Contacts of the helix formed by residues 379 - 398 (chain A) in PDB entry 4IQJ
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 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 3.5 8.0 + - - +
377A GLU* 3.4 10.2 + - - +
378A TRP* 1.3 79.2 - - - +
380A ALA* 1.3 71.9 + - - +
381A GLU* 2.9 25.6 + - + +
382A ALA* 3.3 32.4 + - + +
383A ILE* 3.3 13.2 + - - +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 3.7 30.0 - - + +
326A ILE* 4.0 3.9 - - + +
330A PHE* 3.5 39.7 - - + -
379A THR* 1.3 76.6 + - - +
381A GLU* 1.3 66.5 + - - +
383A ILE* 3.5 18.6 + - - +
384A LEU 3.5 8.0 + - - -
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 3.4 28.5 - - + -
379A THR* 2.9 25.9 + - + +
380A ALA* 1.3 78.8 - - - +
382A ALA* 1.3 63.6 + - - +
384A LEU* 3.3 7.1 + - - +
385A HIS* 3.1 23.3 + - - +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU 5.2 1.3 - - - +
378A TRP* 3.9 23.5 - - + -
379A THR* 3.3 32.8 + - + +
381A GLU* 1.3 78.1 - - - +
383A ILE* 1.3 59.7 + - - +
385A HIS* 3.4 5.5 + - - +
386A ARG* 2.8 31.1 + - - +
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 3.4 31.6 - - + -
322A TYR* 4.0 31.2 - - + -
325A ARG* 3.9 26.2 - - + +
326A ILE* 4.0 18.4 - - + -
378A TRP* 4.5 8.7 - - + +
379A THR 3.3 10.9 + - - +
380A ALA* 3.8 7.9 - - - +
381A GLU 3.3 0.6 - - - -
382A ALA* 1.3 76.2 - - - +
384A LEU* 1.3 63.2 + - - +
386A ARG* 3.3 6.9 + - - +
387A ALA* 3.0 22.9 + - - +
431A LEU* 3.9 5.1 - - + +
444A LEU* 4.0 17.3 - - + -
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 4.2 23.3 - - + -
318A LEU* 5.1 5.6 - - + -
326A ILE* 5.2 3.1 - - + -
330A PHE* 3.5 33.7 - - + -
331A TYR* 4.5 15.3 - - + -
334A VAL* 3.5 28.7 - - + -
354A LEU* 6.0 0.7 - - + -
362A TRP* 4.8 7.2 - - + -
380A ALA 3.5 3.5 + - - +
381A GLU* 3.3 9.8 + - - +
382A ALA 3.2 0.4 - - - -
383A ILE* 1.3 79.1 - - - +
385A HIS* 1.3 52.6 + - - +
387A ALA* 3.1 4.5 + - - +
388A LEU* 2.6 58.8 + - + +
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Residues in contact with HIS 385 (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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366A ARG* 3.0 71.7 + - + +
381A GLU 3.1 12.6 + - - +
382A ALA* 3.9 5.6 - - - +
384A LEU* 1.3 77.1 - - - +
386A ARG* 1.3 65.7 + - - +
388A LEU* 4.2 12.1 - - + -
389A TYR* 3.1 38.2 + + + +
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TRP* 4.1 29.5 - - + -
382A ALA 2.8 19.1 + - - +
383A ILE* 3.4 7.0 - - - +
385A HIS* 1.3 78.3 - - - +
387A ALA* 1.3 62.9 + - - +
389A TYR* 3.7 8.2 - - - +
390A GLU* 2.4 59.7 + - - +
429A GLY 3.7 12.3 + - - -
431A LEU* 3.3 25.2 - - + +
443A PRO* 4.3 9.8 + - - +
444A LEU* 5.2 4.2 - - + +
448A LEU 3.0 27.7 + - - -
449A LEU* 4.1 4.4 - - - +
450A PHE* 3.6 18.3 - - - +
451A GLU* 5.8 1.1 - - - -
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Residues in contact with ALA 387 (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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314A THR* 4.0 24.0 - - + -
315A PHE* 5.5 3.4 - - + -
318A LEU* 4.1 15.5 - - + -
383A ILE 3.0 15.7 + - - +
384A LEU* 3.8 2.5 - - - +
386A ARG* 1.3 77.2 - - - +
388A LEU* 1.3 57.1 + - - +
390A GLU* 3.5 6.5 + - - +
391A LEU* 3.1 36.5 + - + +
431A LEU* 4.2 14.1 - - + -
432A VAL* 3.9 4.0 - - + +
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Residues in contact with LEU 388 (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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311A ARG* 4.3 11.3 + - - +
315A PHE* 4.1 16.6 - - + -
362A TRP* 3.3 71.6 - - + +
365A LEU* 6.0 1.8 - - + -
384A LEU* 2.6 47.2 + - + +
385A HIS* 4.2 12.1 - - + +
387A ALA* 1.3 72.2 - - - +
389A TYR* 1.3 62.3 + - - +
391A LEU* 4.1 5.0 - - - +
392A SER* 3.2 23.2 + - - -
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Residues in contact with TYR 389 (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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385A HIS* 3.1 33.0 + + + +
386A ARG* 3.7 9.2 - - - +
388A LEU* 1.3 74.3 - - - +
390A GLU* 1.3 69.6 + - + +
