Contacts of the helix formed by residues 394 - 407 (chain A) in PDB entry 2JIH
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 GLN 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 5.8 1.1 - - + -
391A ASP* 2.7 48.6 + - - +
392A GLY* 3.3 1.0 - - - -
393A LEU* 1.3 79.7 + - - +
395A ALA* 1.3 54.1 + - - +
396A ALA 3.0 5.6 - - - -
397A PHE* 2.8 36.7 + - + +
398A THR* 3.2 11.9 + - - +
434A LEU* 5.7 3.3 - - + +
491A THR* 3.3 18.8 + - - +
526A PHE* 2.6 60.6 - - + +
527A PRO* 6.3 0.7 - - + -
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.0 19.5 - - + -
356A PHE* 5.1 0.2 - - + -
388A ILE* 3.9 10.0 - - + +
389A GLU 3.8 19.5 - - - +
390A ASP* 4.2 6.3 - - - -
391A ASP* 3.5 5.0 + - - -
392A GLY 2.9 16.9 + - - +
394A GLN* 1.3 76.0 - - - +
396A ALA* 1.3 49.5 + - - +
397A PHE 3.3 0.2 - - - -
398A THR* 3.7 11.5 - - - -
399A THR* 2.6 42.5 + - - -
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.2 37.6 - - + +
288A VAL* 3.6 28.0 - - + -
289A ALA* 3.8 7.1 - - - +
292A LEU* 4.6 0.6 - - - +
393A LEU 3.3 14.8 + - - +
394A GLN 2.9 0.8 + - - -
395A ALA* 1.3 76.4 - - - +
397A PHE* 1.3 59.6 + - + +
399A THR* 3.5 7.2 - - - -
400A ALA* 3.1 24.8 + - - +
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Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 4.4 19.3 - - + -
292A LEU* 3.9 22.4 - - + -
393A LEU 4.5 6.1 - - - -
394A GLN* 2.8 22.7 + - + +
396A ALA* 1.3 76.4 - - - +
398A THR* 1.3 65.7 + - - +
400A ALA* 3.1 6.4 + - - +
401A HIS* 2.8 24.9 + - - +
429A MET* 3.8 11.0 - - + +
434A LEU* 5.5 11.2 - - + -
437A LEU* 3.7 30.1 - - + -
439A HIS* 5.6 6.7 - + - -
527A PRO* 6.4 2.7 - - + -
530A ASP* 6.1 0.9 - - - -
1001A 097 5.1 1.8 - - + -
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Residues in contact with THR 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.3 50.7 - - + +
371A GLY* 3.9 8.3 - - - +
388A ILE* 3.9 12.8 - - + -
389A GLU 5.2 0.6 + - - -
391A ASP* 4.9 1.9 + - - -
394A GLN* 3.2 9.5 + - - +
395A ALA* 3.7 14.4 - - - -
397A PHE* 1.3 76.9 - - - +
399A THR* 1.3 64.0 + - - +
401A HIS* 3.0 3.3 + - - +
402A GLU* 2.9 31.5 + - - +
434A LEU* 5.5 2.1 - - - +
1001A 097 3.9 21.2 - - + +
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Residues in contact with THR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 5.2 1.5 - - - +
286A PHE* 4.5 10.3 - - + -
289A ALA* 4.3 11.4 - - + -
354A ILE* 4.2 19.5 - - + -
356A PHE* 3.4 25.9 - - + -
388A ILE* 3.6 13.1 - - - +
395A ALA 2.6 29.0 + - - -
396A ALA* 3.5 8.8 - - - -
398A THR* 1.3 72.9 - - - +
400A ALA* 1.3 62.0 + - - +
402A GLU* 3.3 1.9 + - - +
403A LEU* 2.9 41.2 + - + +
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Residues in contact with ALA 400 (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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289A ALA* 4.2 8.7 - - + +
292A LEU* 3.7 16.8 - - + -
293A TYR* 2.7 47.2 + - + -
396A ALA 3.1 10.3 + - - +
397A PHE 3.1 8.8 + - - +
399A THR* 1.3 78.3 - - - +
401A HIS* 1.3 62.4 + - - +
403A LEU* 4.6 0.9 - - - -
404A GLY* 3.1 3.5 + - - -
429A MET* 3.6 18.8 - - + -
443A TRP* 4.0 4.4 - - + -
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Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PHE 2.8 12.8 + - - +
398A THR 3.5 7.4 - - - +
400A ALA* 1.3 78.5 - - - +
