Contacts of the helix formed by residues 376 - 391 (chain A) in PDB entry 2JI8
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 ASN 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LYS 4.7 8.5 + - - -
368A ALA* 5.2 6.7 - - - +
370A THR* 3.9 20.9 + - + +
374A MET 3.8 0.6 + - - -
375A MET* 1.3 73.3 - - - +
377A TYR* 1.3 54.3 + - - +
378A SER* 2.6 32.0 + - - -
379A ASN* 2.9 34.6 + - - +
380A SER* 2.6 27.5 + - - -
545A ILE* 4.0 3.7 - - - +
546A ASP* 5.6 0.9 - - + -
549A ALA* 4.2 17.3 - - + -
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 1.3 75.7 - - - +
378A SER* 1.3 59.1 + - - +
380A SER* 3.6 4.5 - - - -
381A LEU* 3.2 35.9 + - + +
402A ASN* 3.5 28.4 - - + +
403A ALA* 3.8 7.9 - - - -
406A ASN* 3.7 26.7 - - + +
410A ILE* 3.6 3.5 - - - +
477A MET* 3.7 32.7 + - + -
479A ASN* 3.3 24.0 + - - -
483A TYR 4.4 0.3 + - - -
545A ILE* 4.1 10.7 - - + +
549A ALA* 4.0 17.7 - - + -
550A GLY* 3.7 22.7 - - - -
1566A TPP 2.6 26.2 + - - -
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 4.5 3.5 - - - +
365A LYS* 3.7 44.1 + - - +
366A MET* 3.4 14.4 - - - +
376A ASN* 2.6 17.0 + - - -
377A TYR* 1.3 73.1 - - - +
379A ASN* 1.3 58.7 + - - -
382A GLY* 2.9 28.1 + - - -
406A ASN* 5.4 2.4 + - - -
409A MET* 5.5 1.7 - - - +
410A ILE* 3.8 13.9 - - - +
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Residues in contact with ASN 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS 4.5 2.0 - - - +
366A MET* 3.5 24.1 - - - +
368A ALA 3.4 23.4 + - - +
369A GLU* 4.7 0.2 - - - +
370A THR* 2.9 36.2 + - - +
375A MET* 3.8 3.0 - - - +
376A ASN* 2.9 34.8 + - - +
378A SER* 1.3 72.2 - - - +
380A SER* 1.3 83.8 + - - +
382A GLY* 3.7 0.9 + - - -
383A VAL* 3.5 21.8 + - - +
522A PRO* 4.1 24.8 - - + +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A MET* 3.8 18.6 - - - -
376A ASN 2.6 21.6 + - - -
377A TYR 3.5 2.8 + - - -
379A ASN* 1.3 83.0 + - - +
381A LEU* 1.3 69.5 + - - +
383A VAL* 3.2 12.9 + - - +
384A VAL* 3.8 2.5 + - - +
477A MET* 3.4 22.8 - - - +
525A LEU* 3.3 29.2 - - - +
543A ALA* 5.7 0.2 - - - -
545A ILE* 3.7 16.6 - - - -
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.2 26.6 + - + +
380A SER* 1.3 76.7 + - - +
382A GLY* 1.3 58.8 + - - +
383A VAL 3.1 2.0 - - - -
384A VAL* 3.0 21.7 + - + +
385A ARG* 2.8 27.2 + - - +
403A ALA 4.7 2.2 - - - +
406A ASN* 3.8 24.0 - - + -
407A THR* 3.4 32.8 - - + +
410A ILE* 3.8 16.6 - - + +
411A VAL* 4.1 3.9 - - + +
449A VAL* 3.6 21.5 - - + -
475A ILE* 6.2 0.2 - - + -
477A MET* 3.8 25.8 - - + -
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Residues in contact with GLY 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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366A MET* 3.8 25.5 - - - +
378A SER 2.9 21.0 + - - -
379A ASN 4.1 2.9 - - - -
380A SER 3.2 0.6 - - - -
381A LEU* 1.3 78.2 - - - +
383A VAL* 1.3 60.2 + - - +
385A ARG* 3.5 6.1 - - - +
386A ASP* 3.2 31.6 + - - +
410A ILE* 4.0 0.8 - - - +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASN 3.5 16.1 + - - +
380A SER 3.2 8.7 + - - +
381A LEU 3.1 0.4 - - - -
382A GLY* 1.3 74.8 - - - +
384A VAL* 1.3 64.9 + - - +
386A ASP* 3.3 8.9 + - - +
387A PHE* 3.0 23.0 + - + +
522A PRO* 3.5 30.1 - - + +
525A LEU* 4.2 11.0 - - + -
526A LYS* 3.5 44.2 - - + +
529A LEU* 4.9 6.7 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER 4.2 9.0 - - - +
