Contacts of the helix formed by residues 366 - 377 (chain A) in PDB entry 2IUK
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 THR 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LYS 4.9 2.2 - - - +
362A SER* 2.6 33.7 + - - +
363A GLY 3.7 2.7 + - - +
365A MET* 1.3 79.1 - - + +
367A ASP* 1.3 60.9 + - - +
368A GLU* 4.1 8.1 - - - -
369A GLU* 3.0 20.0 + - - +
370A PHE* 3.1 26.2 + - - +
509A LYS* 4.4 0.2 - - - -
837A PRO* 3.7 15.3 - - + +
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET 3.5 0.8 + - - -
366A THR* 1.3 74.3 - - - +
368A GLU* 1.3 66.5 + - + +
369A GLU 3.4 0.2 - - - -
370A PHE* 3.7 3.4 + - - +
371A ALA 3.3 10.2 + - - -
470A LYS* 4.4 12.5 + - - +
471A PRO* 3.3 29.9 - - + +
495A PRO* 4.1 12.3 - - - +
496A ALA 5.3 2.1 + - - +
505A TRP* 3.2 42.2 - - - -
509A LYS* 3.2 18.2 + - - -
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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
----------------------------------------------------------
366A THR* 3.3 3.9 - - - -
367A ASP* 1.3 82.3 - - + +
369A GLU* 1.3 58.2 + - - +
371A ALA* 3.9 1.6 - - - +
372A ARG* 2.9 27.5 + - - +
464A LYS* 3.2 27.3 + - - +
468A THR* 3.7 9.8 - - + +
469A LEU 3.1 30.1 - - - +
470A LYS* 2.9 29.7 + - - -
837A PRO* 4.8 14.1 - - + +
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 4.0 1.1 - - - +
363A GLY* 3.9 15.0 - - - +
366A THR* 3.0 23.9 + - - +
367A ASP 3.4 0.2 - - - -
368A GLU* 1.3 76.2 - - - +
370A PHE* 1.4 63.1 + - - +
371A ALA 3.2 1.3 - - - -
372A ARG* 2.8 47.0 + - - -
373A GLU* 3.0 46.8 + - - +
726A TYR* 4.1 0.7 - - - -
732A ASN* 5.2 0.7 - - - +
837A PRO* 3.2 17.6 - - + +
838A VAL* 3.1 30.3 - - + +
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Residues in contact with PHE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLY 5.2 2.1 + - - -
366A THR 3.1 18.0 + - - +
367A ASP 3.7 3.1 - - - +
368A GLU 3.6 0.2 - - - -
369A GLU* 1.4 74.7 - - - +
371A ALA* 1.3 59.1 + - - +
373A GLU* 4.0 8.9 + - - +
374A VAL* 3.7 17.4 - - + +
433A LEU* 5.6 3.1 - - + -
459A THR* 3.7 31.9 - - + -
461A LEU* 5.0 2.9 - - + -
471A PRO* 3.5 28.0 - - + -
474A ILE* 4.0 11.4 - - + -
505A TRP* 4.7 0.2 - + - -
509A LYS* 4.0 39.7 - - + -
512A VAL* 3.9 15.7 - - + -
513A ILE* 3.6 39.1 - - + +
732A ASN* 6.0 3.1 - - - +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASP 3.3 12.2 + - - +
368A GLU 4.0 0.9 - - - +
369A GLU 3.2 0.4 - - - -
370A PHE* 1.3 78.5 - - - +
372A ARG* 1.3 64.2 + - - +
373A GLU 3.2 1.4 + - - -
374A VAL* 3.2 19.4 + - - +
375A ILE 4.2 0.5 + - - -
461A LEU* 3.8 29.4 - - + -
469A LEU* 3.6 40.5 - - + +
471A PRO* 3.8 6.1 - - + -
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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 2.9 21.2 + - - +
369A GLU* 2.8 48.0 + - - +
371A ALA* 1.3 74.6 - - - +
373A GLU* 1.3 57.5 + - - +
374A VAL 3.3 0.2 - - - -
375A ILE* 3.1 16.4 - - - +
376A ALA* 3.0 33.2 + - - +
469A LEU* 5.1 1.3 - - - +
726A TYR* 3.3 26.7 + - - -
833A ASN* 2.7 49.4 + - + +
834A ARG 4.2 2.0 + - - -
835A THR 3.2 11.6 + - - +
836A GLY* 3.7 15.7 - - - -
837A PRO* 4.6 1.3 - - + -
838A VAL* 3.1 14.5 - - - +
840A LEU* 3.6 18.6 + - - +
842A TYR* 4.6 4.4 - - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL* 4.4 1.4 - - - +
369A GLU* 3.0 41.0 + - - +
370A PHE* 4.2 7.0 - - - +
371A ALA 3.2 0.8 + - - -
372A ARG* 1.3 75.4 - - - +
374A VAL* 1.3 61.3 + - - +
375A ILE 3.2 0.4 - - - -
376A ALA 4.2 0.2 - - - -
377A GLY* 2.8 33.5 + - - +
378A VAL* 4.1 6.1 + - - +
379A ASN 4.1 6.4 + - - +
726A TYR* 3.1 38.8 - - + -
732A ASN* 3.1 28.0 + - - +
733A ARG* 4.0 15.5 + - - +
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.7 22.7 - - + +
371A ALA* 3.2 14.3 + - - +
373A GLU* 1.3 78.2 - - - +
375A ILE* 1.3 58.7 + - + +
379A ASN 3.7 6.1 - - - +
380A PRO* 3.2 26.3 - - - +
382A VAL 3.7 19.1 - - - +
383A ILE* 3.7 20.4 - - + +
433A LEU* 4.0 27.6 - - + -
459A THR* 6.6 0.4 - - + -
461A LEU* 4.0 23.1 - - + -
513A ILE* 6.0 2.7 - - + -
516A ASP* 5.6 1.3 - - - +
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Residues in contact with ILE 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 ALA 4.3 1.3 - - - +
372A ARG* 3.1 21.5 - - - +
374A VAL* 1.3 81.7 - - - +
376A ALA* 1.3 56.4 - - - +
377A GLY 3.8 0.2 - - - -
380A PRO* 4.0 5.4 - - - -
383A ILE* 4.4 10.3 - - + -
469A LEU* 3.9 33.7 - - + -
631A ILE* 4.2 20.6 - - + -
633A ASP 3.7 9.6 - - - +
634A TYR* 3.4 39.9 - - + -
635A PRO* 3.7 4.6 - - + +
636A TYR* 3.5 13.9 + - - +
833A ASN* 3.5 38.8 - - + +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ARG* 3.0 21.8 + - - +
373A GLU* 4.2 0.7 - - - -
375A ILE* 1.3 78.1 - - + +
377A GLY* 1.3 65.7 + - - +
380A PRO* 4.7 1.8 - - - -
635A PRO* 3.8 19.5 - - + -
726A TYR* 2.8 19.1 + - - -
833A ASN 3.8 21.1 - - - +
842A TYR* 3.3 25.0 - - + -
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Residues in contact with GLY 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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373A GLU* 2.8 33.3 + - - -
375A ILE 3.8 0.4 - - - -
376A ALA* 1.3 83.3 - - - +
378A VAL* 1.3 64.8 + - - -
379A ASN 3.3 2.5 - - - -
380A PRO* 3.3 14.6 - - - +
718A ALA 4.3 4.2 - - - +
726A TYR* 3.7 17.3 - - - -
842A TYR* 4.6 4.2 - - - -
844A LEU* 4.7 1.6 - - - +
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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