Contacts of the helix formed by residues 390 - 403 (chain B) in PDB entry 2D2O
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 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B GLU* 5.1 4.0 - - - -
383B PHE* 3.6 3.1 - - - -
389B ILE* 1.3 77.9 - - - +
391B ALA* 1.3 60.7 + - - +
392B GLU* 3.2 18.3 + - + -
393B ARG* 3.1 42.4 + - + +
394B PHE* 2.9 26.7 + - - +
512B LYS* 3.4 51.5 - - + +
515B ASN* 3.2 14.1 - - - +
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Residues in contact with ALA 391 (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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383B PHE* 3.4 14.3 - - + -
390B HIS* 1.3 72.7 - - - +
392B GLU* 1.3 57.8 + - - +
394B PHE* 3.3 2.5 + - - +
395B ASP* 2.9 28.8 + - - +
510B ALA* 4.0 3.5 - - - +
511B ASP 3.6 17.7 - - - +
512B LYS* 4.5 0.2 - - - +
515B ASN* 2.7 21.3 + - - +
516B LEU 3.3 28.5 - - - +
517B TYR* 4.0 9.1 - - + -
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 5.0 1.8 - - - +
390B HIS* 3.2 12.9 + - + -
391B ALA* 1.3 73.7 - - - +
393B ARG* 1.3 65.3 + - - +
395B ASP* 3.5 2.8 + - - +
396B ALA* 3.1 22.5 + - - +
510B ALA* 3.4 30.8 - - + +
511B ASP* 3.8 2.3 - - - +
512B LYS* 3.1 49.3 + - - +
513B GLN* 4.9 3.5 + - - -
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 4.1 27.9 + - - +
100A GLY* 5.6 1.6 - - - -
101A PHE 5.8 1.4 + - - -
107A LYS 5.2 2.0 + - - -
64B GLU* 3.0 38.3 + - - +
382B ARG* 4.8 1.6 - - - +
389B ILE* 3.7 29.2 - - + +
390B HIS* 3.1 28.8 + - + +
392B GLU* 1.3 73.9 - - - +
394B PHE* 1.3 65.9 + - - +
396B ALA* 3.3 2.9 + - - +
397B GLU* 3.0 52.7 + - - +
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B SER* 3.5 32.3 - - - -
380B VAL* 4.1 2.7 - - + -
383B PHE* 3.3 48.7 - + + -
384B PHE* 3.8 13.5 - + - -
389B ILE* 3.9 8.9 - - + +
390B HIS 2.9 14.3 + - - +
391B ALA 3.3 7.6 - - - +
392B GLU 3.2 0.2 - - - -
393B ARG* 1.3 74.0 - - - +
395B ASP* 1.3 65.7 + - - +
397B GLU* 3.2 4.0 + - - +
398B LEU* 3.0 53.7 + - + +
442B PHE* 3.6 25.6 - + - -
517B TYR* 3.9 25.1 - + - -
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Residues in contact with ASP 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER 4.8 6.1 - - - +
391B ALA 2.9 17.5 + - - +
392B GLU* 3.6 5.6 - - - +
394B PHE* 1.3 75.6 - - - +
396B ALA* 1.3 56.5 + - - +
398B LEU* 3.5 4.6 + - - +
399B THR* 2.8 41.3 + - - -
507B SER* 2.5 35.8 + - - -
510B ALA* 3.7 19.3 - - + +
517B TYR* 3.7 25.6 + - + -
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Residues in contact with ALA 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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62B SER 4.5 0.4 - - - -
63B ASP* 3.6 16.8 - - + +
64B GLU* 3.5 42.0 - - + +
392B GLU 3.1 14.5 + - - +
393B ARG* 3.5 9.9 - - - +
394B PHE 3.1 0.2 - - - -
395B ASP* 1.3 73.6 - - - +
397B GLU* 1.3 60.2 + - - +
399B THR 3.3 0.5 + - - -
400B ARG* 2.9 32.5 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 5.8 2.0 - - - +
378B GLU* 5.8 0.2 - - - +
379B SER* 2.7 37.1 + - - +
382B ARG* 3.0 36.4 + - - -
389B ILE* 3.8 10.4 - - - +
393B ARG* 3.0 58.1 + - - +
394B PHE 3.2 3.8 + - - +
396B ALA* 1.3 75.6 - - - +
398B LEU* 1.3 64.3 + - - +
400B ARG* 3.6 7.9 + - - +
