Contacts of the helix formed by residues 386 - 403 (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 ASN 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ASP* 3.1 23.7 + - + +
385B SER* 1.3 77.5 - - - +
387B GLU* 1.3 58.8 + - - +
388B GLU* 3.1 26.9 + - - +
389B HIS* 2.9 55.7 + - + +
390B MET* 3.0 14.1 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B SER 3.3 7.7 + - - +
386B ASN* 1.3 72.7 + - - +
388B GLU* 1.3 60.1 + - + +
390B MET* 3.4 8.5 + - + +
391B THR* 2.9 38.8 + - - +
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Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS* 3.6 26.4 + - - +
386B ASN* 3.1 16.1 + - - +
387B GLU* 1.3 79.4 - - + +
389B HIS* 1.3 66.0 + - - +
391B THR* 3.8 6.5 - - - -
392B LEU* 3.2 28.1 + - - +
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Residues in contact with HIS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS* 3.5 46.7 + - + +
381B ASN 3.6 10.3 + - - -
382B PHE* 3.6 29.9 - + + -
383B ASP* 3.0 39.5 + - + +
386B ASN* 2.9 43.1 + - + +
388B GLU* 1.3 78.6 - - - +
390B MET* 1.3 57.9 + - - +
392B LEU* 3.3 6.3 + - - +
393B LEU 3.0 22.3 + - - -
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Residues in contact with MET 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LYS 3.3 25.4 - - - +
277B PHE* 3.3 36.3 - - + -
281B ASP* 5.2 4.3 - - - +
382B PHE* 4.1 8.3 - - - -
384B TYR* 3.6 56.3 - - + +
385B SER 5.3 0.2 - - - -
386B ASN 3.0 15.0 + - - +
387B GLU* 3.8 10.1 - - + +
389B HIS* 1.3 74.9 - - - +
391B THR* 1.3 59.8 + - - +
393B LEU* 3.2 6.2 + - - +
394B LYS* 2.9 39.5 + - - +
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Residues in contact with THR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B THR* 3.9 26.2 - - + -
359B LEU* 5.9 1.1 - - + -
387B GLU* 2.9 30.7 + - - +
388B GLU* 3.8 8.0 - - - -
389B HIS 3.3 0.2 - - - -
390B MET* 1.3 76.4 - - - +
392B LEU* 1.3 64.3 + - + +
394B LYS* 3.3 21.2 + - - +
395B MET* 3.0 28.8 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE* 4.3 9.4 - - + +
374B SER* 3.7 37.2 - - - +
375B PHE* 4.1 17.7 - - + +
378B LYS* 3.4 41.5 - - + +
388B GLU 3.2 10.1 + - - +
389B HIS* 3.3 7.6 + - - +
391B THR* 1.3 80.2 - - + +
393B LEU* 1.3 58.6 + - - +
395B MET* 3.2 27.7 + - + +
396B ILE* 2.9 32.2 + - - +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 3.6 28.3 - - + -
375B PHE* 3.8 28.0 - - + -
382B PHE* 3.6 27.1 - - + -
384B TYR* 4.2 10.3 - - + -
389B HIS 3.0 14.2 + - - +
390B MET* 3.2 10.1 + - - +
392B LEU* 1.3 76.6 - - - +
394B LYS* 1.3 58.1 + - - +
396B ILE* 3.2 5.5 + - + +
397B LEU* 2.8 45.1 + - + +
468B VAL* 5.7 4.0 - - + -
471B LEU* 4.0 14.4 - - + -
472B PHE* 4.4 15.5 - - + -
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Residues in contact with LYS 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 3.6 20.6 - - + -
281B ASP* 2.8 44.2 + - + +
284B ILE* 4.7 11.5 - - + +
285B LEU* 3.9 21.7 - - + +
355B GLY* 5.6 4.4 - - - -
359B LEU* 3.6 18.8 - - + +
390B MET* 2.9 27.9 + - - +
391B THR* 3.7 20.0 + - - +
393B LEU* 1.3 76.0 - - - +
395B MET* 1.3 63.2 + - - +
397B LEU* 3.3 9.3 + - - +
398B ILE* 3.0 23.0 + - - +
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Residues in contact with MET 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B THR* 4.0 20.9 - - + +
359B LEU* 3.7 18.2 - - + -
362B ALA* 3.7 16.4 - - + -
367B ARG* 3.8 16.2 - - - +
371B ILE* 3.6 39.7 - - + -
391B THR* 3.0 25.2 + - - +
392B LEU* 3.2 26.7 + - + +
394B LYS* 1.3 76.8 - - - +
396B ILE* 1.3 61.2 + - - +
398B ILE* 3.2 7.9 - - - +
399B LYS* 3.0 29.0 + - - +
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Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE* 4.0 18.6 - - + +
372B MET* 3.8 27.4 - - + -
375B PHE* 3.4 39.9 - - + -
392B LEU 2.9 16.8 + - - +
393B LEU* 3.5 10.1 - - + +
395B MET* 1.3 76.9 - - - +
397B LEU* 1.3 58.6 + - + +
399B LYS* 3.2 6.2 + - - +
400B CYS* 2.8 33.7 + - - -
