Contacts of the helix formed by residues 393 - 410 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C TRP* 4.2 18.2 - - + -
388C PHE 5.3 0.9 + - - -
389C ARG 4.7 0.2 + - - -
391C LEU* 3.7 24.8 - - - +
392C GLY* 1.3 80.3 - - - +
394C SER* 1.3 61.3 + - - +
395C GLU 3.4 2.7 - - - -
396C LEU* 3.4 22.9 + - + -
397C ILE* 3.2 25.0 + - - +
482C ARG* 3.7 34.3 - - + +
601C C3S 4.2 5.6 - - - -
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Residues in contact with SER 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A VAL* 5.6 0.9 - - - +
481A GLU* 6.5 0.7 - - - -
484A GLN* 3.2 20.6 + - - -
508A THR* 3.9 10.6 - - - +
388C PHE 6.0 1.3 - - - -
389C ARG* 5.9 11.4 - - - -
392C GLY* 3.9 1.6 - - - -
393C CYS* 1.3 73.1 - - - +
395C GLU* 1.3 54.7 + - - +
397C ILE* 3.9 7.8 - - - +
398C SER* 2.7 38.8 + - - -
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Residues in contact with GLU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLN* 4.0 1.2 - - - +
488A HIS* 2.9 27.9 + - - -
508A THR* 2.8 50.8 + - - +
393C CYS 3.4 0.4 - - - -
394C SER* 1.3 82.6 + - - +
396C LEU* 1.3 53.7 + - - +
398C SER* 2.9 15.6 + - - -
399C SER* 2.6 34.8 + - - -
478C GLN* 3.9 14.5 + - - +
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Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C CYS* 3.4 32.4 + - + +
394C SER 3.3 0.4 - - - -
395C GLU* 1.3 76.4 - - - +
397C ILE* 1.3 61.6 + - + +
399C SER* 3.5 3.1 + - - -
400C ILE* 3.0 51.9 + - + +
475C LEU* 3.5 28.0 - - + +
478C GLN* 3.7 24.5 + - + +
479C HIS* 3.9 21.1 - - + +
482C ARG* 4.1 15.7 - - + -
601C C3S 4.3 20.6 - - + -
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C MET* 3.8 25.6 - - + +
388C PHE* 3.9 30.7 - - + +
391C LEU* 3.7 27.6 - - + -
393C CYS* 3.2 19.3 + - - +
394C SER* 4.2 6.3 - - - +
395C GLU 3.4 0.2 - - - -
396C LEU* 1.3 76.2 - - + +
398C SER* 1.3 58.1 + - - +
400C ILE* 3.3 5.6 + - + +
401C PHE* 3.0 39.6 + - + -
601C C3S 3.7 35.0 - - + -
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Residues in contact with SER 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLN* 3.4 30.4 - - - -
485A ILE* 6.3 0.2 - - - -
488A HIS* 3.1 19.9 + - - -
385C MET* 3.8 20.0 - - - +
394C SER 2.7 23.9 + - - -
395C GLU* 2.9 15.2 + - - -
397C ILE* 1.3 72.9 - - - +
399C SER* 1.3 59.6 + - - +
401C PHE* 3.3 3.1 + - - +
402C ASP* 2.9 29.1 + - - +
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Residues in contact with SER 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A HIS* 3.1 25.3 + - - -
395C GLU* 2.6 29.8 + - - -
396C LEU* 3.7 4.5 - - - -
398C SER* 1.3 77.8 + - - +
400C ILE* 1.3 55.5 + - - +
402C ASP* 3.3 6.6 + - - +
403C PHE* 2.9 28.6 + - - +
475C LEU* 3.6 20.1 - - - +
478C GLN* 4.1 11.6 + - - -
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Residues in contact with ILE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 5.0 4.0 - - + -
362C LEU* 3.8 30.7 - - + +
365C MET* 3.6 28.5 - - + -
396C LEU* 3.0 41.8 + - + +
397C ILE* 3.6 6.3 - - - +
399C SER* 1.3 77.2 - - - +
401C PHE* 1.3 58.5 + - + +
403C PHE* 3.2 6.7 + - + +
404C SER* 2.9 26.9 + - - -
475C LEU* 3.8 19.5 - - + +
601C C3S 4.2 33.4 - - + -
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Residues in contact with PHE 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C MET* 4.0 17.3 - - + -
369C TYR* 3.6 29.8 + + - +
374C ARG* 3.5 25.1 - - + -
376C VAL* 3.7 26.9 - - + -
383C GLY 4.0 2.9 - - - -
384C GLY 3.9 6.5 - - - -
385C MET* 3.7 47.1 - - + -
388C PHE* 4.1 9.6 - + - -
397C ILE* 3.0 34.2 + - + +
398C SER 3.3 5.6 + - - +
400C ILE* 1.3 77.9 - - + +
402C ASP* 1.3 57.3 + - - +
404C SER* 3.5 1.9 + - - -
405C HIS* 2.9 28.6 + - - +
601C C3S 5.1 5.4 - - + -
