Contacts of the helix formed by residues 393 - 409 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B TRP* 4.2 18.2 - - + -
388B PHE 5.4 1.5 + - - -
389B ARG 5.0 0.2 + - - -
391B LEU* 3.7 31.1 - - - +
392B GLY* 1.3 80.8 - - - +
394B SER* 1.3 65.6 + - - +
395B GLU* 3.3 3.8 - - - -
396B LEU* 3.2 17.8 + - + +
397B ILE* 3.1 25.7 + - - +
482B ARG* 3.5 33.7 - - + +
601B C3S 4.6 2.2 - - - -
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B MET* 5.6 2.4 - - - +
388B PHE 6.1 0.7 - - - -
389B ARG* 5.9 11.2 - - - +
392B GLY* 3.9 1.2 - - - -
393B CYS* 1.3 72.3 - - - +
395B GLU* 1.3 55.6 + - - +
397B ILE* 4.0 8.0 - - - +
398B SER* 2.8 41.8 + - - -
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B CYS* 4.9 1.8 - - - -
394B SER* 1.3 80.8 + - - +
396B LEU* 1.3 56.5 + - - +
398B SER* 2.9 18.7 + - - -
399B SER* 3.0 23.8 + - - +
478B GLN* 4.1 13.6 - - - +
482B ARG* 5.1 14.6 + - - +
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B CYS* 3.2 24.8 + - + +
395B GLU* 1.3 77.3 + - - +
397B ILE* 1.3 60.8 + - + +
399B SER* 3.2 3.2 + - - -
400B ILE* 2.8 50.8 + - + +
475B LEU* 3.5 28.0 - - + +
478B GLN* 3.5 25.7 + - + +
479B HIS* 3.8 28.5 - - + +
482B ARG* 4.1 19.0 - - + +
601B C3S 4.6 11.7 - - + -
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Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B MET* 3.8 22.9 - - + +
388B PHE* 4.0 21.8 - - + +
391B LEU* 3.8 17.5 - - + -
393B CYS* 3.1 22.2 + - - +
394B SER* 3.4 7.2 + - - +
396B LEU* 1.3 75.5 - - + +
398B SER* 1.3 58.2 + - - +
400B ILE* 3.4 7.4 + - + +
401B PHE* 2.9 58.2 + - + -
601B C3S 3.7 42.2 - - + -
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Residues in contact with SER 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B MET* 3.6 29.2 - - - +
394B SER* 2.8 27.6 + - - -
395B GLU* 2.9 16.5 + - - -
397B ILE* 1.3 72.9 - - - +
399B SER* 1.3 56.6 + - - +
401B PHE* 3.6 1.8 - - - +
402B ASP* 2.9 39.1 + - - +
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU* 3.0 21.0 + - - +
396B LEU* 3.4 11.7 - - - -
398B SER* 1.3 75.4 + - - +
400B ILE* 1.3 63.8 + - - +
402B ASP* 3.3 11.7 + - - +
403B PHE* 3.0 22.5 + - - +
475B LEU* 3.6 22.3 - - - +
478B GLN* 3.9 12.9 + - - -
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B MET* 5.2 4.7 - - + -
362B LEU* 3.9 26.0 - - + -
365B MET* 3.6 28.7 - - + -
396B LEU* 2.8 50.8 + - + +
397B ILE* 3.7 8.5 - - + +
399B SER* 1.3 72.2 - - - +
401B PHE* 1.3 63.0 + - + +
403B PHE* 3.3 5.0 + - - +
404B SER* 3.2 21.8 + - - -
475B LEU* 4.0 15.5 - - + +
601B C3S 3.9 35.2 - - + -
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Residues in contact with PHE 401 (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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365B MET* 4.2 19.3 - - + -
369B TYR* 3.7 22.0 + + + +
374B ARG* 3.4 27.8 - - + -
376B VAL* 3.6 28.7 - - + -
383B GLY 4.0 3.4 - - - -
384B GLY 3.8 5.4 - - - -
385B MET* 3.5 47.1 - - + -
388B PHE* 3.9 9.4 - + - -
397B ILE* 2.9 46.4 + - + +
398B SER 3.6 4.9 - - - +
400B ILE* 1.3 78.1 - - + +
402B ASP* 1.3 64.9 + - - +
404B SER* 3.5 1.2 + - - -
