Contacts of the helix formed by residues 383 - 401 (chain B) in PDB entry 1H1Q
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 THR 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B TRP* 4.1 5.4 - - - +
377B ILE* 4.3 22.7 - - + -
381B GLY 4.7 4.2 + - - +
382B TYR* 1.3 78.7 - - - +
384B LEU* 1.3 67.9 + - - +
385B GLU* 3.5 10.5 + - + +
386B SER* 2.7 24.7 + - - -
387B LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 384 (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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361B HIS* 3.6 42.4 - - + +
371B SER* 4.3 14.1 - - - +
372B TRP* 4.0 17.8 - - + +
377B ILE* 5.6 1.2 - - - +
383B THR* 1.3 75.5 - - - +
385B GLU* 1.3 63.4 + - - +
387B LEU* 3.2 8.5 + - + +
388B LYS* 3.1 23.8 + - - +
391B LEU* 4.7 5.8 - - + -
432B LEU* 3.7 32.0 - - + +
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B THR* 3.1 10.0 + - + +
384B LEU* 1.3 77.9 - - - +
386B SER* 1.3 62.2 + - - +
388B LYS* 3.8 24.5 + - - +
389B PRO* 3.9 8.3 - - - +
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B VAL* 5.5 5.1 - - - +
381B GLY 4.1 2.9 + - - -
382B TYR* 3.2 23.9 - - - -
383B THR* 2.7 39.9 + - - -
385B GLU* 1.3 77.6 - - - +
387B LEU* 1.3 64.7 + - - +
389B PRO* 3.5 12.3 - - - +
390B CYS* 5.3 0.5 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B VAL* 4.0 21.1 - - + +
357B GLY* 3.9 28.0 - - - +
358B ALA 4.1 1.3 - - - +
361B HIS* 5.0 0.4 - - + -
372B TRP* 3.7 42.0 - - + -
382B TYR* 4.1 24.0 - - + -
383B THR 2.9 21.7 + - - +
384B LEU* 4.0 6.1 - - + +
386B SER* 1.3 80.0 - - - +
388B LYS* 1.3 52.1 + - - +
390B CYS* 3.1 10.5 + - - +
391B LEU* 2.7 47.7 + - + -
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU 3.1 14.8 + - - +
385B GLU* 4.0 22.1 + - - +
387B LEU* 1.3 68.5 - - - +
389B PRO* 1.3 69.9 - - + +
391B LEU* 3.0 8.4 + - - +
392B MET* 2.6 65.8 + - + +
432B LEU* 4.1 34.9 - - + +
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Residues in contact with PRO 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TYR* 3.0 26.1 + - + +
385B GLU 3.9 6.5 - - - +
386B SER 3.5 12.8 - - - +
387B LEU 3.5 4.7 - - - -
388B LYS* 1.3 98.5 - - + +
390B CYS* 1.3 57.2 + - - +
392B MET* 3.7 9.0 + - + +
393B ASP* 3.4 15.2 + - - +
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Residues in contact with CYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B TYR* 4.8 6.1 - - - -
350B TYR* 3.5 35.7 + - + -
354B VAL* 3.8 22.9 - - + -
355B ILE* 3.9 24.5 - - - -
358B ALA* 3.6 20.0 - - + -
386B SER 5.3 0.6 + - - +
387B LEU* 3.1 9.3 + - - +
389B PRO* 1.3 74.5 - - - +
391B LEU* 1.3 60.8 + - - +
393B ASP* 3.4 0.7 + - - +
394B LEU* 2.8 34.1 + - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA* 3.4 41.0 - - + +
361B HIS* 4.0 27.6 - - + -
362B LEU* 4.0 17.5 - - + -
384B LEU* 4.7 5.2 - - + -
387B LEU* 2.7 32.2 + - + +
388B LYS* 3.0 13.8 + - - +
390B CYS* 1.3 73.6 - - - +
392B MET* 1.3 64.6 + - + +
394B LEU* 4.7 0.2 - - - -
395B HIS* 2.8 26.4 + - - +
430B LEU* 3.8 20.0 - - + -
432B LEU* 4.4 10.1 - - + -
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Residues in contact with MET 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LYS* 2.6 59.0 + - + +
389B PRO* 3.7 7.6 - - + +
391B LEU* 1.3 75.5 - - + +
393B ASP* 1.3 66.5 + - - +
395B HIS* 3.3 6.4 + - + +
396B GLN* 3.1 25.2 + - + +
430B LEU* 4.6 10.8 - - + -
432B LEU* 4.2 18.8 - - + -
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO* 3.2 34.7 - - + +
347B TYR* 3.2 11.4 + - + +
349B LYS* 5.2 2.9 + - - -
350B TYR* 2.6 27.7 + - + +
389B PRO 3.4 6.0 + - - +
390B CYS 3.7 5.6 - - - +
391B LEU 3.3 0.8 - - - -