392A SER* 3.3 7.1 + - - -
393A VAL* 3.2 45.3 + - + +
396A ARG* 6.3 0.4 - - - -
450A PHE* 4.6 9.0 - + + -
451A GLU* 3.3 28.4 + - - -
456A PRO* 3.5 25.7 - - + +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 2.4 44.6 + - - +
387A ALA 3.7 2.5 - - - +
389A TYR* 1.3 81.1 - - + +
391A LEU* 1.3 59.0 + - - +
393A VAL* 3.0 5.7 + - - +
394A ILE* 2.8 33.1 + - + +
430A SER* 2.6 25.3 + - - -
431A LEU* 3.0 15.4 + - - +
432A VAL* 2.9 28.4 + - + +
450A PHE* 3.3 38.4 - - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.8 32.3 - - + +
311A ARG* 3.9 35.7 - - + +
314A THR* 3.6 36.8 - - + +
315A PHE* 4.4 11.4 - - + -
387A ALA 3.1 21.2 + - - +
388A LEU* 4.1 5.4 - - - +
390A GLU* 1.3 80.2 - - - +
392A SER* 1.3 56.9 + - - +
394A ILE* 3.6 5.5 - - + +
395A GLU* 2.8 40.0 + - - +
432A VAL* 3.8 15.3 - - + -
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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
----------------------------------------------------------
311A ARG* 4.4 4.9 - - - +
359A GLU* 3.4 32.3 + - - +
388A LEU 3.2 17.8 + - - -
389A TYR* 3.6 10.3 - - - -
390A GLU 3.2 0.2 - - - -
391A LEU* 1.3 77.8 - - - +
393A VAL* 1.3 59.1 + - - +
395A GLU* 3.9 1.4 - - - +
396A ARG* 3.0 34.2 + - - +
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Residues in contact with VAL 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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389A TYR* 3.2 41.5 - - + +
390A GLU 3.0 6.6 + - - +
392A SER* 1.3 76.1 - - - +
394A ILE* 1.3 63.2 + - - +
396A ARG* 4.0 16.3 - - - +
397A MET* 3.1 49.2 + - + +
450A PHE* 4.0 21.5 - - + -
454A LEU* 5.0 1.6 - - + +
456A PRO* 3.8 26.2 - - + +
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Residues in contact with ILE 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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310A LEU* 3.6 21.3 - - + -
390A GLU 2.8 25.8 + - - +
391A LEU* 3.6 7.0 - - - +
393A VAL* 1.3 77.0 - - - +
395A GLU* 1.3 59.6 + - + +
397A MET* 4.1 2.0 - - - -
398A GLY 3.1 3.5 + - - -
399A PHE* 2.9 31.0 + - + +
400A PRO* 3.9 10.3 - - + +
403A PHE* 3.5 45.3 - - + -
430A SER* 5.0 0.2 - - - +
432A VAL* 4.1 29.2 - - + -
450A PHE* 4.3 7.0 - - + -
454A LEU* 3.9 16.2 - - + -
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Residues in contact with GLU 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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307A ALA* 3.4 44.4 - - + +
310A LEU* 5.9 1.6 - - + -
311A ARG* 2.8 45.0 + - - +
359A GLU* 3.2 15.7 - - - +
391A LEU* 2.8 24.4 + - + +
392A SER 3.9 3.6 - - - +
394A ILE* 1.3 74.2 - - + +
396A ARG* 1.3 64.6 + - - +
398A GLY* 3.1 13.9 + - - -
400A PRO* 4.7 11.1 - - + +
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Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLU* 5.2 3.1 + - - +
389A TYR* 6.3 0.6 - - - -
392A SER* 3.0 21.4 + - - +
393A VAL* 4.0 17.6 - - - +
394A ILE 3.4 0.2 - - - -
395A GLU* 1.3 77.3 - - - +
397A MET* 1.3 68.5 - - - +
398A GLY* 3.4 1.0 + - - -
456A PRO* 3.6 25.6 + - - +
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Residues in contact with MET 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 VAL* 3.1 38.3 + - + +
394A ILE 4.3 0.2 - - - +
396A ARG* 1.3 84.6 - - + +
398A GLY* 1.3 61.2 + - - +
399A PHE* 3.5 40.0 - - + -
454A LEU* 4.1 14.6 - - + -
455A ASN 3.6 14.1 - - - +
456A PRO* 4.5 7.4 - - - +
458A ARG 3.2 28.7 - - - +
459A VAL* 3.6 28.9 - - + +
460A SER 3.8 9.9 - - - +
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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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295A ILE* 3.6 17.3 - - - +
394A ILE 3.1 1.2 + - - -
395A GLU 3.1 16.3 + - - -
396A ARG 3.2 0.6 - - - -
397A MET* 1.3 79.4 - - - +
399A PHE* 1.3 67.4 - - - +
400A PRO* 3.1 12.6 - - - +
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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
------------------------------------------------------------
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