Contacts of the helix formed by residues 387 - 402 (chain A) in PDB entry 5IVH
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 ALA 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A ASP* 2.9 22.1 + - + +
386A THR* 1.3 78.4 - - - +
388A PRO* 1.3 61.9 - - + +
389A GLU* 2.9 37.2 - - + +
390A THR* 2.5 28.4 + - - -
391A LEU 3.2 5.0 + - - -
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Residues in contact with PRO 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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386A THR 3.1 7.4 - - - +
387A ALA* 1.3 82.6 - - + +
389A GLU* 1.3 62.3 + - - +
391A LEU* 4.4 9.4 - - + +
392A GLU* 3.2 26.2 + - - +
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Residues in contact with GLU 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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380A LEU 4.4 15.5 - - - +
381A ALA 4.9 0.2 - - - -
382A ASP* 4.0 13.7 + - - +
387A ALA* 2.8 28.2 + - + +
388A PRO* 1.3 76.3 - - - +
390A THR* 1.3 65.7 + - - +
392A GLU* 4.2 2.3 - - - +
393A MET* 3.1 45.2 + - + +
566A HIS* 5.7 2.5 - - - +
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Residues in contact with THR 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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373A VAL* 4.1 7.2 - - + +
376A VAL* 3.9 14.3 - - + +
381A ALA* 3.9 16.7 - - + -
382A ASP* 2.4 40.2 + - - +
385A ARG* 3.9 27.1 - - + -
387A ALA 2.5 15.8 + - - -
389A GLU* 1.3 76.3 - - - +
391A LEU* 1.3 60.2 + - - +
392A GLU 3.2 1.6 - - - -
393A MET* 3.8 6.6 - - - +
394A GLY* 2.8 26.9 + - - -
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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
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371A THR* 3.7 37.8 - - + +
373A VAL* 4.0 13.2 - - + +
386A THR* 5.0 9.4 - - - +
387A ALA 3.2 7.9 + - - +
388A PRO* 4.4 8.7 - - + +
390A THR* 1.3 78.0 - - - +
392A GLU* 1.3 57.1 + - - +
394A GLY* 3.5 1.4 + - - -
395A ALA* 3.0 24.9 + - - +
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Residues in contact with GLU 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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388A PRO 3.2 18.2 + - - +
389A GLU* 4.2 2.7 - - - +
390A THR 3.2 0.4 - - - -
391A LEU* 1.3 76.3 - - - +
393A MET* 1.3 64.9 + - - +
395A ALA* 3.2 17.2 + - + +
396A LYS* 3.3 28.0 + - - +
565A LYS* 5.4 9.2 + - - -
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Residues in contact with MET 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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376A VAL* 3.9 14.4 - - + -
380A LEU* 3.8 40.8 - - + +
389A GLU* 3.1 37.2 + - + +
390A THR* 3.4 5.8 + - - +
392A GLU* 1.3 74.8 - - - +
394A GLY* 1.3 61.4 + - - +
396A LYS* 3.1 25.3 + - - +
397A ILE 3.4 5.2 + - - -
562A MET* 3.5 41.9 - - + +
565A LYS* 6.3 0.2 - - + -
566A HIS* 3.6 35.2 - - + +
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Residues in contact with GLY 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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371A THR 3.4 19.4 - - - +
372A CYS* 3.7 6.3 - - - +
373A VAL 4.7 0.2 - - - -
376A VAL* 3.7 15.2 - - - +
390A THR 2.8 16.9 + - - -
391A LEU* 3.8 1.3 - - - -
393A MET* 1.3 77.3 - - - +
395A ALA* 1.3 58.1 + - - +
397A ILE* 3.5 5.5 + - - +
398A LYS* 2.7 30.8 + - - +
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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
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371A THR 4.1 1.7 + - - -
391A LEU 3.0 14.0 + - - +
