Contacts of the helix formed by residues 340 - 356 (chain C) in PDB entry 6GYS
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 SER 340 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C ASN* 1.3 80.5 - - - +
341C THR* 1.3 57.5 + - - +
343C VAL* 3.3 9.9 - - - +
344C LEU* 2.9 29.1 + - - +
387C LEU* 5.6 8.3 - - - -
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Residues in contact with THR 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA* 6.0 1.6 - - + -
127C PHE* 5.3 3.1 - - + -
339C ASN* 3.2 16.1 - - - +
340C SER* 1.3 77.0 - - - +
342C GLU* 1.3 60.1 + - - +
344C LEU* 3.5 9.5 - - - +
345C TYR* 2.9 60.1 + - + +
387C LEU* 4.2 26.0 - - - +
399C GLN* 3.4 37.3 + - + +
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Residues in contact with GLU 342 (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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127C PHE* 3.4 16.8 - - + -
128C GLY* 3.8 4.2 - - - -
291C ARG* 3.5 34.5 - - + +
294C TYR* 4.9 8.0 - - + +
295C ARG* 2.6 62.0 + - - +
339C ASN* 2.7 34.7 + - - +
341C THR* 1.3 76.9 - - - +
343C VAL* 1.3 61.5 + - - +
345C TYR* 3.6 8.2 + - - +
346C TRP* 3.5 14.9 + - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C TYR* 4.2 26.0 - - + -
339C ASN 3.3 13.1 + - - +
340C SER* 3.3 18.6 - - - +
342C GLU* 1.3 80.0 - - - +
344C LEU* 1.3 58.5 + - - +
346C TRP* 3.1 10.8 + - + +
347C LYS* 2.8 50.9 + - + +
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C SER* 2.9 19.8 + - - +
341C THR* 3.5 11.0 - - - +
342C GLU 3.2 0.4 - - - -
343C VAL* 1.3 76.3 - - + +
345C TYR* 1.3 64.1 + - - +
347C LYS* 3.1 9.5 + - + +
348C ILE* 2.9 41.3 + - + +
380C PHE* 3.8 31.2 - - + +
383C LYS* 4.4 29.2 - - + +
384C VAL* 4.6 11.9 - - + -
387C LEU* 4.2 26.2 - - + -
403C ALA* 4.9 4.7 - - + -
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Residues in contact with TYR 345 (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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124C ALA* 4.2 11.2 - - + +
127C PHE* 6.4 0.2 - + - -
295C ARG* 3.4 40.2 - - - +
341C THR* 2.9 42.7 + - + -
342C GLU* 3.6 7.2 - - - +
344C LEU* 1.3 77.2 - - + +
346C TRP* 1.3 56.9 + - - +
348C ILE* 3.9 6.5 - - + +
349C ILE* 3.0 44.9 + - + +
398C PHE 4.7 1.7 + - - -
399C GLN* 3.1 31.4 + - - +
402C ILE* 4.6 15.7 - - + +
403C ALA* 4.0 29.8 - - + -
406C GLN* 5.8 4.9 - - + -
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Residues in contact with TRP 346 (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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294C TYR* 3.6 62.6 - + + +
297C CYS* 3.6 36.3 - - + -
298C GLY* 3.7 4.5 - - - -
301C TYR* 5.5 1.1 - - + -
313C HIS* 4.0 9.2 - - + -
316C VAL* 3.6 27.9 - - + +
342C GLU 3.5 4.5 + - - +
343C VAL* 3.1 13.3 + - + +
345C TYR* 1.3 77.2 - - - +
347C LYS* 1.3 58.4 + - + +
349C ILE* 4.2 15.3 - - + -
350C SER* 2.4 62.5 + - - -
353C ARG* 3.4 32.1 - - + -
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Residues in contact with LYS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 5.0 16.2 - - + +
322C HIS* 6.3 0.6 - - - +
343C VAL* 2.8 41.1 + - + +
344C LEU* 3.1 16.6 + - + +
346C TRP* 1.3 77.0 - - + +
348C ILE* 1.3 57.3 + - - +
350C SER* 2.9 7.2 + - - +
351C LEU* 2.9 31.3 + - - +
380C PHE* 3.7 33.6 - - + -
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Residues in contact with ILE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 2.9 37.7 + - + +
345C TYR* 3.9 6.7 - - + +
347C LYS* 1.3 76.8 - - + +
349C ILE* 1.3 59.0 + - + +
351C LEU* 3.2 10.2 + - + +
352C ASP* 2.9 26.7 + - - +
377C LEU* 6.2 1.6 - - + -
380C PHE* 5.0 8.1 - - + -
384C VAL* 5.0 3.4 - - + -
