Contacts of the helix formed by residues 371 - 382 (chain C) in PDB entry 3Q29
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 SER 371 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C LYS* 5.9 4.8 - - - +
367C THR* 3.1 20.6 + - - +
370C SER* 1.3 76.0 + - - +
372C MET* 1.3 64.9 + - - +
373C ASP* 3.5 9.8 + - - +
374C VAL* 3.1 29.0 + - - +
375C PHE* 3.0 22.2 + - - +
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Residues in contact with MET 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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91A TYR* 3.1 32.8 - - + +
302A ALA* 4.0 18.8 - - + -
303A VAL 5.4 1.1 - - - +
309A GLU* 4.5 14.4 - - + +
312A LEU* 4.2 27.4 - - + +
313A ALA* 5.6 2.0 - - - +
318A ILE* 4.4 9.0 - - + -
322A MET* 4.2 22.7 - - + +
371C SER* 1.3 73.9 - - - +
373C ASP* 1.3 58.3 + - - +
375C PHE* 3.3 3.8 + - - -
376C MET* 2.9 50.7 + - + +
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Residues in contact with ASP 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.6 31.2 + - - -
92A PRO* 5.3 3.8 - - - +
306A LYS* 4.5 15.6 + - - +
371C SER* 3.2 9.1 + - - +
372C MET* 1.3 79.3 - - - +
374C VAL* 1.3 61.7 + - + +
376C MET* 3.5 1.9 + - - +
377C LYS* 3.0 49.3 + - - +
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Residues in contact with VAL 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C GLN* 5.2 10.5 - - + -
339C ALA* 4.5 16.4 - - + -
368C ASN* 3.6 30.3 - - - +
369C SER 4.0 15.3 - - - +
370C SER* 4.1 1.3 - - - +
371C SER* 3.1 30.9 + - - +
373C ASP* 1.3 74.8 - - + +
375C PHE* 1.3 55.1 + - - +
377C LYS* 3.2 9.9 + - - +
378C GLY* 2.8 32.9 + - - -
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Residues in contact with PHE 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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322A MET* 4.1 24.0 - - + -
326A GLN* 3.6 21.8 - - - +
179C ILE* 5.5 7.0 - - + -
371C SER 3.0 10.8 + - - +
372C MET* 3.7 11.0 - - - +
374C VAL* 1.3 79.3 - - - +
376C MET* 1.3 58.1 + - - +
378C GLY* 2.9 17.5 + - - -
379C LEU* 2.9 18.3 + - - +
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Residues in contact with MET 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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91A TYR* 3.3 50.5 - - + -
92A PRO* 6.2 0.4 - - + -
93A PHE* 3.4 29.1 - - + +
94A THR* 4.2 4.3 - - + -
111A VAL* 3.9 25.4 - - + -
302A ALA* 4.7 7.0 - - + -
303A VAL 4.6 5.6 - - - +
322A MET* 5.1 2.2 - - + -
372C MET* 2.9 47.7 + - + +
373C ASP 3.7 4.5 - - - +
375C PHE* 1.3 77.7 - - - +
377C LYS* 1.3 63.0 + - + +
379C LEU* 3.0 23.8 + - - +
380C SER 3.4 7.4 + - - -
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Residues in contact with LYS 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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92A PRO* 5.2 18.2 - - + -
93A PHE* 5.3 0.7 - - - -
373C ASP* 3.0 38.0 + - - +
374C VAL* 3.6 6.7 - - - +
376C MET* 1.3 75.9 - - + +
378C GLY* 1.3 56.4 + - - +
380C SER* 3.1 11.2 + - - +
381C LYS* 2.8 32.0 + - - +
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Residues in contact with GLY 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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326A GLN* 4.0 15.5 + - - -
374C VAL 2.8 14.5 + - - -
375C PHE* 2.9 8.4 + - - -
377C LYS* 1.3 78.0 - - - +
379C LEU* 1.3 55.1 + - - +
381C LYS* 3.8 6.8 - - - +
382C ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 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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93A PHE* 3.4 42.3 - - + -
111A VAL* 4.1 19.1 - - + -
260A VAL* 4.7 4.7 - - + -
322A MET* 4.4 15.5 - - + -
325A ALA* 3.7 35.4 - - + +
326A GLN* 3.8 20.2 - - + +
330A ILE* 5.7 1.7 - - - +
375C PHE 2.9 15.2 + - - +
376C MET* 3.0 14.3 + - - +
378C GLY* 1.3 79.6 - - - +
380C SER* 1.3 59.0 + - - +
382C ALA* 3.7 6.3 + - + +
383C LYS* 3.6 15.4 + - - +
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Residues in contact with SER 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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93A PHE* 3.4 23.9 + - - +
96A ASP* 4.1 17.7 - - - -
376C MET 3.4 2.8 + - - -
377C LYS* 3.1 24.3 + - - +
379C LEU* 1.3 77.7 - - - +
381C LYS* 1.3 57.7 + - - +
383C LYS* 3.0 6.9 + - - +
384C GLU* 3.0 37.3 + - - +
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Residues in contact with LYS 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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74C SER* 3.0 13.9 + - - -
377C LYS* 2.8 18.5 + - + +
378C GLY* 3.8 8.5 - - - +
380C SER* 1.3 76.0 + - - +
382C ALA* 1.3 61.1 + - - +
385C GLY* 2.8 39.4 + - - +
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Residues in contact with ALA 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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326A GLN* 5.0 6.5 - - - +
329A GLU* 5.5 2.6 - - - +
73C GLN* 3.6 43.8 - - + +
74C SER* 3.9 15.2 - - - -
378C GLY 2.9 17.7 + - - +
379C LEU* 3.9 8.7 - - + +
380C SER 3.2 0.2 - - - -
381C LYS* 1.3 76.0 - - - +
383C LYS* 1.3 58.5 + - - +
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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