Contacts of the helix formed by residues 391 - 401 (chain A) in PDB entry 1IK2
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 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A SER 3.3 4.4 - - - +
385A ALA* 5.0 1.1 - - - +
390A LEU* 1.3 84.8 - - + +
392A SER* 1.3 66.7 + - - +
393A ALA* 2.9 36.4 + - - +
394A ASP* 3.3 27.9 + - - +
395A LEU* 3.1 23.7 + - - +
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Residues in contact with SER 392 (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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377A GLY 5.9 0.2 - - - -
378A THR* 4.6 26.4 + - - +
381A ALA* 4.9 16.8 - - - -
384A SER 3.5 8.2 + - - -
385A ALA* 4.3 13.6 - - - +
391A ASN* 1.3 77.0 + - - +
393A ALA* 1.3 62.0 + - - +
395A LEU* 3.5 5.4 - - - +
396A LEU* 3.2 29.2 + - - +
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Residues in contact with ALA 393 (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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377A GLY 6.0 0.4 - - - -
378A THR* 5.6 4.9 - - + +
391A ASN* 2.9 14.9 + - - +
392A SER* 1.3 72.2 - - - +
394A ASP* 1.3 63.7 + - - +
396A LEU* 2.8 28.8 + - - +
397A LYS* 3.1 14.7 + - - +
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Residues in contact with ASP 394 (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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390A LEU* 5.2 7.3 - - + +
391A ASN* 3.3 34.0 + - + +
393A ALA* 1.3 78.3 - - - +
395A LEU* 1.3 65.9 + - - +
397A LYS* 3.5 4.2 + - - +
398A GLY 3.4 12.8 + - - -
608A LEU* 3.6 12.4 - - + +
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Residues in contact with LEU 395 (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 PHE* 3.8 18.8 - - + -
364A PHE* 5.8 0.4 - - + -
381A ALA* 4.1 21.3 - - + -
384A SER* 3.3 25.1 - - - +
390A LEU* 5.0 4.4 - - + +
391A ASN 3.1 9.3 + - - +
392A SER* 3.5 7.4 - - - +
394A ASP* 1.3 78.6 - - - +
396A LEU* 1.3 61.2 + - + +
398A GLY 3.0 5.0 + - - -
399A LEU* 2.7 56.9 + - + +
605A VAL* 5.4 1.1 - - + -
608A LEU* 4.0 9.1 - - + +
609A TYR* 3.2 41.7 - - + +
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Residues in contact with LEU 396 (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 MET* 4.8 1.8 - - + -
364A PHE* 3.8 22.7 - - + -
375A PRO* 4.2 27.1 - - + -
376A ASP 4.0 9.6 - - - +
377A GLY 3.2 26.9 - - - +
378A THR* 5.8 0.2 - - - -
381A ALA* 3.8 25.4 - - + -
392A SER* 3.2 20.0 + - - +
393A ALA* 2.8 18.3 + - - +
395A LEU* 1.3 82.8 - - + +
397A LYS* 1.3 60.3 + - - +
399A LEU* 3.8 3.9 - - - +
400A CYS* 2.9 34.2 + - - -
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Residues in contact with LYS 397 (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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393A ALA 3.1 11.9 + - - +
394A ASP* 4.1 4.7 - - - +
395A LEU 3.0 0.2 + - - -
396A LEU* 1.3 76.2 - - - +
398A GLY* 1.3 61.4 + - - +
399A LEU 3.2 0.2 - - - -
400A CYS* 3.3 5.9 + - - +
401A HIS* 2.9 55.2 + - + +
403A ARG* 4.9 11.2 - - - +
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Residues in contact with GLY 398 (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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394A ASP 3.4 4.6 + - - -
395A LEU 3.0 6.8 + - - -
397A LYS* 1.3 80.9 - - - +
399A LEU* 1.3 59.5 + - - +
401A HIS 4.3 10.0 - - - +
402A PRO* 4.7 0.3 - - - +
403A ARG* 4.7 10.8 - - - -
604A THR* 3.5 23.5 - - - +
605A VAL* 3.5 10.7 - - - +
608A LEU* 3.9 20.3 - - - +
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Residues in contact with LEU 399 (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 PHE* 4.1 6.5 - - + -
364A PHE* 4.0 22.9 - - + -
395A LEU* 2.7 46.4 + - + +
396A LEU* 3.8 4.7 - - - +
398A GLY* 1.3 73.5 - - - +
400A CYS* 1.3 67.8 + - - +
401A HIS 3.3 0.5 + - - -
402A PRO* 3.4 14.6 - - - +
420A VAL* 3.8 32.3 - - + +
423A ALA* 6.0 2.7 - - + -
424A THR* 3.1 28.0 - - - +
602A ASN* 4.3 7.0 + - - +
605A VAL* 4.2 15.0 - - + -
609A TYR* 5.0 0.4 - - - +
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Residues in contact with CYS 400 (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 PHE* 4.4 18.2 - - - -
372A GLN* 2.9 32.2 + - - +
373A ALA* 3.3 34.3 - - + +
374A GLU 5.1 2.9 - - - -
375A PRO* 5.2 4.3 - - - -
396A LEU* 2.9 27.6 + - - +
397A LYS* 3.6 3.4 - - - +
399A LEU* 1.3 82.5 - - - +
401A HIS* 1.3 63.9 + - + +
402A PRO* 3.1 10.0 - - - +
414A GLY* 4.2 3.3 - - - -
415A GLN 4.8 1.7 + - - -
420A VAL* 6.1 2.7 - - - -
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Residues in contact with HIS 401 (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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372A GLN* 3.7 28.1 + - + +
397A LYS* 2.9 44.3 + - + +
398A GLY* 4.4 6.0 - - - -
399A LEU 4.3 0.7 - - - -
400A CYS* 1.3 82.8 - - + +
402A PRO* 1.4 67.8 - - - +
403A ARG* 3.0 10.4 + - - +
412A THR* 4.0 24.1 - - + +
413A LYS 6.3 0.2 - - - -
414A GLY 5.2 0.9 - - - +
604A THR* 4.3 4.5 - - - +
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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