Contacts of the helix formed by residues 380 - 389 (chain A) in PDB entry 4M8J
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 ASN 380 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ASN* 4.4 10.9 - - - +
379A LEU* 1.3 76.0 - - - +
381A ILE* 1.3 65.4 + - - +
382A PRO* 3.5 11.1 - - - +
383A GLN* 3.4 33.6 + - - +
384A LEU* 3.3 26.1 + - - +
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Residues in contact with ILE 381 (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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110A ILE* 3.8 20.6 - - + -
113A TYR* 3.9 14.4 - - + -
370A THR* 5.0 3.6 - - + +
373A LEU* 6.0 1.8 - - + -
374A ILE* 3.9 32.5 - - + -
379A LEU* 3.7 29.7 + - + +
380A ASN* 1.3 69.1 - - - +
382A PRO* 1.4 74.8 - - + +
383A GLN 3.2 0.2 + - - -
384A LEU* 3.2 5.8 + - - +
385A ILE* 3.0 51.4 + - + +
393A ALA* 4.0 15.9 - - + +
397A THR* 4.6 10.5 - - + -
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Residues in contact with PRO 382 (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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113A TYR* 3.5 24.5 - - + +
126A TYR* 3.9 16.8 - - - +
380A ASN* 3.6 13.5 - - - +
381A ILE* 1.4 94.3 - - + +
383A GLN* 1.3 58.9 + - - +
385A ILE* 4.1 4.1 - - + +
386A ASP* 3.0 38.1 + - - +
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASN* 3.4 34.3 + - - +
381A ILE 3.2 0.6 - - - -
382A PRO* 1.3 77.6 - - - +
384A LEU* 1.3 81.6 + - - +
386A ASP* 3.4 7.3 + - - +
387A GLN* 3.2 43.4 + - - +
388A TYR* 5.2 1.6 - - - -
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Residues in contact with LEU 384 (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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379A LEU* 3.5 21.1 - - + -
380A ASN 3.3 13.9 + - - +
381A ILE* 3.2 7.0 + - - +
383A GLN* 1.3 94.9 - - - +
385A ILE* 1.3 57.4 + - - +
387A GLN* 4.7 0.2 - - - -
388A TYR* 2.8 49.7 + - + +
389A GLY 3.3 7.1 + - - +
392A ARG* 4.9 4.3 - - + +
393A ALA* 3.8 28.7 - - + +
396A GLU* 3.3 39.9 - - + +
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Residues in contact with ILE 385 (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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110A ILE* 4.6 5.8 - - + -
113A TYR* 3.7 27.8 - - + +
114A TYR* 3.6 22.2 - - + +
381A ILE* 3.0 22.9 + - + +
382A PRO* 4.1 4.0 - - + +
384A LEU* 1.3 75.0 - - - +
386A ASP* 1.3 69.5 + - - +
389A GLY* 3.1 25.6 + - - +
390A VAL* 4.3 22.4 - - + +
393A ALA* 3.8 17.5 - - + -
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Residues in contact with ASP 386 (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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382A PRO* 3.0 27.5 + - - +
383A GLN* 3.8 6.2 - - - +
385A ILE* 1.3 82.0 - - - +
387A GLN* 1.3 59.3 + - + +
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Residues in contact with GLN 387 (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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383A GLN* 3.2 40.9 + - - +
385A ILE 3.1 0.6 - - - -
386A ASP* 1.3 80.4 - - + +
388A TYR* 1.3 98.0 + - + +
389A GLY 3.7 0.2 - - - -
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Residues in contact with TYR 388 (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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217A GLU* 4.9 6.6 - - - +
220A GLN* 5.9 5.2 - - - -
227A HIS* 5.2 6.6 - - - -
383A GLN* 5.2 2.0 - - - -
384A LEU* 2.8 26.1 + - + +
387A GLN* 1.3 117.6 + - + +
389A GLY* 1.3 60.5 + - - +
391A PRO* 5.1 1.9 - - - +
392A ARG* 3.5 59.3 + - + +
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Residues in contact with GLY 389 (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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384A LEU 3.3 8.9 + - - +
385A ILE* 3.1 27.4 + - - -
387A GLN 3.7 0.4 - - - -
388A TYR* 1.3 82.0 - - - +
390A VAL* 1.3 65.6 + - - +
391A PRO* 3.6 4.0 - - - -
392A ARG* 3.7 9.2 + - - +
393A ALA 3.7 1.9 + - - -
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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