Contacts of the helix formed by residues 365 - 383 (chain A) in PDB entry 1IZO
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 GLY 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A MET* 3.6 14.6 - - - -
363A CYS* 3.2 9.4 - - - -
364A PRO* 1.3 80.6 - - - +
366A GLU* 1.3 58.3 + - - +
367A GLY 3.4 2.2 - - - -
368A ILE* 3.3 8.3 + - - +
369A THR* 2.9 33.5 + - - -
501A HEM 3.8 21.7 - - - +
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Residues in contact with GLU 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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284A ARG* 3.1 40.8 + - - +
349A MET* 5.6 0.9 - - - +
351A PRO* 4.8 3.6 - - - +
352A GLN* 3.7 29.1 + - + +
353A GLY 5.1 0.2 - - - +
362A ARG* 3.0 42.6 + - - -
363A CYS* 3.7 12.9 + - - +
364A PRO 3.3 3.2 - - - -
365A GLY* 1.3 77.2 - - - +
367A GLY* 1.3 63.0 + - - +
369A THR* 3.2 3.5 + - - -
370A ILE* 3.1 30.9 + - + +
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Residues in contact with GLY 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN* 3.6 27.9 - - - +
364A PRO 4.7 3.2 + - - -
365A GLY 3.4 0.6 - - - -
366A GLU* 1.3 77.6 - - - +
368A ILE* 1.3 61.9 + - - +
370A ILE* 3.3 9.4 + - - +
371A GLU* 2.9 29.1 + - - +
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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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102A LEU 4.2 4.3 - - - +
103A MET* 3.6 28.2 - - + +
107A HIS* 5.1 0.9 - - + -
108A GLN* 3.6 25.6 - - + +
111A LEU* 3.6 37.7 - - + -
149A TRP* 4.7 2.5 - - + -
244A ILE* 4.9 2.9 - - + -
247A ILE* 4.4 3.6 - - + -
365A GLY* 3.3 7.8 + - - +
366A GLU 3.3 0.4 - - - -
367A GLY* 1.3 75.9 - - - +
369A THR* 1.3 64.7 + - - +
371A GLU* 3.9 1.5 - - - +
372A VAL* 2.9 34.9 + - + +
501A HEM 3.5 39.7 - - + -
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Residues in contact with THR 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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247A ILE* 4.0 14.3 - - + +
250A PHE* 3.9 13.7 - - + -
284A ARG* 4.1 1.6 - - - -
352A GLN* 3.2 31.6 + - - +
365A GLY 2.9 18.8 + - - -
366A GLU 3.2 8.5 + - - -
368A ILE* 1.3 77.1 - - - +
370A ILE* 1.3 58.3 + - - +
372A VAL* 3.5 1.6 + - - +
373A MET* 2.9 54.9 + - + +
501A HEM 3.4 21.9 - - + +
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Residues in contact with ILE 370 (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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277A GLU* 5.9 2.2 - - + +
280A VAL* 4.2 13.0 - - + -
281A GLN* 3.7 15.9 - - - +
284A ARG* 3.5 40.6 - - - +
366A GLU* 3.1 21.6 + - + +
367A GLY* 3.6 9.9 - - - +
369A THR* 1.3 77.9 - - - +
371A GLU* 1.3 65.1 + - - +
373A MET* 3.3 1.4 + - - +
374A LYS* 2.8 59.0 + - + +
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Residues in contact with GLU 371 (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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108A GLN* 4.1 30.0 - - + +
109A LYS* 5.2 4.9 - - + +
112A ALA* 3.9 22.3 - - + +
367A GLY* 2.9 19.8 + - - +
368A ILE 3.9 2.7 - - - +
370A ILE* 1.3 78.5 - - - +
372A VAL* 1.3 62.0 + - + +
374A LYS* 2.5 38.4 + - - +
375A ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 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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108A GLN 5.7 0.2 - - - +
111A LEU* 4.4 17.5 - - + +
112A ALA* 4.7 2.0 - - - +
115A MET* 4.0 28.7 - - + -
142A LEU* 4.1 13.9 - - + -
244A ILE* 5.7 2.7 - - + -
247A ILE* 3.9 28.3 - - + -
251A LEU* 4.6 0.9 - - + -
368A ILE* 2.9 33.4 + - + +
369A THR 4.0 2.5 - - - +
371A GLU* 1.3 75.3 - - + +
373A MET* 1.3 62.6 + - - +
375A ALA* 3.9 5.4 - - - +
376A SER* 2.9 37.5 + - - +
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Residues in contact with MET 373 (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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247A ILE* 4.3 4.5 - - + -
250A PHE* 3.6 30.7 - - + -
251A LEU* 4.0 21.2 - - + +
254A SER* 3.8 12.9 + - - +
280A VAL* 3.7 19.4 - - + +
283A VAL* 3.6 30.1 - - + -
284A ARG* 3.7 28.3 - - + -
369A THR* 2.9 34.4 + - - +
370A ILE 3.6 4.9 - - - +
371A GLU 3.2 0.2 - - - -
372A VAL* 1.3 80.1 - - - +
374A LYS* 1.3 57.8 + - - +
376A SER* 3.9 1.0 - - - -
377A LEU* 2.9 29.5 + - - +
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Residues in contact with LYS 374 (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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273A SER* 6.3 0.8 - - - -
276A ARG* 4.4 22.1 + - + +
277A GLU* 3.7 39.8 - - + +
280A VAL* 3.6 20.4 - - + -
370A ILE* 2.8 29.2 + - + +
