Contacts of the helix formed by residues 378 - 394 (chain A) in PDB entry 3IAY
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LEU* 3.6 6.7 - - - -
376A HIS* 3.6 7.7 - - - +
377A ALA* 1.3 91.4 - - + +
379A GLU* 1.3 65.5 + - - +
380A GLU* 3.3 17.1 + - - +
381A GLU* 3.3 27.5 + - - +
382A MET* 3.2 15.4 + - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PRO* 3.3 8.0 - - - +
339A VAL* 3.0 39.1 + - + +
362A LEU* 3.6 18.2 - - + +
378A THR* 1.3 70.1 - - - +
380A GLU* 1.3 70.2 + - - +
382A MET* 3.1 12.1 + - + +
383A LEU* 3.0 29.2 + - + +
414A ARG* 2.6 54.1 + - - +
418A LEU* 3.4 14.6 - - + +
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 3.3 22.1 - - - +
379A GLU* 1.3 80.9 + - - +
381A GLU* 1.3 62.0 + - - +
383A LEU* 3.4 6.1 + - - +
384A SER* 3.1 25.7 + - - -
418A LEU* 3.9 32.2 - - + +
420A VAL* 3.7 30.1 - - + +
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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
----------------------------------------------------------
375A SER 5.3 0.9 - - - +
376A HIS* 3.9 21.6 + - - +
377A ALA* 4.0 17.1 + - - +
378A THR* 3.3 21.8 + - - +
379A GLU 3.3 0.2 - - - -
380A GLU* 1.3 78.3 - - - +
382A MET* 1.3 64.5 + - - +
384A SER* 3.2 6.7 + - - +
385A ASN* 2.9 40.7 + - - +
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Residues in contact with MET 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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339A VAL* 3.3 43.5 - - + +
340A ILE* 4.0 8.5 - - - +
341A GLN* 4.4 1.3 - - - -
342A ILE* 4.7 8.5 - - + -
360A PHE* 3.7 27.5 - - + +
361A THR* 3.5 27.8 - - - -
362A LEU* 3.7 6.5 - - + -
376A HIS* 3.5 29.1 + - + -
378A THR 3.2 6.9 + - - +
379A GLU* 3.1 16.9 + - + +
381A GLU* 1.3 79.4 - - - +
383A LEU* 1.3 64.1 + - + +
385A ASN* 3.3 2.8 + - - +
386A TRP* 3.0 22.2 + - - +
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Residues in contact with LEU 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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339A VAL* 4.7 12.3 - - + -
342A ILE* 4.4 10.3 - - + -
379A GLU* 3.0 24.0 + - + +
380A GLU 3.8 4.7 - - - +
382A MET* 1.3 78.0 - - + +
384A SER* 1.3 61.9 + - - +
386A TRP* 3.2 4.4 + - - +
387A ARG 3.1 19.1 + - - -
411A LEU* 3.8 31.0 - - + +
414A ARG* 4.5 4.5 - - + -
415A ALA* 4.2 24.2 - - + +
418A LEU* 4.0 25.1 - - + -
420A VAL* 4.5 9.4 - - + -
423A PHE* 3.3 31.3 - - + -
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Residues in contact with SER 384 (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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380A GLU 3.1 17.7 + - - -
381A GLU* 3.8 5.8 - - - -
383A LEU* 1.3 74.8 - - - +
385A ASN* 1.3 65.7 + - - +
387A ARG* 3.4 11.2 + - - +
388A ASN* 3.1 29.8 + - - +
420A VAL* 3.5 19.3 - - - +
422A ASP* 4.3 9.1 + - - -
423A PHE* 4.5 3.3 - - - +
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Residues in contact with ASN 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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360A PHE* 3.8 8.9 - - + -
376A HIS* 3.0 38.5 + - + -
381A GLU* 2.9 29.7 + - - +
382A MET 3.7 0.7 - - - +
384A SER* 1.3 80.8 - - - +
386A TRP* 1.3 57.3 + - - +
388A ASN* 3.3 13.4 + - - +
389A PHE* 2.9 28.1 + - - +
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Residues in contact with TRP 386 (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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318A MET* 3.6 24.0 - - + +
320A PHE* 3.7 27.6 - + - -
342A ILE* 3.4 30.1 - - + +
344A ASN* 2.9 35.1 + - - -
360A PHE* 3.8 13.7 - + + -
382A MET 3.0 14.3 + - - +
383A LEU 3.2 6.9 + - - +
385A ASN* 1.3 72.7 - - - +
387A ARG* 1.3 67.5 + - - +
389A PHE* 3.2 11.1 + + - +
390A ILE* 3.0 47.0 + - + +
398A ILE* 6.2 1.3 - - + -
