Contacts of the helix formed by residues 386 - 403 (chain B) in PDB entry 3H44
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 HIS 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TRP* 3.5 37.3 + + + +
382B GLU* 2.9 40.4 + - - +
383B GLY 2.8 10.3 + - - +
385B LEU* 1.3 89.6 - - + +
387B VAL* 1.3 62.4 + - - +
388B GLU* 3.6 1.6 - - - -
389B ASP* 2.8 32.6 + - - +
390B ILE* 3.1 21.1 + - - +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.2 12.3 - - + -
379B LEU* 3.9 28.9 - - + -
383B GLY 3.7 12.3 - - - +
384B LEU 3.9 10.1 + - - +
385B LEU 3.7 1.6 - - - -
386B HIS* 1.3 73.2 - - - +
388B GLU* 1.3 70.0 + - - +
389B ASP 3.0 0.2 + - - -
390B ILE* 3.0 6.1 + - - +
391B ILE* 3.0 40.6 + - + +
478B VAL* 5.1 1.3 - - + -
480B ILE* 3.8 31.6 - - + -
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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
----------------------------------------------------------
386B HIS 3.6 0.4 - - - -
387B VAL* 1.3 79.1 - - - +
389B ASP* 1.3 65.5 + - - +
391B ILE* 3.3 1.2 + - - +
392B LEU* 3.0 18.1 + - - +
508B GLU* 4.4 4.0 - - - +
509B VAL* 2.9 36.5 - - + +
512B LYS* 3.6 22.9 - - - +
513B TRP* 3.3 35.7 + - + +
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Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TRP* 3.7 19.6 - - + -
386B HIS* 2.8 39.4 + - - +
387B VAL 3.1 0.6 - - - -
388B GLU* 1.3 76.8 - - - +
390B ILE* 1.3 68.0 + - - +
392B LEU* 3.0 13.1 + - - +
393B HIS* 2.9 31.4 + - + -
512B LYS* 5.1 6.1 + - - -
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.0 16.4 - - + -
350B LEU* 3.9 29.6 - - + +
355B TRP* 3.7 34.8 - - + -
356B VAL* 4.1 7.4 - - + -
377B VAL* 4.4 0.7 - - + -
379B LEU* 3.4 31.9 - - + -
383B GLY* 3.5 17.0 - - - +
386B HIS 3.1 8.9 + - - +
387B VAL* 3.0 10.1 + - + +
389B ASP* 1.3 77.1 - - - +
391B ILE* 1.3 64.5 + - - +
393B HIS* 3.0 7.5 + - - +
394B MET* 3.0 29.2 + - + +
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Residues in contact with ILE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.0 7.9 - - + -
315B VAL* 3.8 24.5 - - + -
387B VAL* 3.0 26.3 + - + +
388B GLU 3.6 6.7 - - - +
390B ILE* 1.3 77.7 - - - +
392B LEU* 1.3 52.6 + - - +
394B MET* 2.8 31.2 + - - +
395B PHE* 3.1 32.1 + - + -
476B VAL* 5.8 1.1 - - + -
478B VAL* 3.6 36.8 - - + -
513B TRP* 3.3 35.0 - - + -
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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
----------------------------------------------------------
388B GLU 3.0 8.8 + - - +
389B ASP* 3.0 15.9 + - - +
391B ILE* 1.3 75.0 - - - +
393B HIS* 1.3 57.4 + - + +
395B PHE* 3.2 5.7 + - - +
396B GLN* 2.7 54.9 + - - +
512B LYS* 3.6 50.7 - - + +
513B TRP* 3.6 22.4 - - + +
516B ALA* 4.1 14.4 - - + -
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Residues in contact with HIS 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.2 13.5 - - + +
349B GLU* 3.9 25.4 - - + +
350B LEU* 3.8 19.1 - - + +
353B LYS* 4.4 16.3 + - + +
355B TRP* 4.0 19.3 - + - -
389B ASP* 2.9 26.2 + - + +
390B ILE 3.0 11.0 + - - +
392B LEU* 1.3 79.1 - - + +
394B MET* 1.3 66.0 + - - +
396B GLN* 3.6 18.2 + - - +
397B TYR 3.1 13.7 + - - -
519B ASN* 3.6 24.1 + - - -
522B PHE* 3.7 5.9 - - - -
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Residues in contact with MET 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.4 2.0 - - + -
315B VAL* 3.9 33.2 - - + -
346B LEU* 3.7 23.2 - - + +
350B LEU* 5.2 1.8 - - + -
375B ILE* 3.7 46.2 - - + +
377B VAL* 4.3 21.3 - - + -
390B ILE* 3.0 32.3 + - + +
391B ILE* 2.8 23.5 + - - +
393B HIS* 1.3 70.7 - - - +
395B PHE* 1.3 61.8 + - + +
397B TYR* 2.8 23.6 + - - +
398B ILE* 2.9 17.4 + - + +
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 5.7 0.9 - - + -
317B PHE* 3.6 32.3 - + - -
391B ILE* 3.1 38.7 + - + -
392B LEU* 3.6 5.6 - - - +
394B MET* 1.3 79.6 - - + +
396B GLN* 1.3 58.4 + - - +
