Contacts of the helix formed by residues 355 - 373 (chain C) in PDB entry 6TXA
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 GLU 355 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C PHE* 6.2 0.2 - - - -
330C ASP 5.4 0.5 - - - +
333C ARG* 3.0 46.2 + - - +
334C PHE* 4.2 20.9 + - + +
337C PHE* 4.2 27.1 - - + -
351C ALA* 4.5 11.7 - - + -
352C ARG 3.0 16.3 + - - +
354C LYS* 1.3 80.0 - - + +
356C VAL* 1.3 65.4 + - - +
357C GLY 3.1 2.9 - - - -
358C ASN* 2.9 40.9 + - + +
359C LEU* 3.0 18.0 + - + +
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Residues in contact with VAL 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B GLN* 4.1 23.6 - - + +
352C ARG 4.0 2.6 + - - +
353C ASP* 3.3 18.8 + - - +
354C LYS 3.2 3.1 - - - +
355C GLU* 1.3 75.9 - - - +
357C GLY* 1.3 66.3 + - - +
359C LEU* 3.3 13.4 + - + +
360C TYR* 3.1 44.2 + - + -
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Residues in contact with GLY 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 6.2 4.7 - - - -
354C LYS 3.9 4.7 + - - -
355C GLU 3.1 0.4 - - - -
356C VAL* 1.3 83.9 - - - +
358C ASN* 1.3 62.6 + - - +
360C TYR* 3.2 11.1 + - - +
361C ASP* 3.0 27.2 + - - +
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Residues in contact with ASN 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 3.0 40.2 + - - +
329C PHE* 4.0 14.9 - - + -
333C ARG* 3.6 16.2 - - - +
354C LYS 4.9 2.2 + - - -
355C GLU* 2.9 43.9 + - + +
357C GLY* 1.3 76.4 - - - +
359C LEU* 1.3 58.5 + - + +
361C ASP* 3.4 7.9 + - - +
362C MET* 2.9 25.5 + - - +
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Residues in contact with LEU 359 (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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308C ILE* 3.7 36.3 - - + -
329C PHE* 4.9 4.3 - - + -
334C PHE* 3.6 37.5 - - + -
351C ALA* 4.1 14.6 - - + -
355C GLU* 3.0 15.5 + - + +
356C VAL* 3.6 15.9 - - + +
357C GLY 3.2 0.2 - - - -
358C ASN* 1.3 77.0 - - + +
360C TYR* 1.3 66.2 + - + +
362C MET* 3.2 19.7 + - - +
363C PHE* 3.3 21.9 - - + -
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Residues in contact with TYR 360 (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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356C VAL* 3.1 46.1 + - + -
357C GLY* 3.2 8.0 + - - +
359C LEU* 1.3 75.3 - - + +
361C ASP* 1.3 61.0 + - - +
363C PHE* 3.3 10.4 + + + +
364C HIS* 3.1 24.7 + - - +
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Residues in contact with ASP 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B HIS* 3.3 27.0 + - - +
368B SER* 2.8 31.0 + - - -
372B ARG* 3.2 20.4 + - - +
328C ASN* 4.2 7.3 - - - +
329C PHE* 5.3 1.3 - - + -
357C GLY 3.0 16.9 + - - +
358C ASN* 3.6 9.1 - - - +
359C LEU 3.2 0.2 - - - -
360C TYR* 1.3 77.9 - - - +
362C MET* 1.3 57.3 + - - +
364C HIS* 3.5 7.3 - - - +
365C THR* 2.9 33.7 + - - -
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Residues in contact with MET 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ILE* 4.1 20.0 - - + -
312C LYS* 3.6 30.1 - - + -
313C TRP* 3.8 26.7 - - - -
316C PHE* 3.6 16.4 - - + -
329C PHE* 3.6 35.9 - - + -
358C ASN 2.9 7.5 + - - +
359C LEU* 3.2 15.4 + - - +
361C ASP* 1.3 79.2 - - - +
363C PHE* 1.3 90.0 + - + +
365C THR* 3.4 6.4 + - - -
366C ARG* 3.0 25.2 + - - +
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Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASN* 3.5 25.4 - - + -
307C GLY* 4.9 0.4 - - - -
308C ILE* 3.8 21.1 - - + -
312C LYS* 4.4 12.3 - - - -
359C LEU* 3.3 23.3 - - + -
360C TYR* 3.3 10.3 + + - +
362C MET* 1.3 100.8 - - + +
364C HIS* 1.3 59.7 + - - +
366C ARG* 3.4 22.0 + - - +
367C ASN* 3.0 27.5 + - - +
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Residues in contact with HIS 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN* 5.5 4.7 - - - -
361B ASP* 3.3 30.2 + - - -
364B HIS* 3.6 48.0 - + + +
540B LEU 5.9 1.9 + - - -
541B LEU* 6.1 4.5 - - + -
328C ASN* 6.1 0.7 - - - -
