Contacts of the helix formed by residues 85 - 95 (chain A) in PDB entry 1RC9
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A VAL* 3.9 25.9 - - + +
7A GLU* 3.5 23.8 - - - +
17A GLU* 5.0 8.1 + - - +
84A MET* 1.3 75.1 - - - +
86A TRP* 1.3 66.4 + - - +
87A THR* 4.2 15.7 + - - +
88A ASP* 3.1 34.6 + - - +
89A ILE* 3.2 13.5 + - - +
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Residues in contact with TRP 86 (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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7A GLU* 2.8 44.7 + - + +
9A PRO* 3.8 22.8 - - + +
14A ILE* 3.5 18.3 - - + +
17A GLU* 4.4 7.1 + - + +
18A ILE* 3.7 31.4 - - + -
84A MET 5.2 1.3 - - - -
85A LYS* 1.3 71.6 - - - +
87A THR* 1.3 62.4 + - - +
89A ILE* 3.2 16.3 + - + +
90A ILE* 2.9 36.0 + - + +
93A TRP* 4.4 7.2 - + - -
129A CYS* 3.7 12.1 - - + -
130A ALA 3.6 24.9 - - - -
131A ALA* 4.1 1.3 - - + +
143A PHE* 3.8 35.7 - + + -
144A VAL 4.3 1.6 - - - -
145A CYS* 3.4 24.2 - - - -
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Residues in contact with THR 87 (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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17A GLU* 2.7 31.1 + - - +
21A LEU* 3.5 20.1 - - + +
85A LYS* 3.1 13.3 + - - -
86A TRP* 1.3 78.8 - - - +
88A ASP* 1.3 65.8 + - - +
90A ILE* 5.0 0.2 - - - -
91A HIS* 3.0 48.5 + - + +
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Residues in contact with ASP 88 (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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84A MET* 3.9 18.6 - - + +
85A LYS* 3.1 35.0 + - - +
87A THR* 1.3 84.5 - - - +
89A ILE* 1.3 64.5 + - - +
91A HIS* 3.4 6.7 + - - +
92A ALA* 2.9 24.3 + - - +
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Residues in contact with ILE 89 (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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78A TYR* 3.8 18.4 - - + -
84A MET* 4.0 21.1 - - + +
85A LYS 3.2 16.3 + - - +
86A TRP* 3.6 23.6 - - + +
88A ASP* 1.3 75.7 - - - +
90A ILE* 1.3 65.1 + - - +
92A ALA* 3.1 8.5 + - - +
93A TRP* 3.0 57.1 + - + -
143A PHE* 3.4 47.1 - - + -
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Residues in contact with ILE 90 (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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17A GLU* 6.3 0.2 - - + -
18A ILE* 4.0 33.0 - - + +
21A LEU* 3.6 26.7 - - + -
22A HIS* 3.5 38.4 - - + +
25A LEU* 3.7 20.0 - - + -
86A TRP* 2.9 27.4 + - + +
89A ILE* 1.3 75.1 - - - +
91A HIS* 1.3 57.2 + - - +
93A TRP* 3.2 21.6 + - + +
94A HIS* 2.9 26.5 + - - +
119A ILE* 3.7 6.9 - - + +
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Residues in contact with HIS 91 (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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21A LEU* 3.8 18.4 - - + +
25A LEU* 4.1 25.7 - - + +
87A THR* 3.0 43.2 + - + +
88A ASP* 3.9 8.7 - - - +
89A ILE 3.3 0.2 - - - -
90A ILE* 1.3 76.5 - - - +
92A ALA* 1.3 57.6 + - - +
94A HIS* 3.8 8.2 + - - +
95A ASP* 2.8 45.6 + - - +
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Residues in contact with ALA 92 (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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78A TYR* 3.8 28.9 - - + +
84A MET* 5.7 0.4 - - + -
88A ASP 2.9 14.3 + - - +
89A ILE* 3.1 9.6 + - - +
91A HIS* 1.3 78.6 - - - +
93A TRP* 1.3 64.0 + - - +
95A ASP* 3.5 18.1 + - - +
96A GLU* 4.2 6.1 + - - +
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Residues in contact with TRP 93 (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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76A ASN* 3.6 34.8 - - + -
77A ILE* 2.8 39.4 + - - +
78A TYR* 3.8 16.6 - + + -
86A TRP* 4.4 4.3 - + - -
89A ILE* 3.0 35.1 + - + -
90A ILE* 3.5 28.3 - - + +
92A ALA* 1.3 78.5 - - - +
94A HIS* 1.3 61.3 + - - +
96A GLU* 3.2 26.7 - - - +
115A HIS* 3.8 28.5 - + + +
116A TYR 3.6 6.9 + - - -
119A ILE* 3.6 12.6 - - + -
143A PHE 4.7 2.2 - - - -
144A VAL 5.1 0.4 - - - -
145A CYS* 3.9 26.7 - - + -
147A TYR* 3.7 17.7 - - - -
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Residues in contact with HIS 94 (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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25A LEU* 3.7 52.3 + - + +
28A SER* 6.1 3.0 - - - -
29A VAL* 5.9 1.4 - - - +
90A ILE 2.9 17.3 + - - +
91A HIS* 3.8 9.5 + - - +
93A TRP* 1.3 73.1 - - - +
95A ASP* 1.3 59.4 + - - +
96A GLU 2.8 12.7 + - - -
97A TYR* 3.0 49.9 + + - +
116A TYR* 3.5 32.3 - + - -
119A ILE* 3.6 17.9 - - + +
120A VAL* 4.5 1.9 - - + +
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Residues in contact with ASP 95 (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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91A HIS* 2.8 36.1 + - - +
92A ALA* 3.7 10.7 - - - +
93A TRP 3.3 1.0 - - - -
94A HIS* 1.3 73.2 + - - +
96A GLU* 1.3 59.2 + - - +
97A TYR* 2.9 22.6 + - - -
98A LYS* 3.2 41.0 + - + +
99A ASP* 5.3 0.7 - - - +
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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