403C ALA* 4.4 18.2 - - + +
406C GLN* 3.7 38.8 - - + +
407C ILE* 4.5 15.3 - - + +
410C VAL* 3.7 25.7 - - + +
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Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C GLY* 4.1 30.3 - - - +
301C TYR* 4.1 23.0 - - + -
302C LEU* 5.3 13.2 - - + -
345C TYR* 3.0 30.7 + - + +
346C TRP* 4.2 13.0 - - + +
348C ILE* 1.3 77.4 - - + +
350C SER* 1.3 57.1 + - - +
352C ASP* 3.1 9.2 + - - +
353C ARG* 2.8 24.9 + - - +
406C GLN* 4.5 20.6 - - + +
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Residues in contact with SER 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 4.3 11.2 - - - +
346C TRP* 2.4 62.3 + - - -
347C LYS* 2.9 16.6 + - - +
349C ILE* 1.3 70.8 - - - +
351C LEU* 1.3 58.8 + - - +
353C ARG* 3.2 24.5 + - - +
354C ASP* 2.9 33.3 + - - +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 4.7 10.5 - - + +
320C LEU* 5.4 4.3 - - + +
347C LYS 2.9 18.6 + - - +
348C ILE* 3.4 9.4 - - + +
349C ILE 3.2 0.2 - - - -
350C SER* 1.3 75.4 + - - +
352C ASP* 1.3 58.9 + - - +
354C ASP* 3.2 15.4 + - + +
355C LEU* 2.8 31.3 + - - +
373C ILE* 3.8 40.2 - - + +
376C GLU* 4.5 11.9 - - - +
377C LEU* 3.7 29.6 - - + -
380C PHE* 4.2 20.0 - - + -
410C VAL* 4.4 7.4 - - + -
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Residues in contact with ASP 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C TYR* 2.9 28.7 + - + -
302C LEU* 5.7 0.7 - - - +
348C ILE 2.9 13.1 + - - +
349C ILE* 3.2 12.3 - - - +
351C LEU* 1.3 73.5 - - - +
353C ARG* 1.3 58.2 + - - +
355C LEU* 3.0 13.4 + - - +
356C ASP* 2.6 53.9 + - - +
409C THR* 6.0 1.6 - - - +
410C VAL* 4.3 11.8 - - + +
413C LYS* 4.5 15.9 + - - +
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Residues in contact with ARG 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C TYR* 3.6 21.5 - - + -
313C HIS* 2.5 63.0 + - + -
314C THR* 5.4 0.9 - - - +
316C VAL* 2.7 29.6 + - - +
317C SER 2.4 31.5 + - - -
318C SER* 3.6 9.5 - - - +
319C LEU 4.3 0.2 - - - +
346C TRP* 3.4 14.7 - - + -
349C ILE 2.8 13.7 + - - +
350C SER* 3.2 26.5 + - - +
352C ASP* 1.3 77.1 - - - +
354C ASP* 1.3 66.2 + - - +
356C ASP 3.7 6.8 + - - -
357C GLN* 4.1 10.6 + - - +
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Residues in contact with ASP 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C SER* 3.3 27.3 - - - -
319C LEU* 3.0 29.3 + - - +
320C LEU* 3.8 10.0 + - + +
350C SER 2.9 18.0 + - - +
351C LEU* 3.2 15.3 + - + +
353C ARG* 1.3 85.1 + - - +
355C LEU* 1.3 64.4 + - - +
357C GLN* 4.7 8.3 + - - +
358C TYR* 4.7 7.6 - - - -
369C THR* 6.4 1.6 - - + -
373C ILE* 5.1 8.8 - - + +
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Residues in contact with LEU 355 (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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351C LEU 2.8 17.5 + - - +
352C ASP* 3.0 19.5 + - - +
354C ASP* 1.3 77.4 - - - +
356C ASP* 1.3 72.9 + - - +
357C GLN 3.5 0.4 - - - -
358C TYR* 3.1 27.4 - - - -
370C LEU* 4.8 0.7 - - + -
373C ILE* 3.7 27.1 - - + -
410C VAL* 3.7 37.7 - - + +
413C LYS* 5.0 6.1 - - + -
414C LEU* 3.8 18.2 - - + -
417C MET* 3.6 31.8 - - + +
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Residues in contact with ASP 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C TYR* 3.5 20.5 + - - +
352C ASP* 2.6 27.2 + - - +
353C ARG 3.7 3.8 + - - -
354C ASP 3.5 0.6 - - - -
355C LEU* 1.3 88.7 - - - +
357C GLN* 1.3 59.9 + - - +
358C TYR* 3.2 4.2 - - - +
359C LEU* 3.3 43.4 - - + +
413C LYS* 3.8 23.5 + - - +
417C MET* 3.9 14.2 - - - +
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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