464B MET* 4.4 10.5 - - + +
468B VAL* 3.6 31.6 - - + -
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B MET* 3.9 7.0 - - + -
267B MET* 4.0 28.7 - - + -
271B CYS* 5.9 0.4 - - - -
273B LEU* 3.9 30.3 - - + -
277B PHE* 4.0 25.1 - - + -
285B LEU* 4.1 15.0 - - + -
393B LEU* 2.8 32.4 + - + +
394B LYS* 3.5 9.6 - - - +
395B MET 3.2 0.4 - - - -
396B ILE* 1.3 78.4 - - + +
398B ILE* 1.3 60.1 + - - +
400B CYS* 3.4 5.0 + - + +
401B CYS* 3.2 28.8 + - - -
468B VAL* 5.0 9.9 - - + -
472B PHE* 5.2 5.4 - - + -
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Residues in contact with ILE 398 (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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260B VAL* 5.0 5.6 - - + -
264B MET* 3.7 16.5 - - + +
285B LEU 4.8 1.6 - - - +
288B ALA* 3.7 43.1 - - + +
289B ALA* 3.9 8.5 - - + +
292B HIS* 4.5 4.7 - - + -
359B LEU* 3.6 37.0 - - + +
360B ILE 4.6 0.2 - - - +
362B ALA* 4.9 0.7 - - + -
363B THR* 4.2 15.0 - - + -
394B LYS 3.0 12.9 + - - +
395B MET* 3.2 16.4 - - - +
397B LEU* 1.3 74.8 - - - +
399B LYS* 1.3 69.6 + - + +
401B CYS* 3.4 1.5 + - - +
402B ASP* 2.9 23.5 + - + +
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Residues in contact with LYS 399 (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 3.4 30.6 + - - +
363B THR* 4.6 6.8 + - - +
364B ASP 5.4 0.2 + - - -
365B MET* 3.6 21.6 - - - +
368B HIS* 2.9 49.7 + - - +
371B ILE* 4.0 26.2 - - + -
372B MET* 5.1 0.2 - - - -
395B MET 3.0 21.7 + - - +
396B ILE* 3.6 9.2 - - - +
398B ILE* 1.3 78.8 - - + +
400B CYS* 1.3 64.2 + - - +
402B ASP* 3.3 7.8 + - - +
403B ILE* 3.2 28.3 + - - +
464B MET* 4.1 12.7 - - - -
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Residues in contact with CYS 400 (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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263B MET* 5.4 0.4 - - - -
267B MET* 4.5 10.8 - - - -
396B ILE* 2.8 24.0 + - - +
397B LEU* 3.5 8.3 - - - +
399B LYS* 1.3 77.8 - - - +
401B CYS* 1.3 62.3 + - - +
403B ILE* 3.6 1.9 - - - +
404B SER* 3.0 26.4 + - - -
464B MET* 3.6 28.5 - - - -
465B PHE* 3.7 29.3 - - + -
468B VAL* 3.9 28.9 - - - -
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Residues in contact with CYS 401 (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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259B CYS* 5.9 0.2 - - - +
260B VAL* 3.5 35.3 + - + +
263B MET* 3.7 7.6 - - + -
264B MET* 3.4 45.8 - - + -
267B MET* 3.9 15.0 - - - -
397B LEU 3.2 18.7 + - - +
398B ILE 3.9 2.7 - - - +
400B CYS* 1.3 77.8 - - - +
402B ASP* 1.3 64.1 + - - +
404B SER* 2.8 25.8 + - - -
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Residues in contact with ASP 402 (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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101B ZN 2.1 37.5 - - - -
251B PHE* 5.4 1.4 - - - -
256B HIS* 2.9 22.2 + - - -
260B VAL* 3.7 11.6 - - + +
292B HIS* 2.8 11.8 + - + +
363B THR* 3.9 24.9 - - + +
365B MET* 5.8 1.0 - - - +
398B ILE* 2.9 19.1 + - + +
399B LYS* 3.3 8.3 + - - +
401B CYS* 1.3 78.4 - - - +
403B ILE* 1.3 68.0 + - + +
404B SER 3.5 1.6 + - - -
405B ASN* 5.0 4.9 + - - +
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Residues in contact with ILE 403 (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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1B IBM 3.7 28.9 - - - +
251B PHE* 6.5 0.2 - - - -
365B MET* 4.6 18.4 - - + -
399B LYS* 3.3 15.7 - - - +
400B CYS 3.6 1.8 - - - +
402B ASP* 1.3 91.2 - - - +
404B SER* 1.3 56.9 + - - +
405B ASN* 3.3 8.5 + - - +
406B GLU 4.6 0.5 + - - -
456B PHE* 3.9 19.2 - - + -
460B VAL* 4.0 12.6 - - + -
461B LEU* 3.3 40.8 - - + +
464B MET* 3.5 23.3 - - + -
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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
------------------------------------------------------------
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