Contacts of the helix formed by residues 113 - 120 (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 THR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.1 23.6 - - - +
99A ASP* 3.5 28.5 - - + +
100A PHE* 4.0 23.7 - - + -
106A ALA* 3.8 21.9 + - + +
111A ALA 3.8 1.2 + - - +
112A VAL* 1.3 79.9 - - - +
114A GLY* 1.3 60.9 + - - +
116A TYR* 3.1 5.7 + - - +
117A THR* 3.0 32.1 + - - +
157A THR* 5.9 2.4 - - - -
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Residues in contact with GLY 114 (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* 4.0 1.9 - - - +
96A GLU* 3.5 0.2 + - - -
112A VAL* 3.8 7.2 - - - +
113A THR* 1.3 79.3 + - - +
115A HIS* 1.3 63.6 + - - +
117A THR* 3.4 8.3 - - - -
118A GLN* 3.2 12.8 + - - +
152A ASN* 3.1 26.8 + - - -
157A THR* 6.4 0.7 - - - -
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Residues in contact with HIS 115 (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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60A HIS* 4.0 20.8 + - - -
75A GLU 4.7 1.3 - - - -
76A ASN* 3.0 43.0 + - + +
77A ILE* 4.1 14.0 + - + +
93A TRP* 3.8 30.6 - + + -
96A GLU* 2.8 35.6 + - - +
112A VAL* 4.3 12.4 - - + +
114A GLY* 1.3 71.9 - - - -
116A TYR* 1.3 63.8 + - - +
118A GLN 3.5 0.3 + - - -
119A ILE* 3.2 28.0 + - - +
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Residues in contact with TYR 116 (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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29A VAL* 4.2 14.7 - - + +
30A ASN 5.0 5.4 + - - -
93A TRP 3.6 13.8 + - - +
94A HIS* 3.5 46.2 - + - +
96A GLU* 3.0 18.6 + - + -
97A TYR* 3.5 26.5 - - + +
100A PHE* 3.6 36.0 - + + -
113A THR* 3.6 6.7 - - - +
115A HIS* 1.3 78.2 - - - +
117A THR* 1.3 73.7 + - + +
119A ILE* 3.0 15.1 + - - +
120A VAL* 3.1 40.4 + - + +
160A PRO* 5.1 0.2 - - + -
161A TYR* 4.5 8.8 + - - -
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Residues in contact with THR 117 (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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100A PHE* 3.6 23.3 - - + -
113A THR* 3.0 23.0 + - - +
114A GLY* 3.4 9.9 + - - -
116A TYR* 1.3 87.6 - - + +
118A GLN* 1.3 56.2 + - - +
120A VAL* 3.7 5.2 - - - -
121A TRP* 3.1 33.1 + - - +
152A ASN* 2.8 23.5 + - - -
157A THR* 3.5 28.1 - - - +
160A PRO* 3.9 10.3 - - + +
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Residues in contact with GLN 118 (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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39A MET* 4.4 2.6 - - - +
74A GLY* 3.4 23.6 - - - -
75A GLU 4.1 3.9 - - - +
76A ASN* 3.8 13.5 - - - +
114A GLY 3.2 19.3 + - - +
115A HIS 3.9 0.4 - - - +
116A TYR 3.1 0.6 - - - -
117A THR* 1.3 74.8 + - - +
119A ILE* 1.3 67.3 + - - +
120A VAL 3.3 0.3 + - - -
121A TRP* 3.3 10.5 + - - +
124A SER* 3.0 21.7 + - - -
147A TYR* 3.4 44.3 - - + +
151A GLY* 3.0 31.2 + - - +
152A ASN* 3.8 11.2 + - - +
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Residues in contact with ILE 119 (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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22A HIS* 3.9 20.0 - - + +
25A LEU* 4.2 20.9 - - + -
26A ARG* 2.9 24.9 + - - +
39A MET* 3.7 4.3 - - - +
76A ASN* 3.8 10.8 - - - +
90A ILE* 3.7 18.2 - - + +
93A TRP* 3.6 16.4 - - + -
94A HIS* 3.6 36.6 - - + +
115A HIS 3.2 11.4 + - - +
116A TYR* 3.0 9.1 + - - +
118A GLN* 1.3 77.3 - - - +
120A VAL* 1.3 68.9 + - + +
147A TYR* 3.9 10.3 - - - +
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Residues in contact with VAL 120 (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 4.4 9.0 - - - +
26A ARG* 3.5 13.0 - - + +
29A VAL* 3.6 27.6 - - + -
36A MET* 3.3 13.6 - - + +
94A HIS* 4.5 2.9 - - + -
116A TYR* 3.1 49.1 + - + +
117A THR* 4.1 2.7 - - - +
119A ILE* 1.3 90.9 - - + +
121A TRP* 1.3 62.3 + - - +
122A TYR 3.2 3.3 + - - -
160A PRO* 3.7 23.5 - - + +
161A TYR* 3.7 5.0 - - + -
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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