Contacts of the helix formed by residues 255 - 260 (chain A) in PDB entry 4ACR
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 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.9 3.1 - - + -
42A LYS* 2.6 25.3 + - - -
77A LEU* 3.4 44.7 - - + +
80A ARG* 3.6 22.7 - - + -
81A SER* 4.1 10.1 - - - -
84A GLU* 2.4 32.6 + - - -
251A MET* 3.3 21.0 + - - +
254A VAL* 1.3 88.5 - - + +
256A CYS* 1.3 62.7 - - - +
257A ALA 3.2 2.5 - - - -
258A HIS* 3.4 41.7 + + - +
259A CYS* 3.6 15.9 + - - -
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Residues in contact with CYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.2 1.6 - - - -
62A CYS* 2.0 59.5 - - + -
63A PRO* 5.0 1.3 - - + -
251A MET* 3.1 21.6 + - - +
252A LYS* 3.5 31.6 - - + +
254A VAL 3.4 1.2 - - - -
255A TYR* 1.3 76.1 - - - +
257A ALA* 1.3 64.3 + - - +
259A CYS* 3.4 1.0 + - - +
260A LEU* 3.1 28.8 + - - +
416A TRP* 3.6 11.1 - - + -
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL 4.0 11.2 + - - +
255A TYR 3.2 0.4 - - - -
256A CYS* 1.3 78.7 - - - +
258A HIS* 1.3 63.9 + - + +
260A LEU 3.4 0.5 + - - -
261A GLY 3.4 4.0 + - - -
262A VAL* 2.9 46.0 + - - +
265A ALA 4.7 8.3 - - - +
416A TRP* 3.5 45.6 - - + +
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Residues in contact with HIS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.3 34.0 - - + +
38A ILE* 3.6 41.7 - - + +
68A CYS* 5.0 0.3 - - - +
69A CYS* 4.4 2.7 - - - -
77A LEU* 5.5 4.9 - - + -
254A VAL* 3.7 10.6 + - + -
255A TYR* 3.6 46.0 - + + +
257A ALA* 1.3 80.2 - - + +
259A CYS* 1.3 62.4 + - - +
260A LEU 3.4 0.3 + - - -
261A GLY* 3.5 8.1 + - - -
262A VAL 4.4 0.2 + - - -
263A PRO* 3.4 32.3 + - + -
265A ALA 5.6 2.5 - - - -
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Residues in contact with CYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 5.0 2.0 - - + -
62A CYS* 4.3 19.3 - - - -
67A THR* 2.5 35.5 + - - +
68A CYS* 3.1 6.2 + - - +
69A CYS* 2.0 52.7 - - + -
74A GLU* 5.1 3.4 - - - -
77A LEU* 3.6 20.0 - - - -
251A MET* 4.5 2.0 - - - -
255A TYR 3.6 5.5 + - - +
256A CYS 3.4 7.7 + - - +
257A ALA 3.3 0.2 - - - -
258A HIS* 1.3 81.3 - - - +
260A LEU* 1.3 60.7 + - + +
261A GLY* 3.2 4.1 + - - -
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 5.3 1.1 - - - +
59A LEU* 4.8 3.6 - - + -
62A CYS* 4.0 17.3 - - + -
63A PRO* 3.7 37.5 - - + +
65A GLY* 5.5 6.3 - - - +
66A TYR 4.3 15.4 - - - +
67A THR* 4.7 6.1 - - - +
256A CYS 3.1 18.7 + - - +
257A ALA 3.4 2.0 + - - +
258A HIS 3.3 0.6 - - - -
259A CYS* 1.3 81.0 - - + +
261A GLY* 1.3 58.3 + - - +
262A VAL* 3.6 5.3 + - + +
416A TRP* 3.7 21.3 - - + -
419A MET 3.6 24.7 - - - +
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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