - - +
410A LEU* 3.7 13.0 - - - +
467A PRO* 5.0 4.2 - - - +
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Residues in contact with LEU 407 (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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362A LEU 4.5 1.1 - - - +
363A VAL* 3.9 35.2 - - + +
366A CYS* 4.0 17.8 - - + -
403A PHE* 3.1 39.1 + - + +
404A SER* 3.3 8.2 + - - +
406A SER* 1.3 80.2 + - - +
408A SER* 1.3 57.7 + - - +
409A ALA 3.1 2.0 - - - -
410A LEU* 3.1 29.6 + - + +
411A HIS 3.7 2.9 + - - -
412A PHE* 3.8 28.1 + - + -
420A TYR* 4.7 3.1 - - + -
467A PRO* 3.7 33.9 - - + -
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A CYS* 4.7 8.9 - - - +
369A TYR* 4.3 10.5 - - - -
371A ALA* 3.6 27.4 - - - +
404A SER 3.0 12.8 + - - -
405A HIS* 2.7 27.9 + - - -
407A LEU* 1.3 76.7 - - - +
409A ALA* 1.3 59.9 + - - +
411A HIS* 3.2 28.6 + - - +
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Residues in contact with ALA 409 (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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405A HIS* 3.5 7.6 + - + +
406A SER* 3.5 15.2 + - - +
407A LEU 3.1 0.4 - - - -
408A SER* 1.3 80.3 + - - +
410A LEU* 1.3 62.2 + - + +
411A HIS* 3.1 22.5 + - - -
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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