Contacts of the helix formed by residues 84 - 89 (chain X) in PDB entry 2RAX
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 CYS 84 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57X CYS* 4.0 0.2 - - - -
59X PHE* 3.9 6.7 - - - -
60X CYS* 3.5 24.5 - - - -
77X HIS* 3.7 4.9 - - + +
81X SER* 3.5 14.9 + - - +
82X SER 3.2 7.0 - - - +
83X GLY* 1.3 78.2 - - - +
85X ALA* 1.3 63.6 + - - +
86X PHE* 3.4 24.0 + - - -
87X LEU* 3.6 18.1 + - + +
88X SER* 4.4 4.2 + - - -
111X ASN* 5.8 0.7 - - - +
341X ZN 2.3 36.8 - - - -
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Residues in contact with ALA 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 3.5 27.0 - - + -
83X GLY 3.7 4.0 + - - +
84X CYS* 1.3 72.1 - - - +
86X PHE* 1.3 62.8 + - - +
87X LEU 3.2 2.2 - - - -
88X SER* 3.4 25.1 + - - +
89X VAL* 4.1 4.2 + - - +
104X LEU* 4.3 17.7 - - + +
107X GLU* 4.8 12.1 - - + -
111X ASN* 5.6 1.4 - - - +
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Residues in contact with PHE 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X ARG* 4.2 9.2 - - - -
40X GLU 3.7 20.0 - - - -
41X ALA* 3.3 33.2 - - - -
42X GLY* 3.8 3.4 - - - -
57X CYS* 5.5 0.2 - - - -
58X PHE* 3.8 27.6 - + - -
59X PHE* 3.9 13.4 - - + -
74X ILE* 4.9 7.2 - - + -
77X HIS* 4.9 1.1 - + - -
84X CYS* 3.3 19.3 - - - -
85X ALA* 1.3 77.5 - - - +
87X LEU* 1.3 70.2 + - + +
88X SER 3.2 0.8 + - - -
89X VAL* 3.1 27.5 - - + +
92X GLN* 5.0 5.6 - - - -
93X PHE* 3.3 42.8 - + - -
341X ZN 4.5 1.3 - - - -
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X ILE* 4.8 11.2 - - + +
77X HIS* 3.6 49.8 - - + +
78X LYS* 4.1 27.1 - - + +
81X SER 4.4 5.8 - - - +
82X SER* 4.9 5.8 - - - +
84X CYS* 3.6 14.8 + - - +
85X ALA 3.2 1.0 - - - -
86X PHE* 1.3 99.7 - - + +
88X SER* 1.3 61.0 + - - +
89X VAL 3.5 3.9 - - - +
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Residues in contact with SER 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X CYS 4.4 2.6 + - - -
85X ALA* 3.5 22.3 + - - +
86X PHE 3.2 0.8 - - - -
87X LEU* 1.3 79.9 - - - +
89X VAL* 1.3 64.6 + - - +
90X LYS* 3.3 13.2 + - - +
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Residues in contact with VAL 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 5.0 2.3 + - - -
85X ALA 4.5 8.3 - - - +
86X PHE* 3.1 21.6 - - + +
87X LEU 4.7 2.8 - - - +
88X SER* 1.3 77.5 + - - +
90X LYS* 1.3 62.2 + - - +
91X LYS* 3.6 24.1 - - + +
92X GLN* 5.7 0.2 - - - -
93X PHE* 3.7 25.6 - - + -
96X LEU* 4.8 9.6 - - + -
104X LEU* 4.0 28.7 - - + -
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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