392A GLU* 3.2 16.5 + - + +
394A GLY* 1.3 76.3 - - - +
396A LYS* 1.3 58.0 + - + +
398A LYS* 3.7 11.7 - - + +
399A LYS* 3.0 31.7 + - - +
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Residues in contact with LYS 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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392A GLU* 3.5 26.6 + - - +
393A MET* 3.1 11.8 + - - +
395A ALA* 1.3 73.3 - - + +
397A ILE* 1.3 67.7 + - - +
399A LYS* 3.1 12.2 + - - +
400A ALA 3.2 8.1 + - - -
558A GLN* 3.7 34.9 - - + +
561A SER* 3.0 42.4 + - - +
562A MET* 4.2 16.9 + - + +
564A GLU* 4.6 14.2 + - - +
565A LYS* 5.9 5.1 - - - +
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Residues in contact with ILE 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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372A CYS* 3.5 21.8 - - + +
375A PHE* 3.5 35.0 - - + +
376A VAL* 3.7 9.2 - - + +
393A MET 3.4 1.2 + - - -
394A GLY 3.5 5.6 - - - +
396A LYS* 1.3 74.5 - - - +
398A LYS* 1.3 60.1 + - - +
400A ALA* 2.8 28.0 + - - +
401A HIS* 3.4 12.5 + - - -
415A LEU* 3.7 24.7 - - + -
558A GLN* 4.8 1.2 + - - +
559A TRP* 3.8 22.6 - - + +
562A MET* 3.4 39.2 - - + -
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Residues in contact with LYS 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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369A LEU 3.5 18.6 - - - +
370A GLU* 3.0 34.1 + - - +
371A THR* 4.3 4.5 - - - +
372A CYS* 3.7 15.5 - - + -
394A GLY 2.7 21.9 + - - +
395A ALA* 3.7 11.9 - - + +
396A LYS 3.2 0.2 - - - -
397A ILE* 1.3 74.6 - - - +
399A LYS* 1.3 57.3 + - - +
401A HIS* 5.4 0.7 - - - -
402A VAL* 3.0 44.6 + - + +
407A PRO* 6.4 1.1 - - - -
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Residues in contact with LYS 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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395A ALA 3.0 17.3 + - - +
396A LYS* 3.1 4.9 + - - +
397A ILE 2.9 0.2 + - - -
398A LYS* 1.3 76.5 - - - +
400A ALA* 1.3 64.3 + - - +
401A HIS 3.1 1.7 + - - -
402A VAL 3.5 12.9 - - - +
558A GLN* 4.6 13.5 - - - +
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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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396A LYS 3.2 9.9 + - - +
397A ILE* 2.8 11.9 + - - +
399A LYS* 1.3 76.2 - - - +
401A HIS* 1.3 68.2 + - + +
403A THR* 6.0 0.5 - - - +
555A LYS* 3.1 46.4 - - + +
558A GLN* 4.3 21.3 - - + +
559A TRP* 4.7 2.0 - - + +
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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
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369A LEU* 5.4 0.2 - - + -
397A ILE* 3.4 19.2 + - + +
398A LYS* 4.7 0.7 - - - +
399A LYS 3.1 0.2 - - - -
400A ALA* 1.3 81.3 + - + +
402A VAL* 1.3 66.0 + - + +
403A THR* 3.5 7.9 + - - +
411A ASN* 3.0 31.2 - - + +
414A ASP* 3.1 28.8 + - - +
415A LEU* 3.6 38.9 - - + -
418A HIS* 3.3 35.7 - + - +
555A LYS* 3.6 14.8 - - + +
559A TRP* 2.9 34.1 + + - -
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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
----------------------------------------------------------
369A LEU* 4.3 28.7 - - + +
372A CYS* 5.1 0.2 - - - -
398A LYS* 3.0 41.2 + - + +
399A LYS* 3.5 15.8 - - - +
401A HIS* 1.3 76.1 - - + +
403A THR* 1.3 62.3 + - - +
404A GLY 3.9 19.2 - - - +
405A GLU 5.1 0.4 - - - -
406A THR* 4.4 17.0 - - - +
407A PRO* 4.4 7.6 - - + -
411A ASN* 3.8 13.5 - - - +
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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