Contacts of the helix formed by residues 370 - 380 (chain C) in PDB entry 7JUR
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 370 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C GLU 4.3 0.2 - - - -
369C VAL* 1.3 70.8 - - - +
371C PHE* 1.3 65.1 + - - +
372C ALA* 3.3 2.7 - - + +
373C GLY* 3.5 22.0 - - - +
374C TRP* 3.0 18.8 + - - +
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Residues in contact with PHE 371 (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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151C LEU* 5.4 3.8 - - + -
165C ILE* 3.5 33.4 - - + -
168C LYS* 5.8 9.0 - - + -
169C VAL* 5.0 5.8 - - + -
198C VAL* 3.7 25.8 - - + -
199C ASN 4.1 10.5 - - - -
202C GLY* 3.6 28.0 - - - +
204C ILE* 3.2 35.0 - - + -
369C VAL* 3.0 16.3 + - + +
370C ASP* 1.3 73.4 - - - +
372C ALA* 1.3 66.0 + - - +
374C TRP* 3.2 18.8 + + - +
375C LEU* 3.0 28.1 + - + +
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Residues in contact with ALA 372 (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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199C ASN 4.8 0.2 - - - -
200C SER 3.3 27.1 - - - +
201C ARG 3.8 15.9 - - - +
202C GLY* 4.3 2.7 - - - -
370C ASP* 3.3 1.3 - - + -
371C PHE* 1.3 85.0 - - - +
373C GLY* 1.3 62.6 + - - +
375C LEU* 3.4 4.8 + - - +
376C CYS* 3.1 29.2 + - - +
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Residues in contact with GLY 373 (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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370C ASP* 3.2 25.0 + - - +
371C PHE 3.2 0.6 - - - -
372C ALA* 1.3 77.9 - - - +
374C TRP* 1.3 55.0 + - - +
376C CYS* 4.4 3.0 - - - +
377C SER* 2.6 36.1 + - - -
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Residues in contact with TRP 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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151C LEU* 6.3 0.8 - - - +
154C VAL* 5.9 7.7 - - + +
158C ALA* 4.3 11.7 - - + -
160C ARG 4.4 2.0 - - - -
161C ILE* 4.2 17.6 - - + +
162C PRO* 3.8 26.7 - - + -
165C ILE* 3.3 47.5 - - + +
370C ASP* 3.0 16.3 + - - +
371C PHE* 3.2 23.5 + + - +
373C GLY* 1.3 74.4 - - - +
375C LEU* 1.3 67.2 + - + +
377C SER* 3.0 13.1 + - - -
378C THR* 2.7 65.7 + - + -
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Residues in contact with LEU 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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148C GLY* 4.3 6.5 - - - -
151C LEU* 6.3 0.2 - - + -
154C VAL* 3.8 15.7 - - + -
198C VAL* 3.5 31.0 - - + -
199C ASN* 3.2 37.5 - - - +
200C SER* 3.8 7.2 - - - +
371C PHE* 3.0 25.9 + - + +
372C ALA 3.7 3.8 - - - +
374C TRP* 1.3 89.1 - - + +
376C CYS* 1.3 63.4 + - - +
378C THR* 3.0 15.1 + - - -
379C ILE* 3.1 40.3 + - + +
381C LEU* 4.9 1.3 - - + -
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Residues in contact with CYS 376 (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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200C SER* 3.7 26.7 - - - -
372C ALA 3.1 16.0 + - - +
373C GLY* 4.4 3.6 - - - +
375C LEU* 1.3 79.0 - - - +
377C SER* 1.3 57.9 + - - +
380C GLY* 3.1 22.7 + - - -
381C LEU* 3.1 50.6 + - - -
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Residues in contact with SER 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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373C GLY 2.6 24.7 + - - -
374C TRP* 3.0 15.4 + - - -
376C CYS* 1.3 77.1 - - - +
378C THR* 1.3 60.8 + - - +
380C GLY* 4.3 4.0 + - - -
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Residues in contact with THR 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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154C VAL* 5.1 3.1 - - + +
157C LYS* 4.2 12.4 - - + +
158C ALA* 3.7 37.2 - - + +
374C TRP* 2.7 50.6 + - + -
375C LEU* 3.0 4.7 + - - -
377C SER* 1.3 80.8 + - - +
379C ILE* 1.3 65.4 + - + +
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Residues in contact with ILE 379 (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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147C ASP 4.9 0.2 - - - +
148C GLY* 3.8 25.1 - - - +
153C GLN* 5.3 1.3 - - + +
154C VAL* 4.3 19.5 - - + +
157C LYS* 4.1 33.1 + - + -
375C LEU* 3.1 39.4 + - + +
378C THR* 1.3 79.6 - - + +
380C GLY* 1.3 60.6 + - - +
381C LEU* 3.6 27.4 - - + -
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Residues in contact with GLY 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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376C CYS 3.1 13.8 + - - -
377C SER 4.8 3.4 - - - -
378C THR 3.5 2.0 - - - -
379C ILE* 1.3 80.5 - - - +
381C LEU* 1.3 62.3 + - - +
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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