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Residues in contact with ASP 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ILE* 5.0 3.1 - - - +
488A HIS* 3.6 43.8 - - + +
489A LEU* 4.3 10.9 + - - +
374C ARG* 6.2 0.7 - - - +
398C SER 2.9 17.2 + - - +
399C SER* 3.5 5.9 - - - +
401C PHE* 1.3 74.9 - - - +
403C PHE* 1.3 61.6 + - - +
405C HIS* 3.2 8.1 + - - +
406C SER* 2.9 34.6 + - - -
471C LYS* 5.3 7.8 - - - +
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Residues in contact with PHE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C LEU* 3.8 21.3 - - + -
363C VAL* 3.9 14.8 - - + -
399C SER 2.9 14.5 + - - +
400C ILE* 3.2 8.9 + - + +
402C ASP* 1.3 79.3 + - - +
404C SER* 1.3 63.8 + - - +
406C SER* 3.3 15.7 + - - -
407C LEU* 3.4 37.6 + - + +
420C TYR* 5.1 3.1 - + - -
467C PRO* 4.0 28.3 - - + -
468C PRO 5.7 0.4 - - - -
471C LYS* 4.2 22.0 - - + -
472C LEU* 3.6 35.7 - - + -
475C LEU* 3.7 24.2 - - + -
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Residues in contact with SER 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C LEU 5.0 2.2 - - - -
365C MET* 3.5 28.9 - - - +
366C CYS* 3.4 33.5 + - - +
369C TYR* 3.6 12.6 - - - +
400C ILE 2.9 17.3 + - - -
401C PHE 3.8 4.7 - - - -
403C PHE* 1.3 80.5 - - - +
405C HIS* 1.3 61.0 + - - +
407C LEU* 3.5 4.4 + - - +
408C SER* 3.3 23.9 + - - -
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Residues in contact with HIS 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 6.4 2.0 - - + -
369C TYR* 2.7 29.9 + - - +
371C ALA* 3.3 34.1 - - + +
374C ARG* 3.4 39.1 + - + +
401C PHE 2.9 18.8 + - - +
402C ASP* 3.5 10.3 - - - +
404C SER* 1.3 75.6 - - - +
406C SER* 1.3 64.1 + - - +
408C SER* 3.5 2.3 + - - -
409C ALA* 3.3 23.6 + - + +
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Residues in contact with SER 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 6.0 2.4 - - - +
402C ASP* 2.9 22.3 + - - -
403C PHE* 3.3 13.4 + - - -
405C HIS* 1.3 76.8 - - - +
407C LEU* 1.3 63.8 + - - +
409C ALA* 3.4 18.8 + - - +
410C LEU* 3.7 13.5 - - - +
465C LYS 6.1 1.1 - - - -
467C PRO* 4.6 16.8 - - - -
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C LEU 4.8 0.7 - - - +
363C VAL* 3.9 33.9 - - + +
366C CYS* 4.1 15.3 - - + -
403C PHE* 3.4 38.6 + - + +
404C SER* 4.0 6.5 - - - +
405C HIS 3.4 0.2 - - - -
406C SER* 1.3 80.7 - - - +
408C SER* 1.3 57.0 + - - +
410C LEU* 3.1 28.6 + - + +
411C HIS 3.7 0.2 + - - -
412C PHE* 3.7 32.6 - - + +
420C TYR* 4.7 9.9 - - + -
466C LEU* 5.0 1.3 - - + -
467C PRO* 3.7 33.2 - - + -
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Residues in contact with SER 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C CYS* 4.4 15.2 - - - +
369C TYR* 3.9 17.9 - - - -
371C ALA* 3.3 29.8 - - - +
404C SER 3.3 12.6 + - - -
405C HIS 3.5 8.8 + - - -
407C LEU* 1.3 75.1 - - - +
409C ALA* 1.3 64.5 + - - +
410C LEU 3.2 0.4 - - - -
411C HIS* 3.2 24.2 + - - +
412C PHE* 4.7 4.9 - - - +
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C ALA* 6.0 1.6 - - - -
405C HIS* 3.3 16.4 + - + +
406C SER* 3.4 14.6 - - - +
407C LEU 3.1 0.4 - - - -
408C SER* 1.3 78.9 + - - +
410C LEU* 1.3 64.4 + - + +
411C HIS* 3.1 15.5 + - - -
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Residues in contact with LEU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C SER 3.7 16.4 - - - +
407C LEU* 3.1 12.3 + - + +
409C ALA* 1.3 79.0 - - + +
411C HIS* 1.3 55.4 + - - +
412C PHE* 4.1 16.6 - - + -
459C ARG* 2.6 42.7 + - - -
462C ILE* 4.2 18.8 - - + -
465C LYS* 3.5 48.5 - - + +
466C LEU* 3.8 28.7 - - + -
467C PRO* 5.3 0.9 - - + -
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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
------------------------------------------------------------
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