371A GLU* 2.5 45.7 + - - +
373A MET* 1.3 75.4 - - - +
375A ALA* 1.3 66.5 + - - +
377A LEU* 3.2 3.7 + - - +
378A ASP* 2.9 25.2 + - - +
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Residues in contact with ALA 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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112A ALA* 4.0 19.5 - - + +
115A MET* 4.7 6.5 - - + -
116A THR* 3.7 24.7 + - - +
119A TRP* 4.4 3.5 - - - -
371A GLU 3.0 17.9 + - - +
372A VAL* 3.9 4.3 - - - +
374A LYS* 1.3 75.7 - - - +
376A SER* 1.3 63.0 + - - +
378A ASP* 3.3 9.8 - - - +
379A PHE* 3.2 20.1 + - - +
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Residues in contact with SER 376 (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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115A MET* 4.1 7.4 - - - +
119A TRP* 2.9 40.3 + - - +
251A LEU* 3.8 26.1 - - - +
372A VAL* 2.9 22.4 + - - +
373A MET 4.0 0.2 - - - -
375A ALA* 1.3 73.1 - - - +
377A LEU* 1.3 68.3 + - - +
379A PHE* 3.2 5.9 + - - +
380A LEU* 3.2 28.3 + - - +
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Residues in contact with LEU 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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254A SER* 5.0 9.2 - - - -
258A LEU* 3.9 21.5 - - + -
268A LEU* 4.1 13.9 - - + -
276A ARG* 4.1 20.6 - - + +
279A PHE* 3.6 45.5 - - + -
280A VAL* 4.3 4.7 - - + -
373A MET 2.9 19.2 + - - +
374A LYS* 3.2 5.1 + - - +
376A SER* 1.3 76.0 - - - +
378A ASP* 1.3 64.4 + - - +
380A LEU* 3.0 11.0 + - + +
381A VAL* 3.0 39.1 + - + +
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Residues in contact with ASP 378 (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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116A THR* 5.7 4.7 - - - +
276A ARG* 3.2 38.2 + - - +
374A LYS 2.9 12.9 + - - +
375A ALA* 3.3 14.1 - - - +
377A LEU* 1.3 77.2 - - - +
379A PHE* 1.3 58.0 + - - +
381A VAL* 4.8 0.9 - - - -
382A HIS* 2.9 51.1 + - - +
383A GLN 3.9 0.3 + - - -
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Residues in contact with PHE 379 (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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119A TRP* 3.4 67.3 - + + -
120A LYS* 5.9 0.7 - - + -
122A ALA* 5.4 0.2 - - + -
123A VAL* 3.6 16.2 - - + -
126A TRP* 3.5 39.7 - + - -
375A ALA 3.2 8.3 + - - +
376A SER 3.2 8.5 + - - +
377A LEU 3.2 0.6 - - - -
378A ASP* 1.3 80.0 + - - +
380A LEU* 1.3 77.9 + - + +
383A GLN* 3.0 43.5 + - + +
384A ILE* 3.6 29.4 + - + +
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Residues in contact with LEU 380 (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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119A TRP* 6.0 1.8 - - + -
126A TRP* 5.3 0.4 - - + -
134A LEU* 5.0 11.2 - - + -
251A LEU* 4.8 6.5 - - + +
254A SER* 5.1 2.2 - - - -
255A ALA* 4.2 31.2 - - + +
258A LEU* 4.3 13.0 - - + +
265A LYS* 4.7 7.1 - - - -
376A SER* 3.4 16.6 - - - +
377A LEU* 3.0 14.6 + - + +
379A PHE* 1.3 98.6 - - + +
381A VAL* 1.3 60.5 + - - +
384A ILE* 3.8 13.4 - - + +
386A TYR* 3.8 26.8 + - + +
410A MET* 4.2 24.9 - - + -
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Residues in contact with VAL 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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258A LEU* 4.2 13.5 - - + -
265A LYS* 4.2 9.4 - - + +
268A LEU* 4.0 23.3 - - + -
269A ARG* 3.4 39.9 + - + +
276A ARG* 5.9 1.1 - - - -
377A LEU* 3.0 40.1 + - + +
378A ASP* 4.1 2.9 - - - +
380A LEU* 1.3 80.2 - - - +
382A HIS* 1.3 86.1 + - + +
384A ILE 4.7 1.5 - - - +
416A LYS* 3.5 8.0 + - - +
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Residues in contact with HIS 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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268A LEU 4.7 7.0 - - - -
269A ARG* 3.9 24.7 + - + -
271A GLY 5.5 3.6 + - - -
276A ARG* 4.3 15.3 - - + -
378A ASP* 2.9 39.0 + - - +
381A VAL* 1.3 105.0 - - + +
383A GLN* 1.3 62.8 + - + +
384A ILE 3.5 2.0 - - - -
416A LYS* 3.4 25.1 - - - +
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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
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120A LYS* 4.0 30.3 - - + +
123A VAL* 3.7 13.7 - - + +
378A ASP 3.9 0.6 + - - -
379A PHE* 3.0 40.9 + - + +
382A HIS* 1.3 79.7 + - + +
384A ILE* 1.3 62.6 + - - +
415A ARG* 3.6 28.0 + - - +
416A LYS* 3.3 16.4 + - - -
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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
------------------------------------------------------------
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