Contacts of the helix formed by residues 367 - 380 (chain B) in PDB entry 2HD1
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 ARG 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B SER* 4.6 11.4 + - - +
358B THR 5.1 0.8 + - - -
361B LEU* 3.4 41.6 + - - +
362B ALA* 4.0 2.6 - - - +
364B ASP* 3.0 15.7 + - + +
365B MET 2.9 1.0 - - - -
366B ALA* 1.3 83.4 - - + +
368B HIS* 1.3 63.2 + - - +
369B ALA 3.5 2.2 - - - -
370B GLU* 3.2 44.4 + - - +
371B ILE* 2.9 37.0 + - + +
395B MET* 3.8 24.2 - - - +
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Residues in contact with HIS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ASP 4.0 1.0 + - - -
365B MET* 3.0 34.6 + - + +
366B ALA 3.5 0.8 - - - -
367B ARG* 1.3 78.5 - - - +
369B ALA* 1.3 62.6 + - + +
371B ILE* 3.8 1.4 - - - +
372B MET* 2.8 57.2 + - + +
399B LYS* 2.9 38.5 + - - +
459B PHE 5.2 2.1 + - - -
460B VAL* 3.8 38.3 + - + +
464B MET* 3.9 16.6 - - + +
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B ALA 5.3 0.8 + - - -
367B ARG 3.5 0.2 - - - -
368B HIS* 1.3 85.4 - - + +
370B GLU* 1.3 58.0 + - - +
372B MET* 3.3 4.2 + - - +
373B ASP* 2.8 44.6 + - - +
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B ALA 5.7 0.2 - - - +
367B ARG* 3.2 58.9 + - - +
368B HIS 3.2 0.2 - - - -
369B ALA* 1.3 79.7 - - - +
371B ILE* 1.3 67.9 + - - +
373B ASP* 3.2 7.0 + - - +
374B SER* 3.1 29.6 + - - +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ALA* 3.5 32.8 - - + +
367B ARG* 2.9 43.0 + - + +
368B HIS 3.9 2.5 - - - +
370B GLU* 1.3 77.0 - - - +
372B MET* 1.3 63.4 + - - +
374B SER* 3.3 7.3 + - - +
375B PHE* 2.9 22.5 + - - +
392B LEU* 4.3 6.6 - - + +
395B MET* 3.6 41.1 - - + -
396B ILE* 4.0 14.6 - - + -
399B LYS* 4.0 20.6 - - + -
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Residues in contact with MET 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B HIS* 2.8 44.1 + - + +
369B ALA* 3.7 6.1 - - - +
371B ILE* 1.3 76.0 - - - +
373B ASP* 1.3 59.9 + - - +
375B PHE* 3.3 6.1 + - - +
376B LYS* 2.8 54.8 + - + +
396B ILE* 3.8 16.2 - - + -
399B LYS* 5.1 0.7 - - - -
463B PRO* 4.2 6.1 - - + +
464B MET* 3.6 48.7 - - + +
467B THR* 3.8 19.1 - - - +
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Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ALA* 2.8 27.3 + - - +
370B GLU* 3.5 7.5 + - - +
372B MET* 1.3 78.6 - - - +
374B SER* 1.3 56.6 - - - +
376B LYS* 3.9 20.7 + - - +
377B GLU* 2.8 33.2 + - - +
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B GLU* 3.1 19.0 + - - +
371B ILE* 3.7 8.2 - - - -
373B ASP* 1.3 75.5 - - - +
375B PHE* 1.3 63.7 + - - +
377B GLU* 3.3 14.0 + - - +
378B LYS* 3.1 29.5 + - - +
392B LEU* 3.7 25.3 - - - +
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Residues in contact with PHE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ILE 2.9 17.5 + - - +
372B MET* 3.5 7.6 - - - +
374B SER* 1.3 77.7 - - - +
376B LYS* 1.3 57.1 + - - +
378B LYS* 3.2 4.8 + - + +
379B MET* 2.8 53.4 + - + +
382B PHE* 4.3 4.7 - + - -
392B LEU* 4.1 21.7 - - + +
393B LEU* 3.8 40.2 - - + -
396B ILE* 3.4 40.8 - - + -
467B THR* 3.3 43.5 - - + -
468B VAL* 4.6 3.1 - - + -
471B LEU* 4.2 4.5 - - + -
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B MET* 2.8 37.1 + - + +
373B ASP* 3.9 23.0 + - - +
375B PHE* 1.3 71.0 - - + +
377B GLU* 1.3 66.5 + - - +
379B MET* 3.1 20.8 + - - +
380B GLU* 3.4 11.1 + - - +
467B THR* 4.1 28.7 - - + +
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B ASP 2.8 19.5 + - - +
374B SER* 3.3 14.1 + - - +
376B LYS* 1.3 78.3 - - - +
378B LYS* 1.3 73.1 + - + +
380B GLU* 3.1 37.1 + - - +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B SER* 3.1 15.4 + - - +
375B PHE* 3.6 4.0 - - + +
377B GLU* 1.3 88.7 - - + +
379B MET* 1.3 63.8 + - - +
380B GLU 3.1 2.9 + - - -
381B ASN 3.5 3.1 + - - -
382B PHE* 3.2 24.1 + - + -
388B GLU* 3.6 36.7 + - - +
389B HIS* 3.5 42.6 + - + +
392B LEU* 3.4 28.7 - - + +
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Residues in contact with MET 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B PHE* 2.8 53.4 + - + +
376B LYS* 3.1 15.2 + - - +
378B LYS* 1.3 73.6 - - - +
380B GLU* 1.3 64.8 + - - +
381B ASN 3.0 3.8 + - - -
382B PHE* 3.3 27.3 + - + +
467B THR* 3.9 21.3 - - + +
470B LYS* 4.7 17.5 - - + +
471B LEU* 3.5 31.4 - - + -
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B LYS 3.4 8.7 + - - +
377B GLU* 3.1 29.2 - - - +
378B LYS 3.1 0.4 - - - -
379B MET* 1.3 79.1 - - - +
381B ASN* 1.3 64.9 + - + +
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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