Contacts of the helix formed by residues 333 - 344 (chain D) in PDB entry 4C3P
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 333 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D ALA 3.2 3.2 - - - +
332D ASN* 1.3 93.4 - - + +
334D TYR* 1.3 65.1 + - - +
335D GLN* 3.5 21.8 + - - +
336D GLU* 2.7 43.4 + - + +
337D THR* 3.1 24.6 + - - -
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Residues in contact with TYR 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ARG* 3.9 16.4 - - - +
290A CYS* 3.2 36.0 - - + -
291A GLY* 4.6 10.8 - - - -
293A LEU* 3.5 22.0 - - + +
333D THR* 1.3 73.0 - - - +
335D GLN* 1.3 69.1 + - + +
337D THR* 3.3 2.4 + - - -
338D TYR* 2.7 36.9 + - - +
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Residues in contact with GLN 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ARG* 4.3 8.5 + - - -
333D THR* 3.0 18.5 - - - +
334D TYR* 1.3 99.8 + - + +
336D GLU* 1.3 67.5 + - - +
338D TYR* 4.0 6.4 - - - +
339D LYS* 3.2 26.0 + - - +
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Residues in contact with GLU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ALA* 3.4 23.6 - - + +
332D ASN* 3.3 36.7 + - - +
333D THR* 2.7 29.6 + - + +
335D GLN* 1.3 74.5 - - - +
337D THR* 1.3 66.0 + - - +
339D LYS* 3.4 4.7 - - - +
340D ARG* 3.0 38.6 + - - +
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Residues in contact with THR 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 3.5 22.0 - - + -
294A ASP* 3.7 14.7 + - - +
329D PHE 2.8 26.8 + - - +
330D GLU* 3.7 1.2 - - - -
331D ALA* 3.2 19.2 + - - -
333D THR 3.1 11.4 + - - -
334D TYR* 3.5 7.2 - - - -
335D GLN 3.2 0.2 - - - -
336D GLU* 1.3 77.9 - - - +
338D TYR* 1.3 68.3 + - - +
340D ARG* 2.7 19.2 + - - +
341D ILE* 3.0 24.5 + - + +
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Residues in contact with TYR 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 3.8 15.2 - - + +
301A ILE* 3.2 39.8 - - + +
302A GLU* 2.8 33.6 + - - -
305A MET* 4.6 16.5 - - + +
306A HIS* 5.5 1.9 - - - -
334D TYR 2.7 20.9 + - - +
335D GLN* 4.0 6.1 - - - +
337D THR* 1.3 73.0 - - - +
339D LYS* 1.3 87.3 + - + +
341D ILE* 2.9 21.8 + - - +
342D SER* 3.1 21.8 + - - -
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Residues in contact with LYS 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D GLN 3.2 19.4 + - - +
336D GLU* 3.4 6.1 - - - +
338D TYR* 1.3 90.3 - - + +
340D ARG* 1.3 56.8 + - + +
342D SER* 2.8 23.5 + - - +
343D ARG* 3.0 47.5 + - - +
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Residues in contact with ARG 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PRO 4.5 7.9 + - - -
329D PHE* 3.9 19.6 - - + +
330D GLU 3.5 19.6 + - - -
331D ALA* 3.8 11.1 - - - +
336D GLU* 3.0 46.6 + - - +
337D THR* 2.7 16.2 + - - +
339D LYS* 1.3 69.1 - - + +
341D ILE* 1.3 59.9 + - - +
343D ARG* 4.6 3.8 - - - +
344D VAL* 2.8 26.0 + - - -
345D GLU* 3.0 55.5 + - - +
346D PHE* 6.0 0.4 - - - +
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 3.1 31.0 - - + +
294A ASP 4.2 5.8 - - - +
296A LEU 3.9 9.9 - - - +
298A PRO* 3.7 21.1 - - + +
301A ILE* 3.4 29.8 - - + -
313D TRP* 4.3 7.1 - - + -
329D PHE* 3.5 33.4 - - + -
337D THR* 3.0 28.8 + - + +
338D TYR* 2.9 8.5 + - - +
340D ARG* 1.3 76.7 - - - +
342D SER* 1.3 61.1 + - - +
344D VAL* 3.3 20.6 - - - +
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Residues in contact with SER 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PRO* 4.6 13.0 - - - -
302A GLU* 4.9 12.1 - - - -
338D TYR* 3.1 18.5 + - - -
339D LYS* 2.8 23.7 + - - +
341D ILE* 1.3 71.8 - - - +
343D ARG* 1.3 57.0 + - - +
344D VAL 3.0 8.1 + - - -
366D HIS* 3.2 30.2 + - - -
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Residues in contact with ARG 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D LYS* 3.0 50.4 + - - +
340D ARG* 4.1 3.1 - - - +
342D SER* 1.3 75.9 + - - +
344D VAL* 1.3 67.9 + - - +
345D GLU* 3.5 34.0 - - + +
366D HIS* 5.6 0.2 - - - -
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Residues in contact with VAL 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PRO* 4.8 0.7 - - + -
313D TRP* 4.1 13.9 - - + -
329D PHE* 4.3 11.4 - - + -
340D ARG 2.8 11.0 + - - -
341D ILE 3.3 15.0 - - - +
342D SER 3.0 8.3 - - - +
343D ARG* 1.3 80.2 - - - +
345D GLU* 1.3 58.2 + - - +
346D PHE* 3.7 22.1 + - + -
364D LEU 3.7 22.7 - - - +
366D HIS* 4.2 26.9 - - + +
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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