Contacts of the helix formed by residues 314 - 323 (chain A) in PDB entry 4HRE
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 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ARG 5.7 0.2 - - - -
307A PHE* 3.7 1.6 - - - -
308A LYS* 4.1 12.8 - - - +
313A LYS* 1.3 77.7 - - - +
315A LEU* 1.3 62.9 + - - +
316A TYR* 3.5 3.6 + - - -
317A TYR* 3.1 35.5 + - - +
318A TYR* 3.3 8.7 - - - -
338A ASP* 2.5 31.1 + - - -
339A ASP* 3.6 26.7 - - - -
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Residues in contact with LEU 315 (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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274A LEU* 3.9 33.0 - - + -
278A MET* 3.5 31.9 - - + -
292A MET* 3.9 24.0 - - + -
300A MET* 4.2 4.9 - - - -
303A ILE* 5.2 2.5 - - + -
304A ARG* 4.1 26.4 + - + +
307A PHE* 3.4 31.2 - - + +
314A SER* 1.3 70.2 - - - +
316A TYR* 1.3 66.0 + - - +
318A TYR* 3.0 11.1 + - - +
319A ILE* 3.0 26.2 + - + +
335A CYS* 4.2 7.6 - - - -
339A ASP* 4.9 3.2 + - - +
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Residues in contact with TYR 316 (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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314A SER* 3.2 8.6 - - - +
315A LEU* 1.3 77.5 - - - +
317A TYR* 1.3 64.6 + - - +
319A ILE 3.7 0.2 + - - -
320A GLN* 3.1 60.0 + - - +
332A LEU* 3.4 44.4 - - + +
335A CYS* 4.0 12.0 - - - -
337A GLY* 3.6 35.4 - - - +
338A ASP* 3.8 24.0 - - + +
339A ASP* 5.6 0.4 + - - -
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Residues in contact with TYR 317 (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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313A LYS* 4.0 46.8 - - + -
314A SER* 3.1 24.2 + - - +
315A LEU 3.1 0.2 - - - -
316A TYR* 1.3 80.6 - - - +
318A TYR* 1.3 68.9 + + - +
320A GLN* 3.3 12.1 + - - +
321A GLN* 2.9 68.7 + - + +
338A ASP* 5.9 0.2 - - - +
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Residues in contact with TYR 318 (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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275A TYR* 3.4 37.5 + + - -
278A MET* 3.6 29.8 - - + -
279A LYS* 6.0 1.8 - - - -
307A PHE* 3.2 34.8 - + + -
311A TYR* 4.0 14.6 + - + +
313A LYS* 3.6 24.0 - - + +
314A SER 3.3 11.2 - - - -
315A LEU 3.0 4.5 + - - +
317A TYR* 1.3 86.2 - + - +
319A ILE* 1.3 57.7 + - - +
321A GLN* 3.0 5.3 + - + -
322A ASP* 2.7 51.0 + - - +
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Residues in contact with ILE 319 (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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278A MET* 3.9 13.0 - - + -
288A LEU* 5.0 2.7 - - + -
292A MET* 3.9 21.1 - - + -
315A LEU* 3.0 32.9 + - + +
318A TYR* 1.3 74.7 - - - +
320A GLN* 1.3 63.8 + - - +
322A ASP* 5.1 0.2 - - - -
323A THR* 2.7 44.3 + - - +
328A GLN* 4.0 2.2 - - + +
331A LEU* 3.5 50.7 - - + +
332A LEU* 3.7 21.8 - - + -
335A CYS* 4.0 9.4 - - + -
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Residues in contact with GLN 320 (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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316A TYR* 3.1 53.2 + - - +
317A TYR* 3.4 12.8 - - + +
318A TYR 3.1 0.6 - - - -
319A ILE* 1.3 80.2 - - - +
321A GLN* 1.3 65.8 + - - +
323A THR 2.9 18.2 - - - +
324A LYS* 4.6 3.6 - - - +
328A GLN* 2.9 28.8 + - - +
332A LEU* 4.2 7.5 - - + +
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Residues in contact with GLN 321 (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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317A TYR* 2.9 60.9 + - + +
318A TYR* 3.0 6.0 + - + +
320A GLN* 1.3 87.2 - - - +
322A ASP* 1.3 65.0 + - - +
323A THR 3.6 0.4 - - - +
324A LYS* 5.4 5.1 - - - +
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Residues in contact with ASP 322 (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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278A MET* 2.8 49.2 - - + +
280A GLY 4.9 1.4 - - - +
282A GLY 3.5 10.0 - - - +
283A THR* 3.3 22.6 + - - +
318A TYR* 2.7 43.3 + - - +
319A ILE 4.6 0.2 - - - +
321A GLN* 1.3 79.6 - - - +
323A THR* 1.3 63.5 + - + +
324A LYS* 5.8 1.6 - - - -
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Residues in contact with THR 323 (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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283A THR* 5.0 2.5 - - + +
285A ASP* 4.8 4.3 - - - +
288A LEU* 4.4 11.0 - - + -
319A ILE* 2.7 25.6 + - - +
320A GLN 2.9 7.3 - - - +
321A GLN 3.6 0.4 - - - -
322A ASP* 1.3 85.8 - - + +
324A LYS* 1.3 62.2 + - - +
327A TYR* 3.7 34.5 - - + -
328A GLN* 2.5 46.9 + - - +
331A LEU* 4.1 12.1 - - + +
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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