398B ILE* 3.6 15.8 - - + +
399B GLN* 2.7 31.9 + - - +
402B ARG* 4.8 4.5 + - - +
471B LEU 4.1 4.7 - - - -
472B ARG* 3.8 4.0 - - - -
473B PRO* 3.5 41.5 - - + -
476B VAL* 4.1 8.7 - - + -
513B TRP* 3.7 35.0 - + + +
516B ALA* 4.1 14.5 - - + +
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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
----------------------------------------------------------
392B LEU* 2.7 46.3 + - - +
393B HIS* 3.6 22.4 + - - +
394B MET 3.2 0.2 + - - -
395B PHE* 1.3 72.7 - - - +
397B TYR* 1.3 63.2 + - - +
399B GLN* 3.1 5.9 + - - +
400B LYS* 3.0 19.9 + - - +
516B ALA* 3.9 8.2 - - + +
517B ASP* 3.1 35.0 + - - +
518B LEU* 5.2 2.2 + - - -
519B ASN* 3.2 32.8 + - + +
522B PHE* 4.0 11.2 - - + -
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.2 40.1 + - - +
338B ILE* 4.0 16.8 - - + -
340B HIS* 4.9 1.0 - - - +
344B GLY 4.1 11.0 - - - -
345B SER* 4.2 3.5 - - - -
346B LEU* 3.6 36.1 - - + -
393B HIS 3.1 9.1 + - - +
394B MET 2.8 14.0 + - - +
396B GLN* 1.3 74.4 - - - +
398B ILE* 1.3 65.3 + - + +
400B LYS* 3.0 18.6 + - + +
401B LEU* 3.2 38.2 + - + +
522B PHE* 3.5 32.2 - + + -
523B LYS 4.1 13.7 + - - -
524B LEU* 4.5 5.6 - - + +
525B PRO* 4.5 6.4 - - - +
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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
----------------------------------------------------------
317B PHE* 4.9 3.6 - - + -
338B ILE* 3.8 22.0 - - + -
375B ILE* 4.4 18.8 - - + -
394B MET* 2.9 23.8 + - + +
395B PHE* 3.7 28.3 - - + +
397B TYR* 1.3 74.1 - - - +
399B GLN* 1.3 57.4 + - - +
401B LEU* 3.0 11.7 + - - +
402B ARG* 2.9 59.6 + - - +
468B LEU* 3.9 15.3 - - + +
471B LEU* 4.0 22.4 - - + +
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Residues in contact with GLN 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE 2.7 13.3 + - - +
396B GLN* 3.1 10.3 + - - +
398B ILE* 1.3 74.5 - - - +
400B LYS* 1.3 66.5 + - - +
401B LEU 3.2 0.2 + - - -
402B ARG* 3.2 32.5 + - - +
403B ALA* 2.8 42.2 + - - +
472B ARG* 5.1 1.9 + - - -
514B GLN 5.7 3.3 - - - +
516B ALA* 3.4 25.4 - - + +
517B ASP 4.0 12.3 - - - +
518B LEU* 4.4 7.0 - - + +
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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
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396B GLN 3.0 11.0 + - - +
397B TYR* 3.0 15.7 + - + +
399B GLN* 1.3 76.0 - - - +
401B LEU* 1.3 65.1 + - + +
403B ALA* 3.2 7.6 + - - +
404B GLU* 3.1 53.1 + - - +
518B LEU* 3.6 26.7 - - + +
519B ASN 5.8 2.2 - - - +
522B PHE* 3.1 37.3 + - + +
523B LYS* 4.4 12.1 - - - +
524B LEU* 4.7 10.5 - - + +
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Residues in contact with LEU 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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333B TYR* 5.8 3.1 - - + +
334B LEU* 4.2 21.1 - - + -
337B LEU* 4.1 17.0 - - + -
338B ILE* 3.8 30.5 - - + -
397B TYR* 3.2 32.5 + - + +
398B ILE* 3.0 8.5 + - - +
400B LYS* 1.3 74.8 - - + +
402B ARG* 1.3 66.6 + - - +
404B GLU* 3.2 4.1 + - - +
405B GLY* 2.8 26.0 + - - -
468B LEU* 4.1 17.3 - - + +
524B LEU* 3.5 31.0 - - + -
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Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 4.8 5.7 + - - +
398B ILE* 2.9 33.3 + - - +
399B GLN* 3.4 39.8 + - - +
401B LEU* 1.3 75.2 - - - +
403B ALA* 1.3 58.3 + - - +
404B GLU 3.0 6.6 + - - -
405B GLY* 3.3 9.0 + - - -
465B GLU* 5.6 10.8 - - + +
468B LEU* 3.2 45.1 + - + +
469B ASP* 4.9 2.9 - - - +
471B LEU 3.5 15.2 + - - -
472B ARG* 3.4 47.4 - - - +
473B PRO* 5.9 1.4 - - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLN* 2.8 31.3 + - - +
400B LYS 3.5 4.9 - - - +
401B LEU 3.1 0.2 - - - -
402B ARG* 1.3 75.7 - - - +
404B GLU* 1.3 62.3 + - - +
518B LEU* 4.3 21.3 - - + -
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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