Contacts of the helix formed by residues 340 - 351 (chain B) in PDB entry 4UHY
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 340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A PRO* 5.4 0.7 - - - +
366A LEU* 4.6 10.6 - - + +
387A ASP* 3.9 30.3 - - + +
339B SER* 1.4 77.0 - - - +
341B ASN* 1.3 65.9 + - - +
342B HIS* 3.8 6.8 + - - +
343B ALA* 3.2 22.2 + - - +
344B ILE* 3.1 22.9 + - - +
395B CYS 3.8 1.2 + - - -
396B ARG* 3.7 40.7 + - - +
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A TYR* 4.2 12.1 - - - +
386A GLN* 2.8 41.3 + - - +
387A ASP* 3.5 5.7 + - - +
388A MET* 3.8 11.7 - - - -
340B THR* 1.3 72.5 - - - +
342B HIS* 1.4 57.0 + - - +
344B ILE* 3.1 15.6 + - - +
345B VAL* 2.9 32.2 + - - +
97C LEU* 3.2 27.8 - - + +
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Residues in contact with HIS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 5.1 1.1 - - + -
320A TYR* 4.5 0.7 - - - -
322A ALA* 3.2 20.8 + - + +
323A PHE 2.7 30.3 + - - -
363A PRO* 4.8 1.0 - - + +
366A LEU* 3.6 13.2 - - + -
387A ASP 2.8 20.2 + - - +
388A MET* 3.1 26.2 - - - +
390A VAL* 3.4 22.5 - - + +
340B THR* 3.2 3.5 - - - +
341B ASN* 1.4 72.8 - - - +
343B ALA* 1.3 53.7 + - - +
345B VAL* 3.0 8.2 + - + +
346B GLN* 2.7 64.1 + - + -
396B ARG 4.6 5.9 + - - +
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.8 2.9 - - - +
339B SER* 3.7 9.0 - - - -
340B THR* 3.2 22.4 + - - +
342B HIS* 1.3 76.8 + - - +
344B ILE* 1.4 56.4 + - - +
346B GLN* 4.0 4.0 - - - -
347B THR* 3.1 34.0 + - - -
359B ALA* 3.6 25.1 - - + +
395B CYS 3.7 17.9 - - - +
396B ARG 3.8 9.8 + - - +
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 4.3 5.8 - - + -
333B LEU* 4.6 13.2 - - + -
334B ALA* 4.3 20.2 - - + +
339B SER* 3.8 18.8 - - - +
340B THR 3.1 17.6 + - - +
341B ASN* 3.1 24.5 + - - +
343B ALA* 1.4 73.1 - - - +
345B VAL* 1.3 54.5 + - - +
347B THR* 3.4 3.9 + - - +
348B LEU* 2.8 33.7 + - + +
97C LEU* 3.8 17.3 - - + +
98C ALA* 4.8 9.2 - - + +
101C SER* 3.7 32.3 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 5.9 0.4 - - + -
303A VAL* 3.8 39.7 - - + -
310A TRP* 3.7 31.0 - - + -
320A TYR* 3.8 24.0 - - + +
322A ALA* 4.7 2.9 - - + -
388A MET* 4.4 11.0 - - + -
341B ASN 2.9 19.5 + - - +
342B HIS* 3.5 8.1 - - + +
344B ILE* 1.3 76.2 - - - +
346B GLN* 1.4 51.5 + - - +
348B LEU* 3.1 8.1 + - + +
349B VAL* 2.8 39.1 + - + +
97C LEU* 4.4 1.1 - - + -
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Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 5.0 4.3 - - + -
324A TYR* 3.6 19.8 - - + +
325A CYS 4.5 7.9 + - - -
363A PRO* 5.3 2.9 - - - +
342B HIS* 2.7 48.7 + - + +
343B ALA* 4.1 5.4 - - - +
345B VAL* 1.4 70.9 - - - +
347B THR* 1.4 53.7 + - - +
349B VAL* 3.4 7.4 + - - +
350B ASN* 2.8 34.4 + - - +
356B ILE* 4.0 11.9 - - + +
357B PRO* 3.0 37.4 + - - +
358B LYS 3.5 14.9 + - - -
359B ALA* 4.4 7.2 - - - +
396B ARG* 4.8 7.5 + - - +
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Residues in contact with THR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B CYS 3.7 13.0 + - - +
330B PRO* 4.9 0.7 - - + -
331B PHE* 4.4 19.3 - - + +
333B LEU* 3.5 23.9 - - + +
343B ALA 3.1 20.3 + - - -
344B ILE* 3.7 3.1 - - - +
346B GLN* 1.4 71.6 - - - +
348B LEU* 1.3 68.1 + - - +
350B ASN* 3.2 11.4 + - - +
351B SER* 3.1 20.4 + - - -
358B LYS* 4.2 7.6 - - + +
359B ALA 3.3 21.2 + - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A VAL* 3.7 37.5 - - + +
310A TRP* 3.3 48.2 - - + +
344B ILE 2.8 21.8 + - - +
345B VAL* 3.5 5.8 - - + +
347B THR* 1.3 73.6 - - - +
349B VAL* 1.3 62.2 + - - +
351B SER* 2.5 34.9 + - - +
352B VAL* 3.6 6.7 + - + +
101C SER* 5.0 9.6 - - - +
104C HIS* 5.1 11.2 - - + -
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Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.9 11.7 - - + -
303A VAL* 3.7 40.8 - - + -
308A VAL* 3.9 16.4 - - + -
345B VAL* 2.8 23.8 + - + +
346B GLN* 3.6 6.5 - - - +
348B LEU* 1.3 71.3 - - - +
350B ASN* 1.3 52.8 + - - +
352B VAL* 3.1 5.8 + - - +
353B ASN* 2.8 35.8 + - + +
356B ILE* 3.8 33.7 - - + -
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Residues in contact with ASN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLN 2.8 14.2 + - - +
347B THR* 3.2 13.5 + - - +
349B VAL* 1.3 77.0 - - - +
351B SER* 1.4 58.9 + - - +
352B VAL 3.1 4.6 + - - -
353B ASN 3.2 22.8 - - - +
354B SER* 3.4 19.6 + - - +
356B ILE 2.6 26.8 + - - +
357B PRO* 4.2 5.0 - - - +
358B LYS* 3.3 40.9 - - - +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B THR* 3.1 9.8 + - - -
348B LEU* 2.5 31.8 + - - +
350B ASN* 1.4 77.8 + - - +
352B VAL* 1.3 63.3 + - - +
108C ASP* 4.6 15.1 + - - +
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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