408A ILE* 6.1 0.7 - - + -
411A LEU* 3.7 27.8 - - + -
423A PHE* 3.8 29.8 - + - -
426A PHE* 4.6 12.3 - + - -
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Residues in contact with ARG 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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383A LEU 3.1 11.9 + - - +
384A SER* 3.6 10.5 - - - +
386A TRP* 1.3 80.5 - - - +
388A ASN* 1.3 74.1 + - - +
390A ILE* 3.3 7.2 + - - +
391A ILE* 3.1 36.7 + - - +
422A ASP* 3.4 47.9 + - - +
423A PHE* 3.5 24.9 - - + +
425A TYR* 2.9 36.4 + - - +
426A PHE* 4.0 12.7 - - + +
430A LYS 4.7 5.3 + - - -
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Residues in contact with ASN 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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384A SER* 3.1 19.0 + - - +
385A ASN* 3.5 16.3 - - - +
387A ARG* 1.3 98.6 - - - +
389A PHE* 1.3 60.4 + - - +
391A ILE* 3.2 10.1 + - - +
392A LYS* 2.9 37.4 + - + +
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Residues in contact with PHE 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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95A SER 4.0 9.9 - - - -
96A SER* 3.9 16.4 - - - -
318A MET* 4.0 18.2 - - + -
344A ASN* 3.9 22.4 - - + -
346A VAL* 4.1 15.3 - - + -
356A ILE* 4.2 2.7 - - + -
358A ASN* 3.5 27.1 - - - -
360A PHE* 3.8 20.0 - + + -
385A ASN 2.9 13.2 + - - +
386A TRP* 3.3 24.2 - + - +
388A ASN* 1.3 72.4 - - - +
390A ILE* 1.3 63.7 + - - +
392A LYS* 3.3 3.1 + - - -
393A VAL* 2.8 57.6 + - + +
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Residues in contact with ILE 390 (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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318A MET* 4.1 19.7 - - + -
386A TRP* 3.0 55.9 + - + +
387A ARG* 3.3 6.3 + - - +
389A PHE* 1.3 77.7 - - + +
391A ILE* 1.3 58.8 + - - +
393A VAL* 4.8 0.7 - - - -
394A ASP* 2.8 27.9 + - - -
395A PRO* 3.2 21.4 - - + +
398A ILE* 4.6 7.0 - - + -
426A PHE* 3.6 46.9 - - + +
459A ARG* 3.8 15.4 + - - +
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Residues in contact with ILE 391 (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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288A SER* 4.2 27.3 + - - +
387A ARG* 3.1 38.4 + - + +
388A ASN* 3.2 12.3 + - - +
390A ILE* 1.3 78.3 - - - +
392A LYS* 1.3 67.6 + - + +
394A ASP* 3.5 14.0 + - - +
425A TYR 3.4 25.4 - - - +
426A PHE* 4.3 9.4 - - - -
427A GLY 4.8 3.6 - - - +
459A ARG* 4.2 9.6 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A SER* 4.6 15.9 - - - +
98A GLU* 3.9 48.9 + - + +
99A ARG 4.9 1.6 + - - -
388A ASN* 2.9 21.6 + - + +
389A PHE* 4.1 3.1 - - - +
391A ILE* 1.3 82.0 - - + +
393A VAL* 1.3 64.8 + - + +
394A ASP* 3.4 3.5 + - - +
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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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96A SER* 3.7 21.5 - - - +
97A PHE 4.0 6.1 - - - +
316A ARG* 2.9 28.4 + - - +
318A MET* 5.7 0.2 - - - -
346A VAL* 4.0 32.3 - - + -
356A ILE* 3.8 7.6 - - + -
389A PHE* 2.8 54.2 + - + +
390A ILE* 4.8 0.7 - - - -
392A LYS* 1.3 73.5 - - - +
394A ASP* 1.3 66.8 + - - +
395A PRO* 4.0 13.7 - - + -
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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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99A ARG* 2.6 52.6 + - + +
148A SER* 3.0 17.9 + - - -
288A SER* 4.6 13.4 + - - +
316A ARG* 4.2 0.2 - - - -
390A ILE 2.8 13.7 + - - -
391A ILE 3.8 10.6 - - - +
392A LYS 3.2 4.4 - - - +
393A VAL* 1.3 79.7 - - - +
395A PRO* 1.3 63.9 - - - +
428A ARG* 2.8 31.2 + - - +
459A ARG* 3.0 11.6 + - - +
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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