402A GLU* 1.3 68.0 + - - +
404A GLY* 2.9 14.6 + - - -
405A HIS* 3.3 2.8 + - - -
411A HIS* 3.6 8.7 - + - -
429A MET* 2.9 29.2 + - + +
430A MET* 3.2 40.5 - - + +
431A ALA 3.4 21.1 + - - -
1001A 097 3.5 35.7 + - + +
1553A ZN 2.2 36.1 - - - -
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLY* 3.1 14.7 + - - -
372A MET* 3.6 15.3 - - - +
373A ALA* 3.3 25.6 + - + +
386A SER* 3.9 19.3 - - - -
388A ILE* 3.5 20.0 - - + -
398A THR* 2.9 19.7 + - + +
399A THR 3.8 3.1 - - - +
401A HIS* 1.3 78.8 - - - +
403A LEU* 1.3 64.5 + - - +
404A GLY 3.1 1.3 - - - -
405A HIS* 3.3 10.0 + - - -
406A VAL* 3.3 13.3 + - - +
1001A 097 2.5 43.4 + - - +
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Residues in contact with LEU 403 (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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260A VAL* 5.5 3.4 - - + -
262A THR* 5.7 0.2 - - - +
286A PHE* 4.4 3.1 - - + -
293A TYR* 3.1 17.7 - - + +
304A LEU* 3.9 34.3 - - + -
352A THR* 4.1 26.7 - - + +
354A ILE* 4.1 26.0 - - + -
378A VAL* 6.4 0.2 - - + -
386A SER* 4.5 7.9 - - - +
399A THR* 2.9 34.5 + - + +
400A ALA* 3.9 0.9 - - - +
402A GLU* 1.3 73.9 - - - +
404A GLY* 1.3 63.7 + - - +
406A VAL* 3.5 11.6 + - + +
407A PHE* 3.1 32.3 + - + -
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Residues in contact with GLY 404 (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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293A TYR* 2.9 14.1 + - - -
400A ALA 3.1 0.8 + - - -
401A HIS 2.9 11.9 + - - -
403A LEU* 1.3 77.5 - - - +
405A HIS* 1.3 52.9 + - - +
407A PHE* 2.8 23.9 + - - +
408A ASN 3.2 0.3 + - - -
409A MET* 3.1 42.7 + - - +
430A MET* 3.9 5.4 - - - -
443A TRP* 4.9 0.2 - - - -
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Residues in contact with HIS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA* 4.1 13.5 - - + -
374A ASP 3.5 15.0 - - - +
375A VAL* 3.0 16.7 - - + +
376A GLY 2.6 29.6 + - - -
401A HIS* 3.3 8.9 + - - -
402A GLU* 3.3 18.8 - - - +
404A GLY* 1.3 70.3 - - - +
406A VAL* 1.3 54.4 + - - +
408A ASN* 2.7 10.2 + - - -
409A MET 3.1 19.5 + - - -
410A PRO* 4.6 1.5 - - + +
411A HIS* 3.5 22.9 - + - -
430A MET* 3.6 9.4 - - + +
1001A 097 3.0 15.9 + - - -
1553A ZN 2.3 32.5 - - - -
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A THR* 4.0 6.7 - - - +
373A ALA* 4.0 1.8 - - + -
374A ASP 3.5 15.3 - - - +
376A GLY* 3.4 4.5 - - - +
377A THR* 3.0 31.4 + - - +
378A VAL* 3.2 41.6 + - + +
384A SER* 3.9 7.9 - - - +
385A CYS 3.9 24.2 - - - +
386A SER* 4.7 0.9 - - - -
402A GLU 3.3 16.1 + - - +
403A LEU* 3.6 21.5 - - + +
404A GLY 3.3 0.6 - - - -
405A HIS* 1.3 75.9 - - - +
407A PHE* 1.3 56.3 + - + +
408A ASN 3.2 0.2 - - - -
454A PHE* 4.2 0.3 - - - -
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Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.5 34.1 - - + -
293A TYR* 3.8 28.3 - + - -
302A VAL* 3.9 15.3 - - + -
304A LEU* 4.8 3.8 - - + -
378A VAL* 4.4 17.7 - - + -
403A LEU* 3.1 24.1 + - + -
404A GLY 2.8 12.6 + - - +
406A VAL* 1.3 75.9 - - + +
408A ASN* 1.3 66.4 + - - +
409A MET* 3.4 4.2 + - + -
451A ILE* 3.2 43.9 - - + -
454A PHE* 3.7 20.2 - + - -
455A LEU* 4.7 6.5 - - + -
463A LEU* 3.6 24.2 - - + -
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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