Contacts of the helix formed by residues 318 - 328 (chain H) in PDB entry 4UJ3
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 CYS 318 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308H TRP* 3.9 12.8 - - + -
313H THR* 3.7 29.6 - - + -
315H ASP* 3.2 23.0 + - + +
317H THR* 1.3 83.7 + - - +
319H PRO* 1.3 68.1 - - + +
320H PHE 4.1 0.7 - - - -
321H LEU* 3.3 27.2 + - - -
322H ASP* 2.7 31.4 + - - +
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Residues in contact with PRO 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H GLU* 3.2 27.0 - - + +
317H THR 3.7 1.8 - - - +
318H CYS* 1.3 90.6 - - + +
320H PHE* 1.3 64.2 + - - +
322H ASP* 4.1 4.1 - - + +
323H LYS* 3.4 20.9 + - - +
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Residues in contact with PHE 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H LEU 5.8 0.2 - - - -
304H GLU* 3.7 18.2 + - + +
305H PHE* 3.5 52.0 - + + -
308H TRP* 3.4 45.1 - + + -
318H CYS 3.3 0.4 - - - -
319H PRO* 1.3 83.0 - - - +
321H LEU* 1.3 92.9 + - + +
323H LYS* 3.7 3.1 + - - +
324H ILE* 3.6 39.9 + - + +
421H ILE* 3.7 25.6 - - + -
441H VAL* 4.0 10.5 - - + -
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Residues in contact with LEU 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308H TRP* 4.9 0.7 - - - +
313H THR 3.6 9.9 - - - +
314H MET* 3.6 34.1 - - + +
315H ASP 3.5 26.2 - - - +
316H ARG 4.2 0.9 - - - +
318H CYS* 3.3 11.3 + - - -
320H PHE* 1.3 110.7 - - + +
322H ASP* 1.3 61.6 + - - +
324H ILE* 3.3 2.5 + - + +
325H TYR* 2.8 52.4 + - + -
417H PHE* 4.1 22.4 - - + -
418H PHE* 5.7 2.5 - - + -
421H ILE* 4.9 5.8 - - + -
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Residues in contact with ASP 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H ARG* 3.7 15.2 + - - +
317H THR* 4.3 7.4 - - - +
318H CYS 2.7 25.0 + - - +
319H PRO* 4.1 5.4 - - + +
321H LEU* 1.3 72.4 - - - +
323H LYS* 1.3 66.3 + - - +
325H TYR* 3.1 4.5 + - - +
326H GLN* 2.9 53.4 + - - +
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Residues in contact with LYS 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B PRO* 6.3 0.9 - - + -
300H SER* 6.1 1.6 - - - -
301H LEU* 3.8 29.2 - - + -
304H GLU* 2.8 31.7 + - - +
319H PRO* 3.4 12.2 + - - +
320H PHE 3.9 3.8 - - - +
322H ASP* 1.3 83.0 - - - +
324H ILE* 1.3 58.4 + - + +
326H GLN* 3.6 4.2 - - - +
327H GLU* 2.8 59.1 + - - +
445H ARG* 4.7 6.1 - - - +
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Residues in contact with ILE 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320H PHE* 3.6 36.7 + - + +
321H LEU* 3.3 7.5 + - + +
322H ASP 3.3 0.6 - - - -
323H LYS* 1.3 77.6 - - + +
325H TYR* 1.3 55.8 + - - +
328H ASP* 2.7 42.9 + - - +
329H ILE* 3.0 14.0 + - + -
417H PHE* 3.3 47.6 - - + -
441H VAL* 4.5 1.1 - - + -
445H ARG* 3.7 31.2 - - + +
448H MET* 4.0 12.6 - - + -
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Residues in contact with TYR 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314H MET 5.3 2.8 + - - -
316H ARG* 4.1 37.2 + - + +
321H LEU* 2.8 46.7 + - + +
322H ASP* 3.5 7.2 - - - +
324H ILE* 1.3 72.6 - - - +
326H GLN* 1.3 63.2 + - + +
329H ILE* 3.4 30.0 + - + -
330H PHE* 2.8 67.5 + + + +
345H LEU* 4.6 0.9 - - + -
349H GLU* 2.6 34.0 + - - +
418H PHE* 3.2 31.7 - + - -
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Residues in contact with GLN 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B GLU* 4.1 11.5 - - - +
322H ASP* 2.9 41.8 + - - +
323H LYS* 3.6 4.9 - - - +
325H TYR* 1.3 76.6 - - - +
327H GLU* 1.3 65.0 + - + +
330H PHE* 3.6 30.3 - - - +
331H PRO* 3.4 16.5 - - - +
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Residues in contact with GLU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B GLN 4.3 4.7 - - - +
327B GLU* 4.1 28.1 - - + +
331B PRO* 3.8 20.2 - - - +
452B LYS* 3.4 21.1 - - - +
323H LYS* 2.8 37.7 + - + +
326H GLN* 1.3 82.8 - - + +
328H ASP* 1.3 69.6 + - - +
331H PRO* 3.4 8.4 - - - +
445H ARG* 2.7 29.3 + - - +
452H LYS* 3.2 22.5 + - - +
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Residues in contact with ASP 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LYS* 3.9 1.2 + - - -
324H ILE* 2.7 19.1 + - - +
326H GLN 3.5 0.2 - - - -
327H GLU* 1.3 84.7 - - - +
329H ILE* 1.3 65.0 + - - +
330H PHE 3.5 0.9 - - - -
331H PRO* 3.2 3.7 - - - +
332H CYS* 3.0 30.3 + - - +
445H ARG* 2.5 56.2 + - - +
448H MET* 3.2 28.7 - - + +
449H SER* 3.6 19.2 + - - -
452H LYS* 5.0 2.4 - - - +
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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