360C TYR 3.1 14.1 + - - +
361C ASP* 3.5 13.9 - - - +
363C PHE* 1.3 73.9 - - - +
365C THR* 1.3 57.0 + - - +
367C ASN* 3.1 10.5 + - - +
368C SER* 2.8 43.5 + - - -
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Residues in contact with THR 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN* 5.6 6.1 + - - +
316C PHE* 4.1 15.7 - - + -
327C ASN* 3.9 22.4 - - - +
328C ASN* 4.0 29.9 + - - +
329C PHE* 4.7 2.2 - - + +
361C ASP 2.9 20.5 + - - -
362C MET* 3.4 7.7 - - - -
364C HIS* 1.3 79.1 - - - +
366C ARG* 1.3 57.8 + - - +
368C SER* 3.3 7.4 + - - -
369C LEU* 2.9 40.9 + - + +
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Residues in contact with ARG 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LYS* 3.7 30.9 - - - +
315C TYR* 3.5 28.0 + - + +
316C PHE* 3.8 14.8 - - + -
362C MET 3.0 13.6 + - - +
363C PHE* 3.4 25.0 + - - +
365C THR* 1.3 76.7 - - - +
367C ASN* 1.3 65.8 + - - +
369C LEU* 3.2 6.0 + - - +
370C HIS* 3.0 46.1 + - + -
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Residues in contact with ASN 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B SER* 5.5 1.0 + - - -
540B LEU* 3.8 32.3 - - - +
363C PHE 3.0 14.3 + - - +
364C HIS* 3.6 10.4 + - - +
366C ARG* 1.3 83.2 - - - +
368C SER* 1.3 57.9 + - - +
370C HIS* 3.3 10.1 + - - +
371C ARG* 2.9 47.0 + - - +
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN* 4.6 5.6 + - - -
361B ASP* 3.0 25.9 + - - -
364C HIS* 2.8 24.2 + - - -
365C THR* 3.5 9.4 - - - -
367C ASN* 1.3 79.7 - - - +
369C LEU* 1.3 57.3 + - - +
371C ARG* 3.3 6.3 + - - +
372C ARG* 2.9 52.1 + - - +
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Residues in contact with LEU 369 (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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316C PHE* 3.9 29.2 - - + -
319C ASP* 5.5 0.2 - - + -
320C CYS* 3.8 30.3 - - - +
323C LEU* 4.3 20.6 - - + -
325C ILE* 4.3 17.7 - - + -
365C THR* 2.9 27.1 + - + +
366C ARG 3.6 5.2 - - - +
368C SER* 1.3 72.8 - - - +
370C HIS* 1.3 60.1 + - - +
372C ARG* 4.9 2.7 - - - +
373C ALA* 2.9 27.0 + - - +
374C TYR* 3.1 39.7 + - + +
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Residues in contact with HIS 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C TYR* 4.9 3.8 + - - -
366C ARG* 3.0 53.3 + - + +
367C ASN* 3.5 13.2 - - - +
369C LEU* 1.3 77.9 - - - +
371C ARG* 1.3 63.9 + - + +
374C TYR* 3.5 30.2 + + + +
375C GLN* 2.8 62.3 + - + +
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Residues in contact with ARG 371 (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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357B GLY* 6.1 5.4 - - - -
537B VAL* 3.0 32.4 + - - +
538B SER* 3.6 20.5 + - - +
540B LEU* 6.3 0.2 - - - +
367C ASN* 2.9 35.9 + - - +
368C SER* 3.3 6.9 + - - +
370C HIS* 1.3 80.7 - - + +
372C ARG* 1.3 64.0 + - + +
375C GLN* 4.5 5.2 - - - +
376C HIS* 4.4 8.8 + - - -
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Residues in contact with ARG 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN* 3.2 49.0 + - - +
329B PHE* 6.3 0.6 - - - -
358B ASN* 3.0 31.1 + - - +
361B ASP* 3.3 26.9 + - - +
157C PHE* 3.7 8.7 - - + -
325C ILE* 3.5 40.0 - - + +
368C SER* 2.9 30.5 + - - +
369C LEU* 4.4 2.4 - - - +
371C ARG* 1.3 80.7 - - + +
373C ALA* 1.3 58.2 + - - +
376C HIS* 3.7 23.6 - - - -
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Residues in contact with ALA 373 (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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150C LEU* 5.6 0.4 - - + -
153C GLY* 5.6 5.0 - - - -
157C PHE* 3.7 23.2 - - + -
323C LEU* 3.7 33.0 - - + -
325C ILE* 4.6 5.4 - - + -
369C LEU 2.9 13.1 + - - +
371C ARG 3.5 0.2 - - - -
372C ARG* 1.3 77.8 - - - +
374C TYR* 1.3 71.7 + - + +
375C GLN 3.3 2.0 - - - -
376C HIS* 3.0 18.9 + - - +
379C GLY* 5.6 1.4 - - - -
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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