Contacts of the helix formed by residues 304 - 311 (chain A) in PDB entry 4P8V
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A THR 3.0 16.5 + - - +
302A LEU 4.0 0.2 + - - -
303A ALA* 1.3 70.6 - - - +
305A TYR* 1.3 57.0 + - - +
307A ILE* 3.1 19.6 + - + +
308A CYS* 2.9 41.5 + - - -
311A LEU* 5.7 2.9 - - + +
336A TYR* 4.4 12.0 - + - -
337A ASP 3.6 20.2 - - - -
338A ASP* 4.4 10.6 - - - +
339A VAL* 4.7 2.9 + - - +
364A MET 3.0 17.3 + - - +
365A ASP* 3.8 12.6 - - - -
366A ASP 4.3 2.2 - - - -
372A CYS* 3.5 24.5 - - + +
374A GLN* 4.8 10.4 + - - -
378A PRO* 3.9 16.6 - - + -
379A LEU* 3.5 37.3 - - + +
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.6 24.3 + - - -
43A PRO* 4.0 26.1 - - + +
44A GLY* 3.4 23.4 + - - -
295A ILE* 3.8 22.1 - - + +
296A THR* 3.7 9.2 - - - +
303A ALA* 3.5 15.6 - - + +
304A TYR* 1.3 78.7 - - - +
306A GLU* 1.3 78.9 + - + +
308A CYS 4.0 1.1 + - - -
309A GLN* 3.9 6.6 - - - +
363A ASP 3.6 21.5 - - - -
364A MET* 3.8 2.9 + - - -
365A ASP 3.5 17.7 - - - -
366A ASP* 3.8 23.0 - - - +
367A PHE* 4.3 0.9 - + - -
371A SER* 2.6 34.7 + - - -
372A CYS* 4.4 4.3 - - - -
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLY* 3.2 14.0 - - - -
294A PRO* 4.4 8.1 - - + -
295A ILE* 2.8 20.8 + - + -
296A THR* 2.6 52.7 + - - +
302A LEU* 3.5 16.3 - - + +
303A ALA 2.8 23.4 + - - +
305A TYR* 1.3 91.5 - - + +
307A ILE* 1.3 67.3 + - - +
308A CYS 3.2 0.4 - - - -
309A GLN* 3.1 10.6 + - - +
310A PHE* 3.0 20.6 + - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A THR 5.6 0.2 - - - -
269A TYR 4.2 2.0 - - - -
270A GLY* 3.6 10.8 - - - +
302A LEU* 3.6 37.9 - - + +
303A ALA 2.9 14.8 + - - +
304A TYR* 3.4 19.7 - - + +
306A GLU* 1.3 77.7 - - - +
308A CYS* 1.3 57.9 + - - +
310A PHE* 3.0 8.7 + - + +
311A LEU* 2.9 47.3 + - + +
334A VAL* 4.4 7.0 - - + -
336A TYR* 3.6 50.7 - - + -
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Residues in contact with CYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A TYR* 2.9 31.4 + - - +
306A GLU 3.2 0.4 - - - -
307A ILE* 1.3 75.9 - - - +
309A GLN* 1.3 63.3 + - - +
311A LEU* 3.7 14.7 + - - +
312A LYS* 3.7 18.9 + - - +
371A SER* 3.5 14.1 - - - +
372A CYS* 2.0 58.3 - - - -
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A PRO* 6.6 0.2 - - + -
305A TYR 3.9 6.1 - - - +
306A GLU* 3.1 10.1 + - - +
308A CYS* 1.3 75.3 - - - +
310A PHE* 1.3 65.7 + - - +
311A LEU 3.2 0.2 - - - -
312A LYS* 3.2 43.4 + - - +
329A LYS* 3.8 5.4 + - - -
370A LYS 5.3 0.2 + - - -
371A SER* 3.1 43.4 + - - +
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Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LEU* 4.4 11.4 - - + -
306A GLU 3.0 12.1 + - - +
307A ILE* 3.0 14.5 + - + +
309A GLN* 1.3 76.4 - - - +
311A LEU* 1.3 73.4 + - + +
314A ALA* 3.7 4.9 - - + +
327A ALA* 3.9 23.1 - - + -
329A LYS* 2.9 58.8 + - + +
332A GLN* 3.6 38.4 - - + -
334A VAL* 3.5 34.3 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 5.7 3.8 - - - +
307A ILE* 2.9 32.4 + - + +
308A CYS* 4.0 13.5 - - - +
309A GLN 3.2 0.6 - - - -
310A PHE* 1.3 79.6 - - + +
312A LYS* 1.3 59.5 + - + +
313A GLY 3.2 0.9 + - - -
314A ALA* 3.0 25.0 + - + +
316A ILE* 4.0 21.0 - - + +
327A ALA* 3.3 33.9 - - + -
336A TYR* 3.6 30.3 - - + +
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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