Contacts of the helix formed by residues 360 - 378 (chain A) in PDB entry 4IE6
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 GLU 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A SER* 2.7 21.3 + - - +
359A PHE* 1.3 72.1 - - - +
361A PRO* 1.3 76.4 - - + +
362A ALA* 4.6 3.8 - - + +
363A VAL* 3.0 26.4 + - + +
364A LEU* 3.3 8.2 + - - +
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Residues in contact with PRO 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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359A PHE 3.2 7.6 - - - +
360A GLU* 1.3 84.3 - - + +
362A ALA* 1.3 62.5 + - - +
364A LEU* 3.3 5.3 + - + +
365A LYS* 3.0 20.8 + - - +
433A GLU* 3.8 44.4 - - + +
434A ILE* 5.3 1.3 - - + -
437A ALA* 3.5 28.5 - - + +
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Residues in contact with ALA 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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360A GLU* 3.1 3.4 + - + +
361A PRO* 1.3 81.6 - - + +
363A VAL* 1.3 60.6 + - + +
365A LYS* 3.7 9.0 - - - +
366A GLN* 3.1 27.7 + - - +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASN* 3.4 43.5 + - + +
358A SER* 4.4 10.3 - - - +
360A GLU* 3.0 22.9 + - + +
362A ALA* 1.3 77.1 - - + +
364A LEU* 1.3 60.8 + - - +
366A GLN* 3.6 16.5 + - - +
367A GLY* 3.0 23.2 + - - -
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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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344A ASN* 4.0 12.1 - - - +
356A LEU* 4.4 4.5 - - + -
358A SER 3.8 16.4 - - - +
359A PHE* 3.6 33.2 - - + +
360A GLU 3.3 8.2 + - - +
361A PRO* 3.7 7.4 - - + +
363A VAL* 1.3 74.9 - - - +
365A LYS* 1.3 64.4 + - - +
367A GLY* 3.2 2.2 + - - +
368A GLU* 3.0 31.0 + - - +
413A VAL* 5.5 2.7 - - + -
417A VAL* 3.5 31.4 - - + -
434A ILE* 4.0 28.9 - - + -
438A ILE* 4.1 14.1 - - + -
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Residues in contact with LYS 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 PRO 3.0 16.4 + - - +
362A ALA* 3.7 9.4 - - - +
364A LEU* 1.3 76.1 - - - +
366A GLN* 1.3 65.3 + - - +
368A GLU* 3.3 5.0 + - - +
369A GLU* 2.9 55.1 + - + +
436A THR 5.7 2.0 - - - -
437A ALA* 3.4 36.2 + - + +
438A ILE* 5.1 0.4 - - - +
440A ALA* 6.4 1.6 - - - -
441A SER* 4.2 2.0 + - - +
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Residues in contact with GLN 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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337A ARG* 5.1 5.6 + - - +
340A LEU* 3.3 44.1 + - + +
341A ALA* 5.4 2.0 - - - +
362A ALA 3.1 15.2 + - - +
363A VAL* 3.7 19.0 + - - +
365A LYS* 1.3 79.8 - - - +
367A GLY* 1.3 56.4 + - - +
369A GLU* 3.4 12.4 + - - +
370A ILE* 3.1 40.4 + - + +
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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
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341A ALA* 4.3 23.5 - - - +
363A VAL 3.0 16.2 + - - -
364A LEU* 3.2 4.2 + - - -
365A LYS 3.2 0.4 - - - -
366A GLN* 1.3 77.7 - - - +
368A GLU* 1.3 60.7 + - - +
370A ILE* 3.5 2.9 + - - +
371A HIS* 3.0 25.8 + - - +
410A MET* 4.9 2.1 - - - +
413A VAL* 5.9 6.5 - - - -
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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
----------------------------------------------------------
364A LEU* 3.0 21.5 + - + +
365A LYS* 3.9 2.5 - - - +
367A GLY* 1.3 74.7 - - - +
369A GLU* 1.3 60.0 + - - +
371A HIS* 3.7 2.2 + - - -
372A ASN* 3.1 20.1 + - - -
413A VAL* 4.0 11.8 - - - +
414A THR* 2.8 42.6 + - - -
417A VAL* 4.4 7.7 - - + +
438A ILE* 4.3 20.2 - - + -
441A SER* 3.6 20.2 - - - +
442A LEU* 6.5 0.9 - - + -
445A ARG* 2.4 52.1 + - - +
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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
----------------------------------------------------------
337A ARG* 4.9 9.0 + - - +
365A LYS* 2.9 54.6 + - - +
366A GLN* 3.7 12.1 - - - +
368A GLU* 1.3 76.9 - - - +
370A ILE* 1.3 60.0 + - - +
372A ASN* 3.3 8.1 + - - +
373A GLU* 3.0 26.3 + - - +
441A SER* 3.4 16.8 + - - +
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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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334A ILE* 5.6 0.9 - - + -
