Contacts of the helix formed by residues 334 - 346 (chain B) in PDB entry 4DJH
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 ASP 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B MET* 4.9 1.0 - - - +
95B ASN* 4.9 3.3 + - - +
271B ARG* 4.6 6.2 - - - +
272B ILE* 4.3 19.3 - - - +
275B LEU* 4.3 13.0 - - + -
330B TYR 3.0 14.6 + - - +
331B ALA 3.4 9.0 - - - +
332B PHE 3.5 1.2 - - - -
333B LEU* 1.3 81.7 - - - +
335B GLU* 1.3 69.3 + - - +
336B ASN* 3.6 17.5 + - - +
337B PHE* 3.0 37.9 + - + -
338B LYS* 3.1 18.3 + - - -
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Residues in contact with GLU 335 (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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271B ARG* 5.0 14.3 - - + +
333B LEU 4.3 0.4 - - - -
334B ASP* 1.3 74.6 + - - +
336B ASN* 1.3 62.5 + - - +
338B LYS* 3.5 13.6 + - + +
339B ARG* 2.8 37.3 + - - +
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Residues in contact with ASN 336 (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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89B LYS* 4.9 13.7 + - - +
90B MET* 4.0 23.6 - - + -
95B ASN* 6.0 0.4 - - - +
334B ASP* 3.2 16.8 + - - +
335B GLU* 1.3 79.7 - - - +
337B PHE* 1.3 67.5 + - - +
339B ARG* 2.9 15.3 + - - +
340B CYS* 2.8 25.3 + - - +
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Residues in contact with PHE 337 (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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80B VAL* 4.2 10.1 - - + -
83B VAL* 4.6 5.4 - - + -
84B ILE* 4.0 15.0 - - + -
90B MET* 3.4 22.4 - - + +
95B ASN* 3.3 28.5 - - - -
98B ILE* 3.6 31.9 - - + -
275B LEU* 4.9 1.8 - - + -
330B TYR* 3.6 30.3 - + + +
334B ASP* 3.0 34.2 + - + +
336B ASN* 1.3 76.7 - - - +
338B LYS* 1.3 65.2 + - - +
340B CYS* 2.9 4.3 + - - +
341B PHE* 2.8 58.5 + + + -
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Residues in contact with LYS 338 (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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345A CYS 5.6 0.7 - - - -
346A PHE* 3.9 28.3 - - + +
347A PRO* 4.3 38.3 - - - +
331B ALA* 3.2 29.5 + - - +
332B PHE* 4.5 17.8 + - - +
334B ASP 3.1 10.5 + - - +
335B GLU* 3.5 11.2 - - - +
337B PHE* 1.3 79.3 - - - +
339B ARG* 1.3 62.3 + - - +
341B PHE* 3.9 7.8 - - - +
342B ARG* 3.3 20.8 + - - +
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Residues in contact with ARG 339 (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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335B GLU* 2.8 24.5 + - - +
336B ASN* 2.9 15.2 + - - +
338B LYS* 1.3 78.8 - - - +
340B CYS* 1.3 64.7 + - + +
342B ARG* 3.2 34.0 - - - +
343B ASP* 3.2 23.8 - - - +
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Residues in contact with CYS 340 (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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83B VAL* 3.6 25.2 - - + +
87B TYR* 4.1 36.1 + - + -
90B MET* 4.2 17.9 - - - -
336B ASN 2.8 18.7 + - - +
337B PHE 3.9 2.0 - - - +
339B ARG* 1.3 73.9 - - - +
341B PHE* 1.3 67.2 + - - +
343B ASP* 3.5 8.2 + - - +
344B PHE* 3.1 23.6 + - - +
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Residues in contact with PHE 341 (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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346A PHE* 3.7 22.9 - + + -
76B GLY 5.3 0.7 - - - -
79B LEU* 3.7 35.7 - - + -
80B VAL* 3.8 29.6 - - + -
83B VAL* 4.1 12.8 - - + -
327B PRO* 4.0 8.3 - - + -
330B TYR* 4.6 1.1 - - + -
331B ALA* 3.7 35.7 - - + -
337B PHE* 2.8 46.2 + + + +
338B LYS* 3.9 2.9 - - - +
340B CYS* 1.3 74.8 - - - +
342B ARG* 1.3 64.8 + - - +
344B PHE* 3.1 5.4 + - - +
345B CYS* 2.8 27.5 + - - +
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Residues in contact with ARG 342 (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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342A ARG* 4.5 20.9 - - + +
346A PHE* 3.6 42.6 - - + -
338B LYS* 3.3 10.5 + - - +
339B ARG* 3.2 34.1 + - - +
341B PHE* 1.3 78.7 - - - +
343B ASP* 1.3 83.0 + - - +
346B PHE* 2.7 43.3 + - + +
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Residues in contact with ASP 343 (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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87B TYR* 4.9 15.0 - - + +
339B ARG* 3.2 11.8 + - - +
340B CYS* 3.9 9.8 - - - +
341B PHE 3.3 0.2 - - - -
342B ARG* 1.3 109.9 + - - +
344B PHE* 1.3 62.3 + - - +
346B PHE 4.5 4.5 - - - -
347B PRO* 3.3 26.8 - - - +
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Residues in contact with PHE 344 (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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79B LEU* 3.1 34.3 - - + -
82B PHE* 3.3 48.2 - + + -
83B VAL* 4.9 5.2 - - + -
87B TYR* 5.3 9.4 + + + +
340B CYS 3.1 15.3 + - - +
341B PHE* 3.1 4.8 + - - +
343B ASP* 1.3 81.3 - - - +
345B CYS* 1.3 70.1 + - - +
347B PRO* 3.8 7.6 - - - +
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Residues in contact with CYS 345 (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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332A PHE* 4.3 14.4 - - - -
346A PHE* 4.5 12.6 - - + -
79B LEU* 4.3 21.1 - - - -
341B PHE 2.8 20.1 + - - +
342B ARG 4.1 0.2 - - - +
344B PHE* 1.3 82.9 - - - +
346B PHE* 1.3 92.8 + - + +
347B PRO* 3.5 6.2 - - - +
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Residues in contact with PHE 346 (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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331A ALA* 4.6 11.9 - - + -
332A PHE* 5.5 2.0 - + - -
338A LYS* 3.6 34.4 - - + +
341A PHE* 3.8 39.5 - + + -
342A ARG* 3.9 26.0 - - + +
345A CYS* 4.7 7.4 - - + -
346A PHE* 4.5 18.2 - + - -
342B ARG* 2.7 28.6 + - - +
343B ASP* 4.5 0.9 - - - -
345B CYS* 1.3 108.1 - - + +
347B PRO* 1.3 66.1 - - - +
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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