Contacts of the helix formed by residues 355 - 369 (chain A) in PDB entry 2KR6
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 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A SER 4.6 0.9 - - - +
354A THR* 1.3 92.2 - - + +
356A GLU* 1.3 64.6 + - - +
357A SER 2.9 4.0 + - - -
358A ARG* 3.1 8.0 + - + +
359A ALA* 2.9 25.4 + - + +
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Residues in contact with GLU 356 (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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354A THR* 3.1 14.9 - - - +
355A PRO* 1.3 82.6 - - - +
357A SER* 1.3 53.6 + - - +
359A ALA* 4.2 7.2 - - + -
360A ALA* 2.8 39.5 + - + +
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Residues in contact with SER 357 (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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354A THR* 3.5 14.1 + - - -
356A GLU* 1.3 81.6 - - - +
358A ARG* 1.3 61.2 + - - +
360A ALA* 3.6 3.3 - - - +
361A VAL* 3.0 29.7 + - - +
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Residues in contact with ARG 358 (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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355A PRO* 3.1 9.3 + - + +
357A SER* 1.3 75.7 - - - +
359A ALA* 1.3 62.6 + - - +
361A VAL* 3.2 7.1 + - + +
362A GLN* 2.8 39.8 + - - +
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Residues in contact with ALA 359 (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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355A PRO* 2.9 19.1 + - + +
356A GLU* 4.0 9.4 - - + +
358A ARG* 1.3 75.9 - - - +
360A ALA* 1.3 53.5 + - - +
362A GLN* 4.0 4.0 - - - +
363A GLU* 2.8 47.6 + - + +
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Residues in contact with ALA 360 (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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356A GLU* 2.8 27.1 + - + +
357A SER* 3.6 4.9 - - - +
359A ALA* 1.3 74.7 - - - +
361A VAL* 1.3 53.1 + - + +
363A GLU* 3.7 4.4 - - - +
364A LEU* 2.8 48.2 + - + +
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Residues in contact with VAL 361 (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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357A SER* 3.0 18.3 + - - +
358A ARG* 3.7 7.2 - - + +
360A ALA* 1.3 76.3 - - + +
362A GLN* 1.3 63.3 + - - +
364A LEU* 3.0 22.5 + - + +
365A SER* 3.1 17.6 + - - +
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Residues in contact with GLN 362 (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* 2.8 27.1 + - + +
359A ALA* 4.0 4.3 - - - +
361A VAL* 1.3 74.2 - - - +
363A GLU* 1.3 63.9 + - + +
365A SER* 3.2 9.6 + - - -
366A SER* 3.1 24.7 + - - +
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Residues in contact with GLU 363 (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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359A ALA* 2.8 34.4 + - + +
360A ALA* 3.7 5.4 - - - +
362A GLN* 1.3 75.7 - - + +
364A LEU* 1.3 58.0 + - - +
366A SER* 3.7 9.0 - - - +
367A SER* 2.8 34.5 + - - -
377A ARG* 3.8 24.6 - - - +
378A GLY 4.6 2.1 - - - +
379A VAL* 3.5 28.3 - - + +
380A LYS* 6.2 3.1 - - - +
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Residues in contact with LEU 364 (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 ALA* 2.8 34.8 + - + +
361A VAL* 3.0 13.9 + - + +
363A GLU* 1.3 78.2 - - - +
365A SER* 1.3 53.1 + - - +
367A SER* 2.9 8.7 + - - +
368A ILE* 2.7 63.6 + - + +
380A LYS* 5.3 13.5 - - + +
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Residues in contact with SER 365 (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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361A VAL* 3.1 15.0 + - - +
362A GLN* 3.6 10.3 - - - -
364A LEU* 1.3 77.6 - - - +
366A SER* 1.3 56.8 + - - +
368A ILE* 4.8 1.3 - - - -
369A LEU* 2.7 48.1 + - - +
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Residues in contact with SER 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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362A GLN* 3.1 15.1 + - - +
363A GLU* 4.0 11.7 - - - -
365A SER* 1.3 80.0 - - - +
367A SER* 1.3 57.4 + - - +
370A ALA* 3.2 15.3 - - - +
371A GLY 5.1 2.5 - - - +
372A GLU* 4.3 21.6 + - - +
374A PRO* 4.6 9.7 - - - +
379A VAL* 5.5 0.7 - - - -
381A LEU* 2.9 22.9 - - - +
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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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363A GLU 2.8 17.8 + - - -
364A LEU* 2.9 22.0 + - - +
366A SER* 1.3 78.7 - - - +
368A ILE* 1.3 64.3 + - - +
379A VAL* 3.5 30.3 - - - +
380A LYS* 2.6 40.1 + - - +
381A LEU* 3.3 20.2 - - - +
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Residues in contact with ILE 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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364A LEU* 2.7 56.7 + - + +
365A SER* 4.8 1.8 - - - -
367A SER* 1.3 81.6 + - - +
369A LEU* 1.3 74.5 + - + +
370A ALA* 3.1 6.0 + - - +
380A LYS* 4.7 4.3 - - + +
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Residues in contact with LEU 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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365A SER* 2.7 29.4 + - - +
368A ILE* 1.3 81.2 - - + +
370A ALA* 1.3 66.0 + - - +
371A GLY* 3.1 14.1 + - - +
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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