Contacts of the helix formed by residues 382 - 387 (chain A) in PDB entry 2R5N
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 LEU 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A SER* 3.0 9.3 + - - +
380A ALA 3.9 8.5 - - - +
381A ASP* 1.3 78.3 - - - +
383A ALA* 1.3 58.5 + - - +
384A PRO* 3.3 7.2 - - - -
385A SER* 3.0 10.1 + - - +
386A ASN* 2.7 50.7 + - - +
433A THR* 3.8 10.8 - - - +
434A PHE* 3.7 64.6 - - + +
189B ILE* 3.5 30.5 - - + -
190B ASP* 3.4 0.4 + - - -
672B TPP 4.0 15.5 - - + -
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Residues in contact with ALA 383 (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 GLN* 5.6 0.2 + - - -
379A SER* 3.4 2.0 + - - -
382A LEU* 1.3 75.2 - - - +
384A PRO* 1.4 58.7 - - + +
387A LEU* 3.0 29.1 + - - +
388A THR* 3.6 14.5 + - - +
389A LEU* 3.9 26.8 + - + +
404A TYR* 3.4 20.9 - - + +
406A HIS* 5.0 2.5 - - + -
190B ASP* 2.9 24.7 + - - +
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Residues in contact with PRO 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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358A ARG* 4.6 2.4 + - - -
382A LEU 3.3 4.5 - - - -
383A ALA* 1.4 94.8 - - + +
385A SER* 1.3 57.4 + - - +
387A LEU* 3.3 19.7 - - + +
389A LEU* 5.6 0.6 - - + -
670A R5P 4.7 1.2 + - - -
189B ILE* 3.5 32.3 - - + +
190B ASP* 3.5 9.6 - - - +
258B HIS* 5.9 4.3 - - + -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ARG* 3.0 30.3 + - - +
382A LEU* 3.0 15.8 + - - +
384A PRO* 1.3 82.9 - - - +
386A ASN* 1.3 66.0 + - - +
387A LEU* 3.2 2.4 + - - +
434A PHE* 3.9 23.5 - - - -
461A HIS* 3.6 4.1 - - - -
670A R5P 2.9 39.0 + - - -
189B ILE* 4.9 2.3 - - - +
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Residues in contact with ASN 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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358A ARG* 4.3 5.5 - - - +
361A SER* 5.3 0.9 + - - -
379A SER* 2.7 21.4 + - - +
382A LEU* 2.7 24.5 + - - +
385A SER* 1.3 70.9 - - - +
387A LEU* 1.3 69.4 + - - +
388A THR* 4.0 9.2 - - + -
432A SER* 3.0 27.1 + - - +
433A THR* 3.3 28.1 + - - -
434A PHE* 3.7 10.5 - - - +
458A VAL* 4.4 7.3 - - - +
460A THR* 2.9 39.7 + - + +
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Residues in contact with LEU 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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358A ARG* 3.8 28.3 - - + +
359A LYS* 3.8 37.9 - - + +
361A SER* 5.2 0.9 + - - -
362A GLN* 3.3 51.6 + - + +
365A ILE* 4.0 4.2 - - - +
383A ALA 3.0 11.1 + - - +
384A PRO* 3.3 28.5 - - + +
385A SER 3.7 6.1 - - - +
386A ASN* 1.3 83.1 - - - +
388A THR* 1.3 58.4 - - - +
389A LEU 3.5 2.7 - - - -
458A VAL* 6.0 0.2 - - - +
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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