381A LEU* 3.0 23.2 + - + +
383A VAL* 1.3 73.8 - - - +
385A ARG* 1.3 65.6 + - - +
387A PHE* 3.3 1.0 + - - +
388A MET* 2.9 37.9 + - + +
396A LEU* 4.4 12.6 - - + -
411A VAL* 3.9 19.1 - - + -
447A ILE* 4.9 4.7 - - + -
449A VAL* 4.4 7.0 - - + -
475A ILE* 4.0 24.5 - - + -
525A LEU* 4.9 7.0 - - + -
529A LEU* 4.2 18.4 - - + -
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Residues in contact with ARG 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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362A LEU* 6.2 0.6 - - - +
366A MET* 3.9 34.0 - - - +
381A LEU 2.8 12.8 + - - +
382A GLY 3.5 8.7 - - - +
383A VAL 3.3 0.2 - - - -
384A VAL* 1.3 77.7 - - - +
386A ASP* 1.3 87.7 + - - +
388A MET* 3.1 2.1 + - - +
389A LEU* 3.0 48.7 + - + +
410A ILE* 3.5 29.9 + - + +
411A VAL* 4.1 12.5 - - - +
412A ASP* 4.4 18.8 + - + +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLY 3.2 15.8 + - - +
383A VAL* 3.3 8.9 + - - +
385A ARG* 1.3 104.6 + - - +
387A PHE* 1.3 61.9 + - - +
389A LEU* 3.5 9.8 + - - +
390A ALA* 3.3 21.7 + - - +
526A LYS* 6.6 0.2 - - - -
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Residues in contact with PHE 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 VAL* 3.0 17.6 + - + +
384A VAL 3.7 3.8 - - - +
386A ASP* 1.3 76.6 - - - +
388A MET* 1.3 53.6 + - - +
390A ALA* 3.2 3.3 + - + -
391A ASN* 2.7 63.5 + - + +
394A ILE* 3.8 17.5 - - + -
447A ILE* 3.7 32.8 - - + -
529A LEU* 4.1 17.0 - - + -
530A GLU* 3.8 40.8 - - + -
533A VAL* 3.7 30.1 - - + -
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Residues in contact with MET 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 VAL* 2.9 27.8 + - + +
385A ARG 3.8 2.9 - - - +
387A PHE* 1.3 74.3 - - - +
389A LEU* 1.3 63.4 + - - +
390A ALA 3.3 0.2 - - - -
391A ASN 3.9 16.4 - - - +
392A PRO* 3.3 32.8 - - + +
394A ILE* 3.5 30.3 - - + +
396A LEU* 4.2 11.2 - - + -
411A VAL* 3.8 23.3 - - + -
412A ASP 4.1 12.0 - - - +
413A MET* 3.8 24.9 - - + -
414A LEU* 4.5 2.1 + - - +
447A ILE* 3.9 24.5 - - + -
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Residues in contact with LEU 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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257A ASN* 4.8 8.5 - - + +
385A ARG* 3.0 56.3 + - + +
386A ASP* 3.7 10.8 - - - +
388A MET* 1.3 75.7 - - - +
390A ALA* 1.3 59.9 + - - +
392A PRO* 4.0 3.3 - - - +
412A ASP* 4.0 27.1 - - + +
414A LEU* 3.6 41.5 - - + +
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Residues in contact with ALA 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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386A ASP 3.3 10.2 + - - +
387A PHE* 3.2 6.3 + - - +
389A LEU* 1.3 80.7 - - - +
391A ASN* 1.3 71.1 + - - +
392A PRO* 3.5 7.2 - - - +
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Residues in contact with ASN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 2.7 48.5 + - + +
388A MET* 3.4 16.7 - - - +
390A ALA* 1.3 84.8 + - - +
392A PRO* 1.3 64.4 - - - +
393A ASP 3.4 2.5 - - - -
394A ILE* 3.5 32.3 - - + +
533A VAL* 5.2 2.6 - - - +
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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
------------------------------------------------------------
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