Contacts of the helix formed by residues 158 - 167 (chain E) in PDB entry 2RCY
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 158 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ASN 4.8 0.9 - - - +
188A GLY* 4.0 19.7 - - - +
189A LEU* 3.7 23.0 - - + +
193A LEU* 5.6 1.4 - - - +
154E ILE* 3.7 11.0 - - + +
155E LYS* 3.1 34.5 + - - +
157E LYS* 1.3 98.4 + - - +
159E MSE 1.3 63.6 + - - +
160E ASP 3.3 2.9 - - - -
161E ILE* 3.3 11.0 - - - +
162E ALA* 3.1 24.1 + - - +
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Residues in contact with MSE 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E TRP* 3.4 60.1 - - + +
113E MSE 3.8 27.1 - - + +
126E ILE* 3.9 6.2 - - + +
127E TYR* 4.0 22.0 - - - -
128E CYS* 3.6 22.9 - - - -
154E ILE* 3.9 17.5 - - - -
155E LYS 3.5 6.9 + - - +
156E GLU 3.2 17.5 + - - +
158E ASP* 1.3 78.9 - - - +
160E ASP* 1.3 54.0 + - - +
162E ALA* 3.8 1.1 - - - +
163E THR* 2.6 38.6 + - - -
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Residues in contact with ASP 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 4.7 1.2 - - - +
95E ASN* 5.8 3.2 + - - -
111E TRP* 4.3 13.3 - - - -
156E GLU 4.6 5.0 - - - +
157E LYS* 4.1 8.9 - - - +
158E ASP 3.3 0.8 - - - -
159E MSE 1.3 76.2 - - - +
161E ILE* 1.3 59.3 + - - +
163E THR* 3.7 3.3 - - - -
164E ALA* 3.2 23.7 + - - +
254E CYS* 3.7 11.6 - - - +
257E SER* 2.7 43.3 + - - +
258E LYS* 3.4 44.4 - - + +
261E GLY* 5.8 0.2 - - - -
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Residues in contact with ILE 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA 3.6 13.0 - - - +
184A GLY* 4.0 8.7 - - - +
187A ASN* 3.5 46.4 - - + +
189A LEU* 3.8 17.3 - - + +
157E LYS 5.0 2.2 + - - +
158E ASP* 3.3 22.7 - - - +
160E ASP* 1.3 75.6 - - - +
162E ALA* 1.3 64.6 + - - +
164E ALA* 3.2 4.7 + - - +
165E ILE* 3.0 33.6 + - + +
250E VAL* 3.6 24.2 - - + -
254E CYS* 3.6 18.3 - - + -
258E LYS* 6.5 0.2 - - - -
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Residues in contact with ALA 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.4 7.9 - - + -
197A LEU* 4.0 18.8 - - + -
126E ILE* 3.7 27.6 - - + -
154E ILE* 3.7 11.4 - - + -
158E ASP 3.1 19.7 + - - +
159E MSE 3.9 1.6 - - - +
161E ILE* 1.3 78.2 - - - +
163E THR* 1.3 53.1 + - - +
165E ILE* 4.8 0.4 - - - -
166E SER* 2.6 40.4 + - - -
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Residues in contact with THR 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.8 29.2 - - + -
111E TRP* 4.9 2.3 - - - -
113E MSE 3.3 48.9 - - + +
126E ILE* 4.3 0.4 - - - +
159E MSE 2.6 28.3 + - - +
160E ASP* 3.7 6.9 - - - -
162E ALA* 1.3 76.8 - - - +
164E ALA* 1.3 56.4 + - - +
167E GLY* 2.9 7.7 + - - +
168E CYS* 2.9 34.4 + - - -
257E SER* 4.4 5.2 + - - +
264E NAP 6.0 0.2 - - + -
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Residues in contact with ALA 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 5.2 0.4 - - - +
160E ASP 3.2 11.8 + - - +
161E ILE 3.2 10.4 + - - +
163E THR* 1.3 78.8 - - - +
165E ILE* 1.3 58.8 + - - +
168E CYS* 3.4 17.0 - - - +
172E TYR* 3.1 28.2 + - - -
250E VAL* 3.3 34.5 - - + +
253E ALA* 3.9 4.0 - - + -
254E CYS* 3.6 13.2 - - + +
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Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.1 15.5 - - + +
184A GLY* 3.4 35.4 - - - +
189A LEU* 3.8 15.5 - - + -
194A SER* 4.8 4.5 - - - +
197A LEU* 4.4 15.9 - - + -
198A VAL* 3.8 30.1 - - + +
201A THR* 3.8 5.0 - - - +
161E ILE* 3.0 19.0 + - + +
162E ALA* 3.9 3.1 - - - +
164E ALA* 1.3 76.9 - - - +
166E SER* 1.3 59.5 + - - +
167E GLY 3.7 0.2 - - - -
169E GLY* 2.8 27.3 - - - -
172E TYR* 5.0 2.0 - - - -
250E VAL* 3.7 19.5 - - + -
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Residues in contact with SER 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 4.0 13.7 - - - -
201A THR* 3.5 8.9 + - - -
115E ASN* 3.1 25.4 + - - +
124E SER* 2.7 43.6 + - - -
126E ILE* 3.7 17.0 - - - +
162E ALA 2.6 20.1 + - - -
165E ILE* 1.3 73.0 - - - +
167E GLY* 1.3 61.7 + - - +
170E PRO* 3.4 7.3 - - - +
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Residues in contact with GLY 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ILE* 3.9 12.5 - - - +
230A THR* 4.6 1.1 - - - -
113E MSE 4.5 12.6 - - - +
114E PRO 3.6 20.9 - - - -
115E ASN* 4.1 5.4 - - - +
162E ALA 3.8 1.0 + - - -
163E THR* 2.9 13.4 + - - +
166E SER* 1.3 79.5 - - - +
168E CYS* 1.3 60.7 + - - +
170E PRO* 3.4 10.2 - - - +
264E NAP 4.2 10.6 + - - -
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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