392B MET* 1.3 79.7 - - - +
394B LEU* 1.3 64.0 + - - +
396B GLN* 2.9 19.4 + - - +
397B THR* 3.0 11.3 + - - -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 3.5 34.3 - - + +
340B SER* 4.4 5.4 - - - +
347B TYR* 2.9 34.5 + - + +
355B ILE* 4.2 5.8 - - + +
358B ALA* 3.7 13.0 - - + +
359B ALA* 3.3 44.2 - - + +
362B LEU* 3.9 10.3 - - + -
390B CYS* 2.8 20.0 + - - +
391B LEU 4.0 2.2 - - - +
393B ASP* 1.3 69.5 - - - +
395B HIS* 1.3 58.0 + - - +
397B THR* 3.3 8.9 + - + -
398B TYR* 2.7 30.5 + - - +
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Residues in contact with HIS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 3.7 18.4 - - + +
391B LEU 2.8 19.5 + - - +
392B MET* 3.6 7.2 - - + +
394B LEU* 1.3 76.7 - - - +
396B GLN* 1.3 68.8 + - - +
398B TYR* 3.0 6.2 + - - +
399B LEU* 3.0 47.0 + - + +
426B PRO* 5.2 1.1 - - + -
427B PRO* 3.4 33.7 - - + -
428B GLU 3.9 11.5 + - - -
429B THR* 4.3 4.0 - - - -
430B LEU* 3.6 37.1 - - + +
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Residues in contact with GLN 396 (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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392B MET* 3.1 12.7 + - + +
393B ASP* 2.9 12.9 + - - +
395B HIS* 1.3 76.9 - - - +
397B THR* 1.3 63.0 + - - +
399B LEU* 3.1 25.7 + - - +
400B LYS* 3.0 57.8 + - - +
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Residues in contact with THR 397 (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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336B LEU* 6.4 0.2 - - + -
339B LEU* 4.0 32.5 - - + -
343B ASP* 4.7 15.7 + - - +
346B PRO* 5.4 1.2 - - - +
347B TYR* 3.0 33.0 + - + +
393B ASP 3.0 6.3 + - - -
394B LEU* 3.5 13.2 - - + -
396B GLN* 1.3 74.4 - - - +
398B TYR* 1.3 65.9 + - - +
400B LYS* 5.0 2.7 - - - -
401B ALA* 3.1 23.2 + - + +
404B HIS* 5.9 3.8 - - + -
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Residues in contact with TYR 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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332B LEU* 3.6 29.6 - - + +
335B PHE* 4.3 16.8 - + - -
336B LEU* 3.5 31.2 - - + +
339B LEU* 5.4 1.1 - - - -
362B LEU* 4.0 16.8 - - + -
366B THR* 3.9 12.7 - - - +
394B LEU 2.7 20.8 + - - +
395B HIS* 3.0 8.7 + - - +
397B THR* 1.3 76.4 - - - +
399B LEU* 1.3 63.0 + - - +
401B ALA* 3.3 15.5 + - + +
402B PRO* 4.2 2.1 - - - +
421B VAL 4.7 1.1 + - - -
422B SER 5.9 1.6 - - - -
424B LEU* 3.8 13.7 + - - +
425B ASN 4.0 0.2 - - - -
426B PRO* 3.3 49.8 - - + +
427B PRO* 3.7 10.8 - - + -
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B HIS* 3.0 38.2 + - + +
396B GLN* 3.1 33.2 + - - +
398B TYR* 1.3 77.4 - - - +
400B LYS* 1.3 63.1 + - + +
401B ALA 3.7 0.2 + - - -
402B PRO* 3.8 9.0 - - - +
403B GLN* 4.1 6.4 + - - +
426B PRO* 4.4 16.5 - - + +
427B PRO 3.9 18.2 - - - +
428B GLU* 4.8 8.3 - - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLN* 3.0 46.9 + - - +
397B THR* 3.9 3.1 - - - +
399B LEU* 1.3 77.0 - - + +
401B ALA* 1.3 65.9 + - - +
402B PRO* 3.2 2.9 - - - -
403B GLN* 2.6 37.8 + - + +
404B HIS* 3.3 10.6 + - + +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PHE* 4.8 3.1 - - + -
339B LEU* 4.3 22.7 - - + -
397B THR* 3.1 13.7 + - - +
398B TYR* 3.5 15.0 - - + +
400B LYS* 1.3 73.6 - - - +
402B PRO* 1.3 71.6 - - + +
403B GLN 3.0 1.4 + - - -
404B HIS* 3.2 12.6 + - - +
406B GLN 4.7 0.2 - - - +
407B GLN* 3.0 17.3 + - - -
410B ARG* 3.5 20.6 - - + +
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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
------------------------------------------------------------
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