401B ALA* 3.0 24.9 + - - +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PHE* 5.5 9.0 - - + +
379B SER* 3.7 28.5 - - - +
394B PHE* 3.0 53.2 + - + +
395B ASP* 3.7 4.5 - - - +
397B GLU* 1.3 75.8 - - - +
399B THR* 1.3 58.8 + - - +
401B ALA* 3.2 7.3 + - + +
402B ARG* 2.9 29.8 + - - +
442B PHE* 3.7 15.3 - - + -
446B TYR* 3.6 30.5 + - + +
517B TYR* 3.9 19.3 - - + +
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Residues in contact with THR 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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61B GLY* 4.1 10.7 - - - -
62B SER 3.5 40.1 + - - +
68B TYR* 4.2 12.1 - - + -
395B ASP* 2.8 33.4 + - - -
396B ALA 3.3 2.9 + - - -
398B LEU* 1.3 76.4 - - - +
400B ARG* 1.3 62.0 - - - +
402B ARG* 3.1 23.7 + - - +
403B MET* 3.1 24.7 + - + +
507B SER* 3.9 5.9 + - - -
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Residues in contact with ARG 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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96A PHE* 4.9 9.3 - - - -
97A GLY 4.4 3.2 + - - -
98A GLU* 3.1 22.3 + - - +
99A THR* 2.5 30.5 + - - +
100A GLY* 4.1 10.7 - - - -
101A PHE* 5.9 1.8 - - - -
111A PHE* 5.9 1.8 - - - -
63B ASP* 4.0 18.3 + - + +
68B TYR* 4.2 15.3 - - - +
396B ALA 2.9 18.1 + - - +
397B GLU* 3.9 7.6 - - - +
399B THR* 1.3 76.6 - - - +
401B ALA* 1.3 62.0 + - - +
403B MET* 3.4 11.2 + - - +
404B LEU* 3.4 27.2 + - + +
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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
----------------------------------------------------------
373B ASN* 6.1 0.9 - - - +
375B LEU* 4.7 23.8 - - + -
376B PHE* 6.1 0.7 - - - +
397B GLU 3.0 19.7 + - - +
398B LEU* 3.5 7.0 - - + +
399B THR 3.2 0.2 - - - -
400B ARG* 1.3 75.3 - - - +
402B ARG* 1.3 64.0 + - - +
404B LEU* 3.0 30.3 + - - +
405B TYR* 4.2 9.8 + - + -
413B LEU* 5.9 1.3 - - - +
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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
----------------------------------------------------------
26B ARG* 4.0 6.3 + - - +
60B ALA* 3.2 25.9 + - - +
61B GLY* 4.3 2.0 - - - -
70B GLU* 6.3 0.2 - - - -
398B LEU 2.9 13.1 + - - +
399B THR* 3.1 32.9 + - - +
401B ALA* 1.3 75.5 - - - +
403B MET* 1.3 87.7 + - + +
404B LEU 3.4 0.9 + - - -
405B TYR* 3.5 15.9 + - - +
410B ALA* 4.5 15.3 - - + +
413B LEU* 6.4 1.1 - - - -
446B TYR* 4.7 8.4 + - - +
447B LEU* 4.0 16.4 - - + -
505B VAL* 3.4 39.2 + - - +
506B ARG* 3.7 22.4 - - - +
507B SER* 5.0 4.9 + - - +
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Residues in contact with MET 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.2 14.0 + - - -
14B TYR* 4.3 12.7 - - + +
26B ARG* 3.6 43.1 + - - +
60B ALA* 4.8 8.5 - - + +
68B TYR* 3.5 55.9 - - + -
70B GLU* 4.6 4.5 - - - +
399B THR* 3.1 17.5 + - + +
400B ARG 3.8 6.1 - - - +
401B ALA 3.2 0.4 - - - -
402B ARG* 1.3 117.8 - - + +
404B LEU* 1.3 63.5 + - - +
405B TYR 3.3 0.8 + - - -
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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
------------------------------------------------------------
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