Contacts of the helix formed by residues 385 - 404 (chain A) in PDB entry 5HI7
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 MET 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A LEU* 3.7 27.4 - - + -
380A GLN* 2.9 36.9 + - + +
383A GLN* 4.3 12.8 - - + +
384A GLY* 1.3 76.9 - - - +
386A PHE* 1.3 61.2 + - - +
387A PRO* 3.7 2.2 - - - -
388A GLN* 3.4 29.4 - - + +
389A ALA* 3.0 29.3 + - - +
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Residues in contact with PHE 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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381A LEU* 3.9 32.3 - - + -
384A GLY* 3.6 21.2 + - - -
385A MET* 1.3 72.1 - - - +
387A PRO* 1.3 72.4 - - + +
389A ALA 3.2 0.2 + - - -
390A MET* 2.8 28.6 + - - +
421A CYS* 3.3 11.1 - - - -
424A ASN* 3.5 54.5 - - + -
425A ILE* 3.6 20.6 - - + -
428A SER* 4.9 5.8 - - - -
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Residues in contact with PRO 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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385A MET* 4.7 0.7 - - - -
386A PHE* 1.3 96.5 - - + +
388A GLN* 1.3 81.8 - - - +
390A MET* 3.9 2.1 - - + +
391A LYS* 3.1 23.7 + - - +
425A ILE* 4.2 13.0 - - + -
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Residues in contact with GLN 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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380A GLN* 3.2 28.3 - - - +
385A MET* 3.4 35.3 - - + +
386A PHE 3.3 0.2 - - - -
387A PRO* 1.3 94.8 - - - +
389A ALA* 1.3 64.9 + - - +
391A LYS* 3.3 5.6 + - - +
392A ASN* 3.1 22.2 + - - +
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Residues in contact with ALA 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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377A GLY* 3.3 22.0 - - - +
380A GLN* 3.6 10.9 + - + -
381A LEU* 3.4 20.9 - - + +
385A MET 3.0 22.3 + - - +
386A PHE 3.7 2.9 - - - +
388A GLN* 1.3 74.9 - - - +
390A MET* 1.3 57.8 + - - +
392A ASN* 3.2 1.4 + - - +
393A LEU* 2.8 37.7 + - + +
421A CYS* 3.9 7.0 - - - -
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Residues in contact with MET 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE 2.8 21.1 + - - +
387A PRO* 3.9 4.7 - - + +
389A ALA* 1.3 72.6 - - - +
391A LYS* 1.3 57.6 + - - +
393A LEU* 4.5 1.8 - - - -
394A ARG* 3.0 47.0 + - + +
418A LEU* 4.0 28.9 - - + +
421A CYS* 3.5 24.4 - - - -
422A ASP* 3.9 31.2 - - + +
425A ILE* 3.6 17.5 - - + -
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Residues in contact with LYS 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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387A PRO 3.1 18.5 + - - +
388A GLN* 3.6 7.0 - - - +
389A ALA 3.3 0.2 - - - -
390A MET* 1.3 78.4 - - - +
392A ASN* 1.3 62.1 + - - +
394A ARG* 3.6 4.8 + - - +
395A LEU* 3.1 27.6 + - + +
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Residues in contact with ASN 392 (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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355A MET* 4.4 9.2 - - - +
373A VAL* 3.1 29.5 - - + +
376A VAL* 3.9 12.5 - - - +
377A GLY* 3.8 18.4 - - - +
380A GLN* 2.8 32.9 + - - +
388A GLN* 3.1 13.7 + - - +
391A LYS* 1.3 78.4 - - - +
393A LEU* 1.3 59.9 + - - +
395A LEU* 3.2 9.0 + - - +
396A ALA* 2.8 27.3 + - - +
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Residues in contact with LEU 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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374A MET* 4.1 10.5 - - + +
377A GLY* 4.0 25.1 - - - +
378A LYS* 4.1 4.0 - - - +
381A LEU* 4.5 5.6 - - + -
389A ALA* 2.8 28.1 + - + +
390A MET 4.0 1.1 - - - +
392A ASN* 1.3 72.5 - - - +
394A ARG* 1.3 57.8 + - - +
396A ALA* 3.4 5.7 + - - +
397A PHE* 2.9 27.4 + - - +
414A LEU* 3.8 23.2 - - + +
417A LEU* 3.9 41.1 - - + +
418A LEU* 3.5 18.9 - - + +
421A CYS* 4.0 16.6 - - + -
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Residues in contact with ARG 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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390A MET* 3.0 41.0 + - + +
391A LYS* 3.9 4.5 - - - +
393A LEU* 1.3 74.6 - - - +
395A LEU* 1.3 59.8 + - - +
397A PHE* 3.1 7.3 + - - +
398A ASP* 2.9 36.6 + - - +
418A LEU* 3.7 18.2 - - + -
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Residues in contact with LEU 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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355A MET* 6.1 0.7 - - - -
369A ARG* 3.7 26.2 - - - +
373A VAL* 3.9 20.4 - - + -
