Contacts of the helix formed by residues 320 - 330 (chain A) in PDB entry 5H1Y
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 THR 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ILE* 4.8 0.9 - - - -
264A CYS 3.3 13.2 - - - +
265A PRO 4.1 2.5 - - - +
266A SER* 3.6 31.9 - - - +
267A ARG* 3.8 4.9 - - + +
270A ALA* 4.5 1.1 - - + -
297A CYS 3.1 6.1 + - - +
298A ILE* 3.8 16.4 - - + +
299A GLY 4.2 0.2 + - - -
319A ALA* 1.3 76.4 - - - +
321A PRO* 1.3 77.0 - - - +
322A GLY 3.3 0.8 + - - -
323A ARG* 3.3 35.2 + - - +
324A LEU* 3.2 21.0 + - - +
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Residues in contact with PRO 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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263A ILE* 3.8 18.6 - - + -
264A CYS 3.2 13.2 - - - +
265A PRO* 4.6 0.7 - - + +
320A THR* 1.3 87.4 - - - +
322A GLY* 1.3 56.1 + - - +
323A ARG* 5.6 0.4 - - - +
325A MET* 3.0 31.9 + - - +
349A MET* 4.0 8.3 - - - -
354A PHE* 3.9 37.2 - - + -
357A ASP* 4.4 12.6 - - + +
358A ILE* 4.2 16.8 - - + -
361A ILE* 3.6 17.5 - - + +
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Residues in contact with GLY 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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320A THR 3.3 0.8 - - - -
321A PRO* 1.3 81.6 - - - +
323A ARG* 1.3 75.2 + - - +
325A MET* 3.8 5.7 - - - +
326A ASP* 3.2 23.0 + - - +
354A PHE* 5.4 5.2 - - - -
357A ASP* 3.9 15.6 + - - -
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Residues in contact with ARG 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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267A ARG* 2.9 29.9 - - - +
297A CYS* 3.8 19.5 - - - +
298A ILE 3.5 4.5 - - - +
299A GLY* 3.3 34.1 - - - +
306A GLN* 4.6 4.5 - - - +
320A THR* 3.3 25.0 + - - +
322A GLY* 1.3 82.2 - - - +
324A LEU* 1.3 66.4 + - - +
326A ASP* 3.6 6.1 + - - +
327A LEU* 3.1 29.3 + - + +
354A PHE* 6.2 2.0 - - - -
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Residues in contact with LEU 324 (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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261A LEU* 3.5 37.7 - - + -
263A ILE* 4.4 5.8 - - + -
297A CYS* 3.7 8.9 - - - -
317A MET* 4.5 14.6 - - - -
319A ALA* 3.8 13.2 - - + -
320A THR 3.2 16.0 + - - +
321A PRO 4.1 2.0 - - - +
323A ARG* 1.3 77.3 - - - +
325A MET* 1.3 66.4 + - - +
327A LEU* 3.1 2.1 + - - -
328A LEU* 2.9 41.6 + - + +
333A VAL* 4.1 18.4 - - + -
335A LEU* 5.2 0.9 - - + -
361A ILE* 3.9 22.7 - - + -
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Residues in contact with MET 325 (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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321A PRO 3.0 20.5 + - - +
322A GLY* 3.8 5.4 - - - +
324A LEU* 1.3 76.9 - - - +
326A ASP* 1.3 66.5 + - + +
328A LEU* 3.1 8.0 + - + +
329A GLN* 2.9 43.3 + - + +
357A ASP* 3.4 46.7 - - - +
360A THR* 3.9 30.1 - - + -
361A ILE* 4.3 13.7 - - + +
364A TYR* 5.8 0.4 - - + -
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Residues in contact with ASP 326 (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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322A GLY 3.2 15.1 + - - +
323A ARG* 3.7 7.0 - - - +
325A MET* 1.3 81.6 - - + +
327A LEU* 1.3 65.7 + - - +
329A GLN* 3.4 9.1 + - - +
330A LYS* 3.0 68.3 + - - +
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Residues in contact with LEU 327 (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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297A CYS* 3.7 8.7 - - + -
303A VAL* 5.3 12.3 - - + -
306A GLN* 3.6 38.8 - - + +
307A MET* 4.2 12.3 - - + -
323A ARG 3.1 20.2 + - - +
324A LEU* 3.1 4.7 + - - +
326A ASP* 1.3 86.7 - - - +
328A LEU* 1.3 64.4 + - - +
330A LYS* 3.3 5.0 + - + -
331A LYS 3.1 3.3 + - - -
332A MET* 3.0 48.1 + - + -
333A VAL* 3.4 28.9 - - + +
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Residues in contact with LEU 328 (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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324A LEU* 2.9 36.9 + - + +
325A MET* 3.5 6.7 - - - +
327A LEU* 1.3 76.0 - - - +
329A GLN* 1.3 58.2 + - - +
331A LYS* 3.0 22.9 + - - +
333A VAL* 3.4 36.9 - - + +
334A SER* 4.6 0.2 - - - -
335A LEU* 3.7 25.1 - - + +
361A ILE* 4.1 26.5 - - + -
364A TYR* 3.6 49.6 - - + -
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Residues in contact with GLN 329 (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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325A MET* 2.9 41.5 + - + +
326A ASP* 4.0 7.7 - - - +
328A LEU* 1.3 77.0 - - - +
330A LYS* 1.3 61.6 + - + +
331A LYS* 3.4 13.2 + - - +
360A THR* 3.9 20.6 - - - +
364A TYR* 3.1 25.4 + - + +
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Residues in contact with LYS 330 (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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326A ASP* 3.0 52.7 + - - +
327A LEU* 3.9 5.8 - - + +
328A LEU 3.2 0.4 - - - -
329A GLN* 1.3 76.9 - - + +
331A LYS* 1.3 71.6 + - - +
332A MET* 3.1 28.9 + - + +
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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