Contacts of the helix formed by residues 304 - 312 (chain C) in PDB entry 4AY1
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 TYR 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C THR 3.0 19.8 + - - +
303C ALA* 1.3 71.9 - - - +
305C TYR* 1.3 57.1 + - - +
307C ILE* 3.0 24.5 + - + +
308C CYS* 3.0 51.6 + - - -
311C LEU* 5.6 2.0 - - + -
336C TYR* 4.8 2.5 - + - -
337C ASP 3.8 17.9 - - - -
338C ASP* 4.6 12.7 - - + +
339C VAL 5.0 0.5 + - - -
364C MET 3.0 14.4 + - - +
365C ASP* 4.0 10.5 - - - -
366C ASP 4.3 3.4 - - - -
372C CYS* 3.5 10.5 - - - -
374C GLN* 2.8 29.0 + - - -
378C PRO* 4.0 10.5 - - + -
379C LEU* 3.5 37.9 - - + +
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Residues in contact with TYR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 3.7 12.3 + - - -
43C PRO* 4.2 21.0 - - + +
44C GLY* 3.4 24.4 + - - -
295C ILE* 3.7 30.7 - - + +
296C THR* 3.7 16.6 - - - +
303C ALA* 3.7 15.6 - - + +
304C TYR* 1.3 78.4 - - - +
306C GLU* 1.3 73.3 + - + +
308C CYS 4.2 0.4 + - - -
309C GLN* 3.8 8.5 + - - +
363C ASP 3.6 21.0 + - - -
364C MET* 3.7 2.4 + - - -
365C ASP 3.5 18.6 - - - -
366C ASP* 3.9 14.8 - - - +
367C PHE* 4.3 1.6 - + - -
371C SER* 2.6 41.1 + - - -
372C CYS* 4.0 7.9 - - - -
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Residues in contact with GLU 306 (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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293C GLY* 3.3 12.5 - - - -
294C PRO* 4.5 9.4 - - + -
295C ILE* 2.7 38.3 + - + -
296C THR* 2.5 38.9 + - - +
302C LEU* 3.6 15.4 - - + +
303C ALA 2.9 22.5 + - - +
305C TYR* 1.3 89.2 - - + +
307C ILE* 1.3 67.6 + - - +
308C CYS 3.3 0.2 - - - -
309C GLN* 3.0 10.6 + - - +
310C PHE* 2.9 20.5 + - - +
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Residues in contact with ILE 307 (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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268C THR 5.5 0.2 - - - -
269C TYR* 4.2 2.0 - - - -
270C GLY* 3.7 11.0 - - - +
302C LEU* 3.6 34.1 - - + +
303C ALA 2.9 12.3 + - - +
304C TYR* 3.4 24.9 - - + +
306C GLU* 1.3 76.9 - - - +
308C CYS* 1.3 63.6 + - - +
310C PHE* 3.1 9.3 + - + +
311C LEU* 2.9 41.3 + - + +
334C VAL* 4.3 11.4 - - + -
336C TYR* 3.6 46.0 - - + -
337C ASP 5.7 0.2 - - - +
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Residues in contact with CYS 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TYR* 3.0 36.9 + - - -
306C GLU 3.3 0.2 - - - -
307C ILE* 1.3 76.1 - - - +
309C GLN* 1.3 64.0 + - - +
311C LEU* 3.6 18.8 + - - +
312C LYS* 3.7 17.2 - - - +
371C SER* 4.3 7.4 - - - +
372C CYS* 2.1 59.0 - - + -
374C GLN* 4.3 0.9 - - - -
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Residues in contact with GLN 309 (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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305C TYR 3.8 5.6 + - - +
306C GLU* 3.0 10.5 + - - +
308C CYS* 1.3 75.2 - - - +
310C PHE* 1.3 65.7 + - - +
312C LYS* 3.1 52.5 + - - +
329C LYS* 4.1 3.5 + - - -
371C SER* 3.0 45.5 + - - +
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Residues in contact with PHE 310 (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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302C LEU* 4.5 11.7 - - + -
306C GLU 2.9 12.1 + - - +
307C ILE* 3.4 12.6 - - + +
309C GLN* 1.3 75.5 - - - +
311C LEU* 1.3 74.2 + - + +
312C LYS 3.5 0.3 - - - +
314C ALA* 3.5 7.8 - - + +
327C ALA* 3.9 24.5 - - + -
329C LYS* 3.0 52.1 + - + +
332C GLN* 3.6 44.0 - - + -
334C VAL* 3.7 32.5 - - + -
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Residues in contact with LEU 311 (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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304C TYR* 5.6 5.2 - - + +
307C ILE* 2.9 32.7 + - + +
308C CYS* 3.8 13.5 - - - +
309C GLN 3.1 0.6 - - - -
310C PHE* 1.3 79.6 - - + +
312C LYS* 1.3 57.9 + - - +
313C GLY 3.1 0.9 + - - -
314C ALA* 2.9 25.6 + - + +
316C ILE* 3.8 21.6 - - + +
327C ALA* 3.3 33.7 - - + -
336C TYR* 3.7 28.9 - - + +
338C ASP* 6.3 0.4 - - + -
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Residues in contact with LYS 312 (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 CYS* 3.7 16.4 - - - +
309C GLN* 3.3 44.4 + - - +
310C PHE 3.1 0.8 - - - -
311C LEU* 1.3 74.2 - - + +
313C GLY* 1.3 57.5 + - - +
329C LYS* 3.2 23.9 + - - +
371C SER 4.7 4.7 + - - -
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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