Contacts of the helix formed by residues 356 - 371 (chain C) in PDB entry 5T0I
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 GLY 356 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C GLY* 3.0 20.7 - - - +
194C THR* 3.1 21.5 + - - -
320C PRO* 3.9 12.6 - - - +
328C ILE* 5.7 0.2 - - - +
355C SER* 1.3 68.5 - - - +
357C ALA* 1.3 63.9 + - - +
358C GLU 3.1 1.8 - - - -
359C VAL* 3.2 27.7 + - - +
360C LYS* 4.3 1.9 + - - +
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Residues in contact with ALA 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C PRO 6.0 0.2 - - - -
193C GLY 4.1 3.1 - - - +
194C THR* 3.5 23.9 + - + +
355C SER* 3.3 9.0 + - - +
356C GLY* 1.3 75.3 - - - +
358C GLU* 1.3 59.0 + - - +
359C VAL 3.1 0.6 + - - -
360C LYS* 3.4 13.1 + - + +
361C GLY* 3.0 19.6 + - - -
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Residues in contact with GLU 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C MET* 5.1 7.0 - - + -
354C ALA* 4.4 15.3 - - + +
355C SER* 3.2 31.2 + - - +
356C GLY 3.1 0.6 - - - -
357C ALA* 1.3 77.0 - - - +
359C VAL* 1.3 52.9 + - - +
361C GLY* 3.3 9.5 - - - +
362C VAL* 2.7 42.2 + - + +
390C VAL* 3.2 38.5 - - + +
393C LYS* 5.1 13.4 + - - +
394C ASP* 5.7 0.9 - - - -
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Residues in contact with VAL 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ARG* 4.5 22.9 - - + -
328C ILE* 3.8 42.4 - - + +
329C LEU* 4.1 21.3 - - + +
332C HIS* 5.0 7.2 - - + +
351C MET* 6.2 3.8 - - + -
355C SER 4.6 2.5 - - - +
356C GLY* 3.4 21.8 - - - +
357C ALA 3.1 0.6 - - - -
358C GLU* 1.3 77.8 - - - +
360C LYS* 1.3 62.7 + - + +
362C VAL* 3.4 19.8 + - - +
363C CYS* 3.6 11.9 + - - -
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Residues in contact with LYS 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C THR* 5.9 5.4 - - + +
198C LEU* 6.1 0.9 - - + -
332C HIS* 3.2 50.6 - - + +
356C GLY 5.4 2.0 - - - +
357C ALA* 3.4 13.8 + - + +
358C GLU 3.3 0.4 - - - -
359C VAL* 1.3 76.3 - - + +
361C GLY* 1.3 54.7 + - - +
362C VAL 3.3 0.2 - - - -
363C CYS* 4.8 3.8 - - - +
364C THR* 2.4 58.9 + - + +
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Residues in contact with GLY 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ALA 3.0 12.0 + - - -
358C GLU* 2.9 20.1 + - - -
360C LYS* 1.3 75.7 - - - +
362C VAL* 1.3 64.8 + - - +
364C THR* 4.0 4.0 - - - -
365C GLU* 3.1 36.1 + - - +
366C ALA* 3.7 1.4 + - - +
390C VAL* 5.0 3.1 - - - +
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Residues in contact with VAL 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU* 5.3 6.7 - - + -
347C ILE* 6.3 3.6 - - + -
351C MET* 4.0 29.6 - - + -
358C GLU* 2.7 24.6 + - + +
359C VAL* 3.5 10.5 - - - +
360C LYS 3.3 0.4 - - - -
361C GLY* 1.3 76.4 - - - +
363C CYS* 1.3 69.0 + - - +
366C ALA* 3.1 24.0 - - - +
386C ALA* 5.0 16.9 - - + +
387C VAL* 6.2 2.7 - - + -
390C VAL* 3.9 24.5 - - + -
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Residues in contact with CYS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU* 3.7 31.6 - - - -
332C HIS* 5.4 8.5 - - + -
333C SER* 4.6 11.0 - - - -
336C MET* 4.6 22.2 - - + -
359C VAL* 3.6 8.3 + - - +
360C LYS* 4.2 5.4 - - - +
361C GLY 3.5 0.2 - - - -
362C VAL* 1.3 82.1 - - - +
364C THR* 1.3 59.8 + - + +
367C GLY* 2.7 35.3 + - - -
196D ILE* 5.3 2.1 - - - +
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Residues in contact with THR 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C MET* 5.5 4.7 - - + -
360C LYS* 2.4 53.5 + - + +