405B HIS* 3.1 22.5 + - - +
601B C3S 5.1 3.6 - - + -
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Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG* 4.5 11.9 + - - +
385B MET* 5.2 4.2 - - - +
398B SER* 2.9 27.9 + - - +
399B SER* 3.4 12.7 + - - +
401B PHE* 1.3 76.5 - - - +
403B PHE* 1.3 58.3 + - - +
405B HIS* 3.2 9.0 + - - +
406B SER* 3.0 32.6 + - - +
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 3.9 21.3 - - + -
363B VAL* 4.0 9.2 - - + -
399B SER 3.0 12.6 + - - +
400B ILE 3.4 9.6 - - - +
401B PHE 3.2 0.2 - - - -
402B ASP* 1.3 76.8 - - - +
404B SER* 1.3 64.3 + - - +
406B SER* 3.0 18.8 + - - -
407B LEU* 3.1 35.6 + - + +
420B TYR* 4.8 2.5 - - - -
467B PRO* 3.8 34.3 - - + -
471B LYS* 4.0 21.3 - - + -
472B LEU* 3.6 38.8 - - + -
475B LEU* 3.8 21.5 - - + -
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU 4.0 4.5 + - - -
365B MET* 3.5 33.6 - - - +
366B CYS* 3.8 13.6 + - - +
369B TYR* 3.6 31.4 - - - -
400B ILE 3.2 6.4 + - - -
401B PHE 3.9 4.0 - - - -
402B ASP 3.4 0.2 - - - -
403B PHE* 1.3 80.3 - - - +
405B HIS* 1.3 57.1 + - - +
407B LEU* 3.2 8.4 + - - +
408B SER* 2.8 30.1 + - - -
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Residues in contact with HIS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TYR* 2.8 32.0 + - - +
371B ALA* 3.5 32.5 - - + +
374B ARG* 3.5 38.2 + - - +
401B PHE 3.1 9.6 + - - +
402B ASP* 3.3 13.5 - - - +
404B SER* 1.3 77.2 - - - +
406B SER* 1.3 60.6 + - - +
408B SER* 2.8 20.1 + - - -
409B ALA* 3.3 10.8 + - + +
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Residues in contact with SER 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASP* 3.0 16.2 + - - +
403B PHE* 3.4 11.1 - - - -
405B HIS* 1.3 75.8 - - - +
407B LEU* 1.3 61.4 + - - +
409B ALA* 3.5 17.5 + - - +
410B LEU* 3.9 12.3 - - - +
465B LYS 5.3 1.2 - - - +
467B PRO* 4.8 15.4 - - - +
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Residues in contact with LEU 407 (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 LEU 4.6 0.7 - - - +
363B VAL* 3.7 35.2 - - + +
366B CYS* 4.0 15.7 - - + -
403B PHE* 3.1 39.0 + - + +
404B SER* 3.6 8.1 - - - +
406B SER* 1.3 76.2 - - - +
408B SER* 1.3 63.1 + - - +
410B LEU* 3.2 22.7 + - + +
411B HIS 3.9 2.8 + - - -
412B PHE* 3.7 32.0 + - + -
420B TYR* 4.2 9.2 - - + -
467B PRO* 3.8 33.2 - - + -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B CYS* 4.8 9.4 - - - +
369B TYR* 4.3 10.5 - - - -
371B ALA* 3.3 32.2 - - - +
404B SER 2.8 15.1 + - - -
405B HIS* 2.8 21.7 + - - -
407B LEU* 1.3 76.0 - - - +
409B ALA* 1.3 60.0 + - - +
410B LEU 3.2 0.2 - - - -
411B HIS* 3.3 26.0 + - - +
412B PHE 5.8 0.7 - - - +
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Residues in contact with ALA 409 (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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405B HIS* 3.3 9.1 + - + +
406B SER* 3.6 13.5 - - - +
407B LEU 3.2 1.0 - - - -
408B SER* 1.3 80.1 + - - +
410B LEU* 1.3 63.4 + - + +
411B HIS* 3.2 22.3 + - - -
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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