391A LYS* 3.1 20.7 + - + +
392A ASN* 3.6 11.2 - - - +
394A ARG* 1.3 75.2 - - - +
396A ALA* 1.3 62.4 + - - +
398A ASP* 3.3 13.4 + - + +
399A ILE* 3.1 40.6 + - + +
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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
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370A GLY 3.6 23.1 - - - +
373A VAL* 3.9 4.0 - - + +
374A MET* 3.8 23.8 - - + +
392A ASN 2.8 20.9 + - - +
393A LEU* 3.6 6.3 - - - +
395A LEU* 1.3 73.5 - - - +
397A PHE* 1.3 52.7 + - - +
399A ILE* 3.3 4.3 + - - +
400A MET* 2.7 41.2 + - - +
414A LEU* 3.8 9.0 - - + -
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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
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393A LEU 2.9 14.7 + - - +
394A ARG* 3.1 9.2 + - - +
396A ALA* 1.3 74.5 - - - +
398A ASP* 1.3 66.8 + - - +
400A MET 4.3 0.4 - - - +
401A ARG* 2.8 50.8 + - + +
411A ILE* 4.2 17.7 - - + -
414A LEU* 3.5 24.2 - - + +
415A ILE* 3.8 31.9 - - + -
418A LEU* 4.0 19.3 - - + -
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Residues in contact with ASP 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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365A SER* 4.9 1.4 + - - -
394A ARG* 2.9 21.7 + - - +
395A LEU* 3.3 17.5 + - + +
397A PHE* 1.3 80.1 - - - +
399A ILE* 1.3 62.8 + - + +
401A ARG* 3.2 18.7 - - - +
402A VAL* 3.9 8.7 - - - +
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Residues in contact with ILE 399 (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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364A GLY 4.2 11.7 - - - +
365A SER* 4.2 7.6 - - - +
366A HIS 3.4 37.2 - - - +
369A ARG* 3.9 40.2 - - + +
370A GLY* 3.7 16.6 - - - -
373A VAL* 4.6 3.4 - - + -
395A LEU* 3.1 30.2 + - + +
396A ALA 3.7 5.2 - - - +
398A ASP* 1.3 77.4 - - + +
400A MET* 1.3 59.2 + - - +
402A VAL* 3.0 11.3 + - - +
403A THR* 3.0 26.1 + - + +
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Residues in contact with MET 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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370A GLY* 3.6 37.2 - - - +
371A VAL* 4.1 2.9 - - - -
374A MET* 3.9 18.4 - - - +
396A ALA 2.7 22.6 + - - +
397A PHE 4.5 0.4 - - - +
399A ILE* 1.3 67.4 - - - +
401A ARG* 1.3 61.9 + - - +
402A VAL 3.1 1.6 - - - -
403A THR* 3.3 7.6 - - - +
404A HIS* 2.7 53.7 + - + +
405A GLY 3.0 8.0 + - - -
410A LEU* 3.5 39.9 - - + +
411A ILE* 3.6 17.4 - - + +
414A LEU* 4.2 7.4 - - + -
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Residues in contact with ARG 401 (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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27A GLY* 4.3 7.1 - - - +
224A ARG* 5.0 0.5 + - - -
397A PHE* 2.8 43.0 + - + +
398A ASP* 3.2 17.3 - - - +
400A MET* 1.3 76.9 - - - +
402A VAL* 1.3 71.7 + - + +
405A GLY* 3.6 17.1 - - - +
411A ILE* 3.9 8.8 - - - +
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Residues in contact with VAL 402 (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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26A PRO* 4.1 15.7 - - + +
27A GLY* 3.4 34.1 - - - +
224A ARG* 3.3 19.9 + - - +
225A ALA 3.8 7.4 - - - +
226A VAL* 3.9 17.7 - - + +
365A SER* 4.0 20.9 - - - +
398A ASP 3.9 13.7 - - - +
399A ILE 3.0 8.3 + - - +
401A ARG* 1.3 83.6 - - + +
403A THR* 1.3 63.1 + - - +
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Residues in contact with THR 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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213A SER* 4.1 8.3 + - - -
215A VAL* 3.3 18.4 - - - +
224A ARG* 3.2 14.5 - - - +
226A VAL* 4.2 7.9 - - + -
365A SER* 3.7 14.1 - - - +
366A HIS* 3.7 34.1 - - - +
367A PRO* 3.7 19.0 - - + +
399A ILE* 3.0 11.0 + - + +
400A MET* 3.3 12.3 - - - +
402A VAL* 1.3 76.3 - - - +
404A HIS* 1.3 82.9 + - - +
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Residues in contact with HIS 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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215A VAL* 3.5 28.0 - - + +
222A LEU* 3.8 5.2 - - - +
224A ARG* 2.8 24.0 + - - -
367A PRO* 3.7 31.2 - - + +
371A VAL* 4.0 11.9 - - + +
400A MET* 2.7 45.8 + - + +
403A THR* 1.3 98.2 + - - +
405A GLY* 1.3 62.2 + - - +
408A HIS* 3.7 40.0 + + + +
410A LEU* 4.2 2.9 - - + +
411A ILE* 4.0 9.4 - - + -
506A DMS 4.9 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
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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