337A ARG* 3.4 71.1 - - + +
338A CYS* 4.2 3.6 - - - +
340A LEU* 4.3 5.8 - - + -
341A ALA* 3.7 26.2 - - + +
366A GLN* 3.1 34.3 + - + +
367A GLY 3.8 4.0 - - - +
369A GLU* 1.3 72.5 - - - +
371A HIS* 1.3 66.8 + - - +
373A GLU* 3.1 7.3 + - + +
374A VAL* 3.0 24.5 + - + +
410A MET* 4.1 11.4 - - + -
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Residues in contact with HIS 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLY 3.0 19.8 + - - +
368A GLU* 3.4 9.3 + - - +
370A ILE* 1.3 75.3 - - - +
372A ASN* 1.3 62.8 + - - +
374A VAL* 3.2 2.3 - - - +
375A GLU* 3.1 25.6 + - - +
407A TRP* 3.3 25.2 + + - -
410A MET* 3.5 25.5 + - + +
411A GLU* 2.6 49.9 + - - +
414A THR* 3.1 27.7 + - - -
445A ARG* 3.5 19.3 + - - +
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Residues in contact with ASN 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 3.1 10.1 + - - +
369A GLU* 3.5 11.1 - - - +
370A ILE 3.2 0.4 - - - -
371A HIS* 1.3 79.1 - - - +
373A GLU* 1.3 62.7 + - - +
375A GLU* 3.2 1.3 + - - -
376A PHE* 3.0 45.6 + - + +
441A SER* 3.0 33.9 + - - +
444A ALA* 4.1 9.1 - - - +
445A ARG* 2.7 43.4 + - - +
448A LEU* 5.7 1.7 - - + +
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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
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328A THR* 4.3 8.3 - - - +
333A TYR* 2.5 33.8 + - - -
334A ILE* 4.1 13.5 - - + +
337A ARG* 3.0 35.8 + - - +
369A GLU 3.0 13.3 + - - +
370A ILE* 3.1 8.8 + - - +
372A ASN* 1.3 74.9 - - - +
374A VAL* 1.3 63.7 + - - +
377A GLU* 3.0 49.5 + - + +
378A TRP* 3.6 3.4 + - + +
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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
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334A ILE* 4.2 14.7 - - + +
338A CYS* 4.0 23.1 - - - -
370A ILE 3.0 14.4 + - - +
371A HIS* 3.2 18.2 - - - +
373A GLU* 1.3 77.0 - - - +
375A GLU* 1.3 67.8 + - - +
378A TRP* 3.3 7.1 - - + +
379A LEU* 3.0 25.3 + - + +
403A LEU* 3.9 37.0 - - + +
407A TRP* 4.1 15.0 - - + -
410A MET* 4.2 12.6 - - - -
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Residues in contact with GLU 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 HIS* 3.1 20.8 + - - +
372A ASN 3.7 3.4 - - - +
374A VAL* 1.3 85.5 - - - +
376A PHE* 1.3 76.0 + - + +
379A LEU* 3.5 5.9 - - - +
380A ARG* 2.7 69.0 + - - +
407A TRP* 2.8 31.6 + - + +
445A ARG* 4.3 1.9 - - - -
449A ARG* 2.9 31.1 + - - -
474A PRO* 5.1 2.9 - - + -
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Residues in contact with PHE 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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372A ASN* 3.0 50.0 + - + +
375A GLU* 1.3 102.2 - - - +
377A GLU* 1.3 69.8 + - + +
378A TRP 3.2 2.0 + - - -
380A ARG* 3.6 16.2 - - - -
381A GLN* 3.2 25.8 + - - +
445A ARG* 3.3 33.4 - - + -
448A LEU* 3.7 34.8 - - + -
449A ARG* 3.8 9.9 - - + -
452A TRP* 3.7 34.0 - + - +
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Residues in contact with GLU 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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107A LYS* 2.6 33.5 + - - -
112A ARG* 2.8 52.0 + - - +
373A GLU* 3.0 33.3 + - + +
376A PHE* 1.3 82.0 - - + +
378A TRP* 1.3 68.2 + - + +
381A GLN* 3.5 10.7 - - - +
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Residues in contact with TRP 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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105A THR* 3.6 29.8 - - + -
112A ARG* 4.4 7.1 - - - +
114A PHE* 3.6 21.9 - + - -
328A THR 3.9 15.6 + - - -
329A GLY* 3.8 13.5 - - - -
330A THR 3.5 33.4 - - - -
331A LEU* 4.3 1.8 - - + -
334A ILE* 3.6 40.9 - - + +
373A GLU* 3.6 15.9 - - - +
374A VAL* 3.3 15.5 + - + +
376A PHE 3.2 1.0 - - - -
377A GLU* 1.3 94.0 - - + +
379A LEU* 1.3 70.2 + - + +
380A ARG 3.4 0.9 - - - -
381A GLN* 3.3 2.4 + - - +
382A PHE* 2.9 25.1 + - - +
396A TRP* 3.9 14.4 - + - -
400A MET* 4.1 14.8 - - + -
403A LEU* 4.5 7.2 - - + -
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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