361C GLY* 4.0 2.3 - - - -
363C CYS* 1.3 76.5 - - + +
365C GLU* 1.3 78.1 + - - +
367C GLY* 3.1 12.3 + - - -
368C MET* 3.8 16.5 + - - +
196D ILE* 4.6 24.4 - - + +
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Residues in contact with GLU 365 (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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361C GLY* 3.1 29.4 + - - +
364C THR* 1.3 90.0 + - - +
366C ALA* 1.3 58.5 + - - +
367C GLY 3.4 0.2 + - - -
368C MET* 3.5 20.9 + - - +
369C TYR* 4.3 6.9 - - - -
393C LYS* 5.6 9.4 - - - +
176D GLU* 4.8 12.0 - - - +
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Residues in contact with ALA 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C GLY 3.7 1.1 + - - +
362C VAL* 3.1 20.6 + - - +
363C CYS 3.7 0.4 - - - -
365C GLU* 1.3 74.2 - - - +
367C GLY* 1.3 61.7 + - - +
368C MET 3.1 2.7 - - - -
369C TYR* 3.2 37.0 + - + +
370C ALA* 4.0 2.4 + - - +
382C ASP* 4.8 2.8 - - - +
386C ALA* 4.1 31.0 - - + +
389C LYS* 5.5 5.6 - - + -
390C VAL* 6.1 1.6 - - + -
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Residues in contact with GLY 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C CYS 2.7 20.5 + - - -
364C THR* 3.1 5.8 + - - -
366C ALA* 1.3 76.3 - - - +
368C MET* 1.3 66.3 + - - +
369C TYR 3.1 0.2 - - - -
370C ALA* 3.4 11.7 + - - +
371C LEU* 3.1 22.9 + - - +
194D ILE* 4.5 6.1 - - - +
196D ILE* 4.9 9.1 - - - +
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Residues in contact with MET 368 (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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364C THR 3.9 10.5 - - - +
365C GLU* 3.7 18.2 - - - +
366C ALA 3.1 1.2 - - - -
367C GLY* 1.3 80.2 - - - +
369C TYR* 1.3 59.6 + - + +
370C ALA 3.4 0.2 - - - -
371C LEU* 3.2 34.9 + - + +
372C ARG 3.1 14.9 + - - -
176D GLU* 5.3 9.9 - - - +
179D GLU* 3.0 45.2 - - + +
191D TYR* 5.7 2.9 - - + -
194D ILE* 4.5 2.0 - - + -
196D ILE* 3.7 34.5 - - + -
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Residues in contact with TYR 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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365C GLU 4.3 6.7 - - - -
366C ALA* 3.2 33.1 + - + +
367C GLY 3.1 0.8 - - - -
368C MET* 1.3 77.2 - - + +
370C ALA* 1.3 60.3 + - - +
371C LEU 3.1 1.6 - - - -
372C ARG* 3.0 22.5 + - - +
373C GLU* 2.8 25.0 - - - +
382C ASP* 3.8 20.9 - - - +
385C MET* 6.5 1.6 - - + -
389C LYS* 3.2 43.9 + - + -
175D GLN* 5.2 12.6 - - + -
176D GLU* 4.6 14.3 + - - -
179D GLU* 4.2 11.0 - - - -
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ALA 4.0 2.1 + - - +
367C GLY* 3.4 12.8 + - - +
369C TYR* 1.3 77.4 - - - +
371C LEU* 1.3 60.2 + - - +
372C ARG 3.2 0.6 + - - -
373C GLU* 3.3 17.8 + - - +
374C ARG 3.9 3.6 + - - -
375C ARG 3.2 26.5 + - - +
376C VAL 4.8 8.5 - - - +
377C HIS* 5.6 0.2 - - - -
378C VAL* 4.6 19.5 - - + +
382C ASP* 4.1 4.2 + - - +
190D LEU* 4.6 1.2 - - - +
194D ILE* 5.0 8.2 - - + +
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Residues in contact with LEU 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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367C GLY 3.1 13.8 + - - +
368C MET* 3.2 38.6 - - - +
369C TYR 3.1 0.8 - - - -
370C ALA* 1.3 75.0 - - - +
372C ARG* 1.3 62.6 + - - +
373C GLU 3.5 0.2 - - - -
374C ARG* 3.9 3.6 + - - +
179D GLU* 4.0 24.7 - - + +
183D LEU* 3.6 23.6 - - + +
190D LEU* 3.2 37.9 - - + +
191D TYR* 3.8 29.2 - - + +
194D ILE* 3.8 19.5 - - + +
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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