Contacts of the helix formed by residues 367 - 377 (chain A) in PDB entry 1MAQ
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 PRO 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A LEU 4.4 1.6 - - - +
366A LYS* 1.3 91.0 - - + +
368A GLU* 1.3 69.6 + - - +
370A VAL* 3.5 11.7 + - + +
371A GLU* 3.1 25.1 + - - +
383A LYS* 3.9 35.0 - - + +
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Residues in contact with GLU 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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366A LYS* 3.0 34.2 - - - +
367A PRO* 1.3 81.0 - - - +
369A GLN* 1.3 64.4 + - + +
371A GLU* 3.4 13.8 - - - +
372A ARG* 3.2 24.7 + - - +
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Residues in contact with GLN 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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364A GLY 4.7 0.4 + - - -
365A LEU* 3.2 27.8 - - + +
366A LYS* 2.8 63.2 + - - +
368A GLU* 1.3 77.5 - - + +
370A VAL* 1.3 59.6 + - - +
372A ARG* 3.4 8.5 - - - +
373A LEU* 3.1 32.4 + - - +
408A VAL* 3.6 38.8 - - + +
409A THR* 4.1 9.5 + - - -
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Residues in contact with VAL 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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365A LEU* 4.3 11.4 - - + -
366A LYS 3.2 12.5 + - - +
367A PRO* 3.6 13.5 - - + +
369A GLN* 1.3 74.5 - - - +
371A GLU* 1.3 65.1 + - - +
373A LEU* 3.3 4.2 + - - +
374A THR* 3.2 25.9 + - - +
381A MET* 3.4 47.6 - - + +
382A THR 4.1 13.0 - - - +
383A LYS* 3.9 30.1 - - + +
385A GLY* 4.5 5.8 - - - -
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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 PRO 3.1 16.0 + - - +
368A GLU* 3.4 17.1 - - - +
370A VAL* 1.3 76.1 - - - +
372A ARG* 1.3 63.1 + - - +
374A THR* 3.3 7.0 + - - -
375A LYS* 3.0 47.8 + - - +
383A LYS* 4.6 16.4 - - - +
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Residues in contact with ARG 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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368A GLU 3.2 10.6 + - - +
369A GLN* 3.4 6.7 - - - +
371A GLU* 1.3 81.7 - - - +
373A LEU* 1.3 57.6 + - - +
375A LYS* 3.1 4.7 + - - +
376A GLU* 2.6 75.3 + - - +
377A PHE* 4.9 0.2 - - - -
406A GLN* 3.8 19.0 + - - +
408A VAL* 3.3 46.7 + - + +
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Residues in contact with LEU 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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365A LEU* 3.8 18.2 - - + -
369A GLN 3.1 11.4 + - - +
370A VAL 3.3 11.4 - - - +
372A ARG* 1.3 78.0 - - - +
374A THR* 1.3 57.3 + - - +
377A PHE* 3.2 18.4 + - + +
378A SER 2.9 20.8 + - - -
379A ILE* 3.0 26.3 + - + +
381A MET* 3.0 31.0 - - + -
400A LEU* 6.3 0.2 - - + -
403A ALA* 3.6 41.1 - - + +
404A ILE* 4.4 10.5 - - + +
408A VAL* 4.0 12.1 - - + -
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Residues in contact with THR 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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27A ASP* 4.2 2.9 - - - +
370A VAL* 3.2 13.9 + - - +
371A GLU* 3.6 9.4 - - - -
372A ARG 3.1 0.6 - - - -
373A LEU* 1.3 77.3 - - - +
375A LYS* 1.3 61.1 + - + +
378A SER* 3.0 25.5 + - - -
379A ILE 2.9 19.8 + - - +
380A TYR* 3.4 40.5 + - + +
381A MET* 4.8 3.1 + - - +
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Residues in contact with LYS 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* 3.0 40.8 + - - +
372A ARG* 3.7 4.5 - - - +
374A THR* 1.3 81.6 - - + +
376A GLU* 1.3 65.3 + - + +
378A SER* 4.7 3.1 + - - -
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Residues in contact with GLU 376 (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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29A ASN* 4.8 6.2 + - - -
372A ARG* 2.6 67.3 + - + +
375A LYS* 1.3 81.0 - - + +
377A PHE* 1.3 82.2 + - + +
378A SER* 5.2 0.7 - - - -
399A TYR* 4.7 0.9 + - - -
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Residues in contact with PHE 377 (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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29A ASN* 4.0 2.1 + - - -
31A LYS 4.6 1.6 - - - +
372A ARG 4.4 0.2 - - - -
373A LEU* 3.2 25.0 + - + +
376A GLU* 1.3 105.3 - - + +
378A SER* 1.3 71.3 + - - +
379A ILE* 3.7 16.2 - - + -
399A TYR* 2.5 46.2 + + - +
402A HIS* 4.2 16.2 - + - -
403A ALA* 3.7 37.9 - - + -
406A GLN* 4.0 24.5 - - + -
408A VAL* 4.7 4.9 - - + -
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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