Contacts of the helix formed by residues 158 - 167 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D ILE* 3.6 13.9 - - + +
155D LYS* 3.3 30.2 + - + +
156D GLU 3.1 1.2 - - - -
157D LYS* 1.3 102.1 + - - +
159D MSE 1.3 58.7 + - - +
160D ASP 3.3 2.9 - - - -
161D ILE* 3.3 16.6 - - + +
162D ALA* 3.0 28.9 + - - +
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Residues in contact with MSE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D TRP* 3.4 65.3 - - + +
113D MSE 3.8 26.2 - - + -
126D ILE* 3.9 13.9 - - + +
127D TYR 4.1 2.7 - - - -
128D CYS* 3.6 27.1 - - - -
154D ILE* 3.8 23.8 - - - -
155D LYS 3.7 5.8 - - - +
156D GLU 3.1 19.6 + - - +
158D ASP* 1.3 78.1 - - - +
160D ASP* 1.3 55.0 + - - +
162D ALA* 3.8 1.3 - - - +
163D THR* 2.6 39.4 + - - +
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLY 4.6 1.4 - - - +
95D ASN* 5.8 2.3 + - - -
111D TRP* 4.2 14.0 - - - -
156D GLU 4.8 4.3 - - - +
157D LYS* 4.2 8.4 + - - +
158D ASP 3.3 0.4 - - - -
159D MSE 1.3 76.4 - - - +
161D ILE* 1.3 56.7 + - - +
163D THR* 3.5 3.7 + - - -
164D ALA* 3.1 25.5 + - - +
254D CYS* 3.9 10.8 - - - +
257D SER* 2.7 41.8 + - - +
258D LYS* 3.3 44.2 - - + +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LYS 5.1 2.0 + - - +
158D ASP* 3.3 31.2 - - + +
160D ASP* 1.3 75.2 - - - +
162D ALA* 1.3 64.1 + - + +
164D ALA* 3.2 1.8 + - - -
165D ILE* 3.1 36.3 + - + +
250D VAL* 3.6 28.7 - - + -
251D GLU* 5.6 1.1 - - - +
254D CYS* 3.7 22.9 - - + -
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ILE* 3.6 31.9 - - + -
154D ILE* 3.7 12.1 - - + -
158D ASP 3.0 19.8 + - - +
159D MSE 3.8 2.0 - - - +
161D ILE* 1.3 76.3 - - + +
163D THR* 1.3 55.6 + - - +
165D ILE* 4.6 4.5 - - - +
166D SER* 2.8 39.9 + - - -
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Residues in contact with THR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLY* 5.2 4.9 - - - -
111D TRP* 4.8 2.1 - - - -
113D MSE 3.4 51.8 - - + +
126D ILE* 4.4 0.4 - - - +
159D MSE 2.6 27.7 + - - +
160D ASP* 3.6 7.9 - - - -
162D ALA* 1.3 75.0 - - - +
164D ALA* 1.3 58.0 + - - +
167D GLY* 2.8 23.7 + - - +
168D CYS* 2.9 24.3 + - - -
257D SER* 4.5 13.2 + - - +
264D NAP 5.8 0.2 - - + -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP 3.1 12.2 + - - +
161D ILE 3.2 9.1 + - - +
163D THR* 1.3 78.3 - - - +
165D ILE* 1.3 58.4 + - - +
168D CYS* 3.5 13.8 - - - +
172D TYR* 3.0 32.6 + - - -
250D VAL* 3.3 32.5 - - + +
253D ALA* 3.8 5.2 - - + -
254D CYS* 3.7 14.6 - - + +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 3.1 36.1 + - + +
162D ALA* 4.2 4.0 - - - +
164D ALA* 1.3 77.7 - - - +
166D SER* 1.3 63.3 + - - +
169D GLY* 2.8 28.9 - - - -
172D TYR* 4.9 2.2 - - - -
250D VAL* 3.7 21.3 - - + -
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D MSE 4.8 0.2 + - - -
115D ASN* 2.9 28.3 + - - +
124D SER* 2.8 43.2 + - - -
126D ILE* 3.8 17.0 - - - +
162D ALA* 2.8 22.1 + - - -
165D ILE* 1.3 75.9 - - - +
167D GLY* 1.3 60.8 + - - +
170D PRO* 3.6 5.7 - - - +
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Residues in contact with GLY 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D MSE 4.4 13.6 - - - +
114D PRO 3.9 18.8 - - - -
115D ASN* 4.1 6.1 - - - +
162D ALA 3.7 0.6 + - - -
163D THR* 2.8 19.8 + - - +
166D SER* 1.3 74.4 - - - +
168D CYS* 1.3 60.4 + - - -
170D PRO* 3.6 10.0 - - - +
264D NAP 4.3 17.1 + - - -
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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