Contacts of the helix formed by residues 53 - 63 (chain B) in PDB entry 4Y2H
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 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PHE* 4.1 2.9 - - - -
229A CYS* 3.2 31.6 - - - +
230A LEU* 5.1 1.8 - - - +
49B GLU 4.6 1.1 + - - +
50B CYS 5.1 2.4 + - - +
51B TYR* 3.4 2.4 - - - +
52B SER* 1.3 82.6 + - - +
54B VAL* 1.3 65.1 + - - +
55B SER* 3.0 35.5 + - - -
56B VAL* 4.0 7.6 + - + +
57B HIS* 3.4 18.1 - - - -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TRP* 3.5 36.6 - - + +
225A PHE* 3.7 25.6 - - + -
226A ALA* 4.0 13.9 - - + -
229A CYS* 3.4 30.7 - - + -
230A LEU* 3.7 26.7 - - + -
53B ASP* 1.3 74.5 - - - +
55B SER* 1.3 63.3 + - - +
57B HIS* 3.2 7.7 + - + +
58B GLU* 2.9 30.0 + - - +
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Residues in contact with SER 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.0 30.1 + - - +
230A LEU* 3.8 9.2 - - - +
53B ASP* 3.0 18.0 + - - -
54B VAL* 1.3 77.5 - - - +
56B VAL* 1.3 53.5 + - - +
58B GLU* 3.3 4.9 + - - +
59B GLU* 2.8 36.0 + - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS 4.1 15.5 - - - +
51B TYR* 3.4 36.6 - - + -
53B ASP* 4.0 5.1 + - + +
54B VAL 3.4 0.2 - - - -
55B SER* 1.3 78.5 - - - +
57B HIS* 1.3 71.6 + - + +
59B GLU* 3.5 4.9 + - - +
60B MET* 3.1 33.2 + - + +
402B 49K 3.4 45.0 - - + +
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Residues in contact with HIS 57 (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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208A TRP* 4.1 8.3 - - + -
51B TYR* 2.8 28.3 + + - -
53B ASP 3.4 21.1 - - - -
54B VAL* 3.2 6.5 + - - +
56B VAL* 1.3 79.5 - - + +
58B GLU* 1.3 65.0 + - - +
60B MET* 3.0 25.5 + - + +
61B ILE* 2.9 30.1 + - + +
92B GLY* 3.9 23.7 - - - -
93B THR* 3.7 28.1 + - + +
116B ILE* 3.5 22.7 - - + +
401B SAH 4.0 11.3 + - - +
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Residues in contact with GLU 58 (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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204A ARG* 3.1 67.3 + - - +
207A PHE* 3.8 27.4 - - + +
208A TRP* 3.8 16.9 + - + -
230A LEU* 4.6 4.2 - - - +
54B VAL* 2.9 18.4 + - - +
55B SER* 3.4 10.1 - - - +
57B HIS* 1.3 75.2 - - - +
59B GLU* 1.3 58.2 + - - +
61B ILE 3.7 0.2 - - - -
62B ALA* 2.8 35.7 + - + +
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Residues in contact with GLU 59 (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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55B SER 2.8 19.8 + - - +
56B VAL* 3.7 7.2 - - - +
58B GLU* 1.3 74.5 - - - +
60B MET* 1.3 61.8 + - - +
62B ALA* 3.8 4.9 - - - +
63B ASP* 3.1 22.9 + - - +
159B TYR* 4.8 4.0 + - - -
317B HIS* 3.5 31.5 - - + +
319B LYS* 5.9 2.6 - - - -
402B 49K 2.9 27.2 + - - +
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Residues in contact with MET 60 (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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51B TYR* 3.9 11.9 - - + -
56B VAL* 3.1 22.9 + - + +
57B HIS* 3.0 32.8 + - - +
59B GLU* 1.3 75.7 - - - +
61B ILE* 1.3 59.0 + - + +
63B ASP* 3.3 12.3 + - - +
66B ARG* 2.9 35.2 + - - +
67B THR* 3.0 6.6 + - - -
155B GLU* 3.8 5.6 - - - +
317B HIS* 4.0 13.5 - - + +
401B SAH 3.5 43.5 - - + +
402B 49K 3.8 30.7 - - + -
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Residues in contact with ILE 61 (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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207A PHE* 3.9 20.6 - - + -
208A TRP* 3.8 21.3 - - + -
211A VAL* 4.3 11.4 - - + -
215A TYR* 2.8 50.2 + - + -
219A MET* 3.9 10.3 - - - -
57B HIS* 2.9 19.8 + - + +
60B MET* 1.3 71.4 - - - +
62B ALA* 1.3 60.3 + - - +
63B ASP 3.2 0.7 - - - -
66B ARG* 4.1 10.1 - - - +
67B THR* 3.7 6.1 - - + +
93B THR* 3.5 26.9 - - + +
95B ILE* 4.2 18.4 - - + -
401B SAH 4.6 3.4 - - - +
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Residues in contact with ALA 62 (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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207A PHE* 3.6 22.6 - - + -
58B GLU* 2.8 25.7 + - + +
59B GLU* 3.8 6.1 - - - +
61B ILE* 1.3 70.0 - - - +
63B ASP* 1.3 58.0 + - - +
64B ARG* 2.9 18.2 + - - +
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Residues in contact with ASP 63 (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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215A TYR* 4.0 1.1 - - - -
59B GLU 3.1 13.7 + - - +
60B MET 3.4 11.7 - - - +
61B ILE 3.2 1.0 - - - -
62B ALA* 1.3 73.0 - - - +
64B ARG* 1.3 58.6 + - - +
65B VAL* 3.4 10.0 + - - +
66B ARG* 3.0 26.1 + - + +
67B THR* 2.9 31.5 + - - -
315B ALA 4.5 1.0 - - - +
316B THR* 3.5 10.5 - - - -
317B HIS* 2.8 49.2 + - + +
318B TRP* 4.1 0.5 - - - -
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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