Contacts of the helix formed by residues 373 - 386 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C GLY* 5.6 1.0 - - - +
371C ILE 3.6 2.6 + - - -
372C PRO* 1.3 74.7 - - - +
374C ALA* 1.3 67.6 + - - +
375C THR* 3.7 17.8 + - - -
376C GLY* 2.9 24.3 + - - -
377C ARG* 3.0 27.7 + - - +
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C ASP* 1.3 73.2 - - - +
375C THR* 1.3 62.6 + - - +
377C ARG* 3.2 32.6 + - - +
378C LEU* 3.2 19.3 + - - +
400C ALA* 3.8 9.1 - - - +
401C ASN* 3.9 20.2 - - - +
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Residues in contact with THR 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C ASP* 3.3 16.5 + - - -
374C ALA* 1.3 77.2 - - - +
376C GLY* 1.3 61.2 + - - +
378C LEU* 3.4 15.5 + - + +
379C GLU* 3.3 28.6 + - + +
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Residues in contact with GLY 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C GLY* 3.8 23.2 + - - -
372C PRO* 4.1 11.4 - - - -
373C ASP* 2.9 21.7 + - - -
375C THR* 1.3 73.5 - - - +
377C ARG* 1.3 63.3 + - - +
379C GLU* 3.3 8.6 + - - +
380C ILE* 3.2 25.5 + - - +
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Residues in contact with ARG 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C PRO* 4.0 22.7 + - + -
373C ASP* 3.0 16.1 + - - +
374C ALA* 3.2 39.7 + - - +
376C GLY* 1.3 73.0 - - - +
378C LEU* 1.3 65.9 + - - +
380C ILE* 3.4 3.5 + - - +
381C LEU* 3.0 27.4 + - - +
400C ALA* 2.6 39.0 + - + -
401C ASN* 4.2 6.7 + - - +
403C THR* 2.9 38.7 + - - +
404C HIS* 3.0 27.9 + - - +
405C GLY 5.4 0.2 - - - -
406C HIS* 4.2 9.2 + - - +
411C LEU* 3.9 20.7 - - + +
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ALA 3.2 9.2 + - - +
375C THR* 3.5 17.9 - - + +
377C ARG* 1.3 78.4 - - - +
379C GLU* 1.3 62.8 + - + +
381C LEU* 3.2 5.9 + - - +
382C GLN* 3.0 53.3 + - - +
396C LEU* 3.9 12.8 - - + -
397C GLU* 3.7 50.5 - - + +
400C ALA* 3.8 11.3 - - + +
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Residues in contact with GLU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ILE 4.4 3.5 - - - +
207C GLY* 3.7 7.3 - - - -
208C GLY* 3.2 32.5 + - - +
209C CYS 5.0 0.3 + - - -
210C ARG* 5.0 17.2 - - - +
375C THR* 3.3 17.6 + - + +
376C GLY* 3.3 10.8 + - - +
378C LEU* 1.3 76.3 - - + +
380C ILE* 1.3 58.0 + - - +
382C GLN* 3.1 16.8 + - - +
383C ILE* 3.0 37.6 + - + +
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C GLY 3.8 10.1 - - - +
372C PRO* 4.1 27.4 - - + -
376C GLY 3.2 16.2 + - - +
377C ARG 3.7 5.6 - - - +
378C LEU 3.4 0.2 - - - -
379C GLU* 1.3 78.3 - - - +
381C LEU* 1.3 57.0 + - - +
383C ILE* 3.3 7.7 + - - +
384C HIS* 2.9 38.0 + - - +
408C GLY* 4.1 15.5 - - - +
411C LEU* 3.8 26.2 - - + -
800C AGS 3.4 50.9 - - + +
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Residues in contact with LEU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C ARG 3.0 21.7 + - - +
378C LEU* 3.2 5.1 + - - +
380C ILE* 1.3 74.6 - - - +
382C GLN* 1.3 53.0 + - - +
384C HIS* 3.9 2.9 - - + -
385C THR* 2.6 41.4 + - - +
396C LEU* 3.9 24.9 - - + +
399C VAL* 3.7 31.9 - - + -
400C ALA* 3.8 20.4 - - + +
411C LEU* 4.3 29.8 - - + +
414C LEU* 4.6 2.2 - - + -
415C CYS* 3.9 25.6 - - - -
452C PHE* 4.9 4.0 - - + -
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Residues in contact with GLN 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C LEU* 3.0 45.7 + - + +
379C GLU* 3.4 17.0 - - - +
381C LEU* 1.3 76.9 - - - +
383C ILE* 1.3 61.5 + - + +
385C THR* 3.8 5.0 + - - -
386C LYS* 3.3 24.4 + - - +
396C LEU* 3.9 17.5 - - + +
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Residues in contact with ILE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C ASP 3.3 23.6 - - - +
205C ASP* 3.5 32.1 - - + +
206C ILE 3.7 3.6 - - - +
207C GLY* 3.6 36.3 - - - +
379C GLU* 3.0 21.7 + - + +
380C ILE* 3.6 5.6 - - - +
382C GLN* 1.3 76.0 - - + +
384C HIS* 1.3 67.3 + - + +
386C LYS* 3.3 30.4 - - + +
387C ASN* 5.2 0.7 + - - -
800C AGS 4.5 5.8 - - + +
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Residues in contact with HIS 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C ILE* 2.9 25.3 + - + +
381C LEU* 4.0 4.5 - - + +
382C GLN 3.4 0.2 - - - -
383C ILE* 1.3 82.7 - - + +
385C THR* 1.3 60.0 + - - +
386C LYS 3.3 1.1 + - - -
387C ASN* 4.4 8.1 + - - -
388C MET* 4.4 9.6 - - - +
411C LEU 5.4 0.4 - - - -
412C ALA* 3.4 30.9 - - + +
415C CYS* 4.4 18.2 - - + -
800C AGS 3.0 55.0 + + - -
234D GLY 4.9 4.0 - - - +
360D PHE* 5.8 0.2 - - - -
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Residues in contact with THR 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C LEU 2.6 24.6 + - - +
382C GLN* 3.8 3.3 + - - -
383C ILE 3.4 0.2 - - - -
384C HIS* 1.3 75.6 - - - +
386C LYS* 1.3 59.4 + - - +
387C ASN 3.1 2.9 - - - -
388C MET* 2.8 55.6 + - + +
390C LEU* 3.7 30.5 - - + +
396C LEU* 3.9 12.4 - - + +
415C CYS* 3.8 19.1 - - - -
452C PHE* 4.6 5.8 - - + -
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Residues in contact with LYS 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C ASP* 5.5 6.9 + - - +
205C ASP* 3.4 25.7 + - - -
382C GLN 3.3 14.7 + - - +
383C ILE* 3.3 21.1 - - + +
384C HIS 3.3 0.6 - - - -
385C THR* 1.3 76.9 - - - +
387C ASN* 1.3 81.8 + - - +
388C MET 4.7 1.8 - - - +
389C LYS* 5.6 1.7 + - - -
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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