Contacts of the helix formed by residues 373 - 385 (chain B) in PDB entry 3HU1
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 ASP 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B GLY* 5.4 1.9 - - - +
371B ILE 3.7 1.8 + - - -
372B PRO* 1.3 74.2 - - - +
374B ALA* 1.3 66.0 + - - +
375B THR* 3.6 17.2 + - - -
376B GLY* 2.9 25.9 + - - -
377B ARG* 3.0 26.9 + - - +
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Residues in contact with ALA 374 (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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373B ASP* 1.3 73.3 - - - +
375B THR* 1.3 63.2 + - - +
377B ARG* 3.3 32.2 + - - +
378B LEU* 3.3 18.4 + - - +
400B ALA* 3.8 9.0 - - - +
401B ASN* 4.0 19.3 - - - +
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Residues in contact with THR 375 (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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373B ASP* 3.3 16.9 + - - -
374B ALA* 1.3 75.6 - - - +
376B GLY* 1.3 62.1 + - - +
378B LEU* 3.3 17.6 + - + +
379B GLU* 3.3 28.2 + - + +
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Residues in contact with GLY 376 (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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208B GLY* 3.7 23.9 + - - -
372B PRO* 4.2 9.2 - - - -
373B ASP* 2.9 22.1 + - - -
375B THR* 1.3 76.8 - - - +
377B ARG* 1.3 55.0 + - - +
379B GLU* 3.2 8.7 + - - +
380B ILE* 3.0 30.5 + - - +
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Residues in contact with ARG 377 (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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372B PRO* 4.1 19.6 + - + +
373B ASP* 3.0 17.1 + - - +
374B ALA* 3.4 39.2 - - - +
375B THR 3.3 0.2 - - - -
376B GLY* 1.3 72.1 - - - +
378B LEU* 1.3 60.7 + - - +
380B ILE* 3.3 4.9 + - - +
381B LEU* 2.9 34.9 + - + +
400B ALA* 2.5 38.7 + - + -
401B ASN* 4.2 6.5 + - - +
403B THR* 2.8 39.2 + - - +
404B HIS* 3.3 35.0 + - - +
406B HIS* 4.2 6.4 + - - +
411B LEU* 3.9 22.1 - - + +
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Residues in contact with LEU 378 (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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374B ALA 3.3 5.9 + - - +
375B THR* 3.3 19.2 + - + +
377B ARG* 1.3 78.1 - - - +
379B GLU* 1.3 57.2 + - + +
381B LEU* 3.3 5.4 + - - +
382B GLN* 3.0 60.0 + - - +
396B LEU* 3.8 12.6 - - + -
397B GLU* 3.7 51.8 - - + +
400B ALA* 3.8 14.3 - - + +
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Residues in contact with GLU 379 (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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206B ILE 4.6 2.8 - - - +
207B GLY* 3.9 7.6 - - - -
208B GLY* 3.6 28.5 + - - +
210B ARG* 4.8 18.9 - - - +
375B THR* 3.3 15.9 + - + +
376B GLY* 3.2 12.3 + - - +
378B LEU* 1.3 78.8 - - + +
380B ILE* 1.3 57.6 + - - +
382B GLN* 3.2 15.3 + - - +
383B ILE* 3.0 39.6 + - + +
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Residues in contact with ILE 380 (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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207B GLY* 3.7 20.0 - - - +
372B PRO* 4.2 23.8 - - + -
376B GLY 3.0 15.8 + - - +
377B ARG 3.3 6.3 + - - +
379B GLU* 1.3 79.0 - - - +
381B LEU* 1.3 56.6 + - - +
383B ILE* 3.2 7.7 + - - +
384B HIS* 2.9 36.5 + - + +
408B GLY* 4.1 17.9 - - - +
411B LEU* 3.8 27.8 - - + -
800B AGS 3.5 41.3 - - + +
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Residues in contact with LEU 381 (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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377B ARG 2.9 20.8 + - - +
378B LEU* 3.3 4.9 + - - +
380B ILE* 1.3 74.8 - - - +
382B GLN* 1.3 52.9 + - - +
384B HIS* 3.5 3.5 + - - -
385B THR* 2.7 40.6 + - - +
396B LEU* 3.7 28.7 - - + +
399B VAL* 3.8 19.3 - - + -
400B ALA* 3.7 33.2 - - + +
411B LEU* 4.2 29.6 - - + +
414B LEU* 4.5 2.5 - - + -
415B CYS* 3.9 24.9 - - - -
452B PHE* 5.2 0.9 - - + -
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Residues in contact with GLN 382 (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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378B LEU* 3.0 44.4 + - + +
379B GLU* 3.6 17.2 - - - +
381B LEU* 1.3 74.5 - - - +
383B ILE* 1.3 64.2 + - + +
385B THR* 3.9 5.1 + - - -
386B LYS* 3.4 23.2 + - - +
396B LEU* 4.0 17.6 - - + +
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Residues in contact with ILE 383 (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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204B ASP 3.2 23.6 - - - +
205B ASP* 3.4 33.4 - - + +
206B ILE 3.7 5.4 - - - +
207B GLY* 3.7 31.6 - - - +
379B GLU* 3.0 25.1 + - + +
380B ILE* 3.6 6.5 - - - +
382B GLN* 1.3 76.6 - - + +
384B HIS* 1.3 69.8 + - + +
386B LYS* 3.4 28.6 - - + +
387B ASN* 5.4 0.5 + - - -
800B AGS 4.7 2.2 - - + -
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Residues in contact with HIS 384 (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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380B ILE* 2.9 25.7 + - + +
381B LEU* 4.0 4.0 - - - +
382B GLN 3.4 0.4 - - - -
383B ILE* 1.3 80.5 - - + +
385B THR* 1.3 61.4 + - - +
386B LYS 3.6 0.7 + - - -
387B ASN* 4.5 7.3 + - - -
388B MET* 4.4 10.6 - - - +
411B LEU 5.4 0.4 - - - -
412B ALA* 3.2 41.5 - - + +
415B CYS* 4.4 18.4 - - + -
800B AGS 3.2 48.4 + + - -
234C GLY 4.8 4.7 - - - +
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Residues in contact with THR 385 (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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381B LEU 2.7 24.0 + - - +
382B GLN* 3.9 3.9 + - - -
383B ILE 3.4 0.2 - - - -
384B HIS* 1.3 77.2 - - - +
386B LYS* 1.3 61.6 + - - +
387B ASN 3.1 4.5 - - - -
388B MET* 3.0 44.9 + - - +
390B LEU* 3.7 29.3 - - + +
396B LEU* 3.8 13.2 - - + +
415B CYS* 3.9 18.6 - - - -
452B PHE* 4.5 10.1 - - + -
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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