Contacts of the helix formed by residues 390 - 401 (chain B) in PDB entry 4YJ5
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 TYR 390 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLN* 5.1 0.2 - - - -
20B ALA 4.4 0.7 - - - -
21B ALA* 4.2 10.8 - - - +
23B ALA 2.6 30.6 + - - -
24B ASP 3.3 18.2 + - - -
25B THR* 3.3 6.5 + - - -
26B PHE* 3.8 31.8 - + + -
29B HIS* 3.5 39.7 + + + +
388B ALA 3.4 2.8 + - - -
389B ILE* 1.3 74.0 - - - +
391B TYR* 1.3 63.9 + - - +
392B LEU* 3.3 24.1 - - + +
393B GLN* 3.3 45.1 + - + -
394B LEU* 3.1 20.1 + - - +
400C ARG* 4.8 2.1 + - - -
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Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 5.8 3.9 + - + +
44B ASN* 4.5 6.8 + - - -
386B GLU* 3.1 35.2 + - - +
389B ILE* 3.0 49.2 + - + +
390B TYR* 1.3 71.0 - - - +
392B LEU* 1.3 63.8 + - - +
394B LEU* 4.2 11.7 - - + -
395B PHE* 2.8 30.2 + - + +
421B PHE* 3.8 24.7 - + + -
445B ARG* 3.5 29.6 - - + -
446B PRO 3.9 2.8 + - - -
447B ARG* 3.5 54.1 + - + +
467B ARG* 5.1 0.7 + - - -
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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
----------------------------------------------------------
21B ALA 4.1 15.3 + - - +
22B MET* 5.8 2.0 - - - -
23B ALA 4.0 7.9 - - - +
24B ASP* 5.2 1.8 - - - -
390B TYR* 3.8 30.7 - - + +
391B TYR* 1.3 76.9 - - - +
393B GLN* 1.3 61.7 + - - +
395B PHE* 4.5 2.2 - - - +
396B GLU* 3.5 19.4 + - - +
396C GLU* 5.4 0.9 - - - +
399C ARG* 5.2 13.9 + - - +
400C ARG* 3.4 57.8 + - + +
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Residues in contact with GLN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.4 14.9 - - + +
390A TYR* 5.1 0.2 - - - -
393A GLN* 2.9 43.4 + - - -
26B PHE* 4.3 3.1 - - - +
390B TYR* 3.3 36.3 + - + +
392B LEU* 1.3 77.8 - - + +
394B LEU* 1.3 61.1 + - - +
396B GLU* 3.4 8.3 + - - +
397B GLU* 2.7 65.9 + - + +
400C ARG* 5.7 2.5 - - - +
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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
----------------------------------------------------------
27A LEU* 5.3 10.3 - - + -
318B ASN* 5.3 10.1 - - - +
355B GLY* 6.5 0.9 - - - -
389B ILE* 3.9 25.6 - - + -
390B TYR 3.1 17.3 + - - +
391B TYR* 3.3 11.0 + - + +
393B GLN* 1.3 77.2 - - - +
395B PHE* 1.3 64.0 + - - +
397B GLU* 3.3 7.8 + - + +
398B LEU* 2.9 49.8 + - + +
445B ARG* 3.9 29.2 - - + +
467B ARG* 5.8 1.3 - - - +
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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
----------------------------------------------------------
391B TYR* 2.8 20.6 + - + +
392B LEU* 4.5 1.6 - - - +
394B LEU* 1.3 74.9 - - - +
396B GLU* 1.3 63.6 + - - +
398B LEU* 3.3 4.6 + - + -
399B ARG* 3.0 62.7 + - + +
414B VAL* 4.3 9.2 - - + -
417B VAL* 3.7 18.6 - - + -
418B GLU* 3.2 50.7 - - + -
421B PHE* 4.0 22.9 - + + -
444B TYR* 3.6 30.5 - + + +
445B ARG* 5.8 0.9 - - - +
399C ARG* 3.7 10.8 - - - +
418C GLU* 4.6 0.7 - - - -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 5.8 0.2 - - - +
392B LEU 3.5 17.1 + - - +
393B GLN* 3.4 8.7 + - - +
394B LEU 3.4 0.4 - - - -
395B PHE* 1.3 79.7 - - - +
397B GLU* 1.3 68.8 + - - +
399B ARG* 3.4 19.2 + - - +
400B ARG* 3.0 54.9 + - + +
396C GLU* 3.6 31.8 - - + +
399C ARG* 5.4 0.2 - - - +
400C ARG* 3.3 22.7 + - - -
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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
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25A THR* 3.4 22.1 - - + +
26A PHE* 2.8 23.4 + - - +
27A LEU* 2.9 37.4 + - + +
393B GLN* 2.7 57.2 + - + +
394B LEU* 3.9 7.0 - - + +
395B PHE 3.2 0.2 - - - -
396B GLU* 1.3 78.9 - - + +
398B LEU* 1.3 58.1 + - - +
400B ARG* 3.8 5.7 - - - +
401B LEU* 3.0 35.5 + - - +
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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
----------------------------------------------------------
27A LEU* 3.8 22.7 - - + -
318B ASN* 3.8 28.9 - - + +
319B ARG* 5.0 1.3 - - - -
394B LEU* 2.9 35.2 + - + +
395B PHE* 3.8 4.0 - - + +
397B GLU* 1.3 72.9 - - - +
399B ARG* 1.3 65.7 + - - +
401B LEU* 3.6 2.6 + - - +
402B ALA* 3.4 22.2 + - - +
443B ARG* 3.6 21.5 - - - +
444B TYR* 3.8 24.0 - - + +
445B ARG* 3.7 30.5 - - + -
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.0 43.4 + - + +
396B GLU* 3.4 24.8 - - - +
398B LEU* 1.3 70.6 - - - +
400B ARG* 1.3 69.8 + - - +
402B ALA* 2.9 22.4 + - - +
414B VAL* 4.3 8.5 - - + -
444B TYR* 4.8 4.8 - - + -
392C LEU* 5.3 4.2 + - - +
395C PHE* 4.1 16.4 - - - -
396C GLU* 2.9 42.0 + - - +
399C ARG* 3.2 30.0 - - - +
418C GLU* 3.2 29.7 + - - +
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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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24A ASP* 4.4 16.7 + - - +
25A THR* 4.0 15.7 - - + +
396B GLU* 3.0 45.2 + - + +
397B GLU* 3.8 4.5 - - - +
399B ARG* 1.3 78.4 - - - +
401B LEU* 1.3 66.6 + - + +
402B ALA 3.2 8.0 + - - +
24C ASP* 3.7 39.2 + - - +
390C TYR* 4.9 1.2 + - - -
392C LEU* 3.7 50.1 - - + +
396C GLU* 6.1 0.2 - - - -
400D ARG* 5.3 2.8 - - - +
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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
----------------------------------------------------------
24A ASP* 6.0 2.0 - - + +
25A THR* 3.6 34.3 - - + +
27A LEU* 4.1 18.8 - - + -
28A GLU* 3.9 35.0 - - + +
319B ARG* 4.4 29.0 - - + +
397B GLU 3.0 19.2 + - - +
398B LEU* 3.9 4.3 - - - +
399B ARG 2.9 0.6 + - - -
400B ARG* 1.3 81.0 - - + +
402B ALA* 1.3 57.8 + - - +
403B PRO* 4.2 2.6 - - - +
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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
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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