Contacts of the helix formed by residues 304 - 311 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B THR 3.0 22.6 + - - +
303B ALA* 1.3 71.5 - - - +
305B TYR* 1.3 63.3 + - - +
307B ILE* 3.0 24.1 + - + -
308B CYS* 3.0 45.8 + - - -
311B LEU* 5.6 3.9 - - + +
336B TYR* 4.7 2.2 - + - -
337B ASP 3.7 19.5 - - - -
338B ASP* 4.4 13.5 - - + +
339B VAL 4.9 0.5 + - - -
364B MET 3.1 12.0 + - - +
365B ASP* 4.0 9.6 - - - -
366B ASP 4.4 1.8 - - - -
372B CYS* 3.8 8.7 - - - -
374B GLN* 3.0 30.2 + - - -
378B PRO* 3.8 13.0 - - + -
379B LEU* 3.5 36.9 - - + +
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 3.7 24.4 + - - -
43B PRO* 4.1 14.6 - - + +
44B GLY* 3.4 25.6 + - - -
295B ILE* 3.7 30.1 - - + +
296B THR* 3.7 6.8 - - - +
303B ALA* 3.7 14.4 - - + +
304B TYR* 1.3 77.1 - - - +
306B GLU* 1.3 72.9 + - + +
308B CYS* 4.1 2.8 + - - +
309B GLN* 3.8 8.7 - - - +
363B ASP 3.6 20.4 - - - -
364B MET* 3.8 4.0 + - - -
365B ASP 3.4 18.4 - - - -
366B ASP* 3.9 13.6 - - - +
367B PHE* 4.3 0.9 - + - -
371B SER* 2.7 40.5 + - - -
372B CYS* 4.0 7.4 - - - -
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLY* 3.2 14.3 - - - -
294B PRO* 4.2 15.0 - - + -
295B ILE* 2.8 33.8 + - + -
296B THR* 2.7 36.6 + - - +
302B LEU* 3.7 14.4 - - + -
303B ALA* 2.9 23.4 + - - +
305B TYR* 1.3 87.7 - - + +
307B ILE* 1.3 65.8 + - - +
308B CYS 3.2 1.8 - - - -
309B GLN* 3.1 9.7 + - - +
310B PHE* 3.0 20.8 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR 4.7 0.4 - - - +
269B TYR 4.2 2.0 - - - -
270B GLY* 3.7 11.7 - - - +
302B LEU* 3.6 37.7 - - + +
303B ALA 2.9 16.7 + - - +
304B TYR* 3.0 20.6 + - + +
306B GLU* 1.3 76.8 - - - +
308B CYS* 1.3 63.1 + - - +
310B PHE* 3.1 8.3 + - + +
311B LEU* 2.9 37.2 + - + +
334B VAL* 4.4 7.2 - - + -
336B TYR* 3.6 49.6 - - + -
337B ASP 5.4 0.4 - - - +
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Residues in contact with CYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TYR* 3.0 35.5 + - - +
305B TYR 4.2 3.6 - - - +
306B GLU 3.2 0.4 - - - -
307B ILE* 1.3 76.1 - - - +
309B GLN* 1.3 64.5 + - - +
311B LEU* 3.6 19.1 + - - +
312B LYS* 3.8 16.3 - - - +
371B SER* 4.3 4.3 - - - +
372B CYS* 2.1 59.0 - - + -
374B GLN* 4.1 1.6 - - - -
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B TYR 3.8 12.3 - - - +
306B GLU* 3.1 9.2 + - - +
308B CYS* 1.3 76.0 - - - +
310B PHE* 1.3 65.6 + - - +
312B LYS* 3.0 51.8 + - - +
329B LYS* 4.1 3.3 + - - -
371B SER* 2.9 40.7 + - - +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B LEU* 4.5 11.9 - - + -
306B GLU 3.0 12.7 + - - +
307B ILE* 3.1 12.3 + - + +
309B GLN* 1.3 75.8 - - - +
311B LEU* 1.3 74.5 + - + +
312B LYS 3.4 0.3 - - - +
314B ALA* 3.6 6.4 - - + +
327B ALA* 3.9 24.2 - - + -
329B LYS* 3.0 54.5 + - + +
332B GLN* 3.7 40.6 - - + -
334B VAL* 3.7 34.5 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TYR* 5.6 5.8 - - + +
307B ILE* 2.9 27.9 + - + +
308B CYS* 3.8 13.2 - - - +
309B GLN 3.3 0.6 - - - -
310B PHE* 1.3 80.2 - - + +
312B LYS* 1.3 56.8 + - + +
313B GLY 3.1 1.0 + - - -
314B ALA* 2.9 26.4 + - + +
316B ILE* 3.8 22.5 - - + +
327B ALA* 3.4 31.6 - - + -
336B TYR* 3.6 36.1 - - + +
338B ASP* 6.2 0.4 - - + -
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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
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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