Contacts of the helix formed by residues 365 - 375 (chain A) in PDB entry 1Q57
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 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ARG* 3.9 11.4 - - - -
362A LEU 3.2 2.5 + - - +
363A ARG 3.0 6.1 + - - -
364A GLN* 1.3 81.9 - - - +
366A ASP* 1.3 64.8 + - - +
367A SER* 3.2 20.1 + - - -
368A LEU* 3.2 15.8 + - - +
369A LYS* 3.2 24.8 + - - +
284C SER* 4.2 0.6 - - - -
300C LEU* 6.0 1.3 - - - -
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Residues in contact with ASP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A SER* 1.3 72.3 - - - +
367A SER* 1.3 66.8 + - - +
369A LYS* 3.2 7.3 + - - +
370A ARG* 3.2 21.7 + - - +
283C GLU* 6.1 1.8 - - - -
284C SER* 3.1 20.8 + - - +
285C VAL* 2.8 35.0 - - + +
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A SER* 3.2 9.0 + - - -
366A ASP* 1.3 81.2 - - - +
368A LEU* 1.3 67.0 + - - +
370A ARG* 3.2 33.5 + - - +
371A GLU* 2.9 26.2 + - - +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A VAL* 4.1 26.5 - - + -
361A ARG 5.6 0.9 - - - +
362A LEU* 3.8 24.5 - - + -
365A SER* 3.2 17.4 + - - +
367A SER* 1.3 79.2 + - - +
369A LYS* 1.3 71.7 + - - +
371A GLU* 3.8 18.8 - - + +
372A ILE* 3.0 31.9 + - + +
381A TRP* 4.4 10.8 - - + -
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Residues in contact with LYS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLU* 4.9 2.2 - - - -
362A LEU* 3.4 23.7 - - + +
363A ARG* 3.3 20.4 - - - +
365A SER 3.2 21.3 + - - +
366A ASP* 3.3 7.7 + - - +
368A LEU* 1.3 83.4 - - - +
370A ARG* 1.3 62.7 + - - +
372A ILE* 3.3 4.1 + - - +
373A ILE* 3.1 25.5 + - + +
278C HIS* 5.7 1.1 - - - -
279C LEU* 2.8 53.1 + - + +
282C GLU 2.9 24.0 + - - -
284C SER* 2.6 33.7 + - - +
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Residues in contact with ARG 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ASP* 3.2 11.8 + - - +
367A SER* 3.3 32.4 + - - +
369A LYS* 1.3 77.6 - - - +
371A GLU* 1.3 88.7 + - - +
373A ILE* 3.3 7.9 + - - +
374A GLU* 3.1 45.0 + - - +
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A SER 2.9 15.1 + - - +
368A LEU* 3.3 23.9 - - + +
370A ARG* 1.3 95.9 - - - +
372A ILE* 1.3 56.9 + - - +
374A GLU* 3.7 3.8 - - - +
375A ASN* 2.9 57.3 + - - +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LEU* 4.0 22.9 - - + -
368A LEU* 3.0 30.6 + - + +
369A LYS* 3.5 9.4 - - - +
371A GLU* 1.3 72.7 - - + +
373A ILE* 1.3 71.0 + - + +
375A ASN* 2.8 15.0 - - - +
376A GLY 3.7 0.3 + - - -
377A LYS* 3.3 15.7 + - + -
378A PHE* 2.8 52.4 + - + +
381A TRP* 3.8 39.7 - - + -
279C LEU* 5.6 2.5 - - + -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LYS 3.1 20.5 + - - +
370A ARG* 3.3 9.6 + - - +
372A ILE* 1.3 79.6 - - + +
374A GLU* 1.3 69.0 + - + +
376A GLY* 3.9 5.0 + - - -
378A PHE* 4.2 18.5 - - + +
379A ASP* 5.0 5.5 - - - +
276C ARG* 4.1 33.9 + - + +
279C LEU* 4.2 21.5 - - + -
280C SER* 4.2 20.9 - - - +
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Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ARG* 3.1 38.3 + - + +
371A GLU* 3.8 2.5 - - - +
373A ILE* 1.3 81.2 - - + +
375A ASN* 1.3 57.5 + - - +
376A GLY* 2.9 12.2 + - - -
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Residues in contact with ASN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A GLU* 2.9 47.0 + - - +
372A ILE* 2.8 23.8 - - - +
374A GLU* 1.3 70.5 - - - +
376A GLY* 1.3 55.1 + - - +
377A LYS* 3.0 39.3 + - - +
380A GLN* 5.3 0.9 + - - -
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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