Contacts of the helix formed by residues 168 - 187 (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 CYS 168 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D THR* 2.9 28.1 + - - -
164D ALA* 3.5 13.7 - - - +
167D GLY* 1.3 73.5 - - - -
169D GLY* 1.3 66.1 + - - +
170D PRO* 3.4 1.6 - - - -
171D ALA* 3.0 25.4 + - + +
172D TYR* 3.3 29.7 + - + +
253D ALA* 4.3 10.5 - - + -
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Residues in contact with GLY 169 (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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165D ILE 2.8 26.7 + - - -
168D CYS* 1.3 76.5 - - - +
170D PRO* 1.4 66.6 - - - +
172D TYR* 2.9 29.8 + - - +
173D VAL* 3.1 18.9 + - - +
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Residues in contact with PRO 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ASN* 4.0 12.1 - - + +
116D THR* 4.7 3.6 - - - +
117D PRO* 3.9 29.4 - - + -
166D SER 3.6 9.2 - - - +
167D GLY 3.6 10.8 - - - +
168D CYS 3.4 4.5 - - - -
169D GLY* 1.4 87.2 - - - +
171D ALA* 1.3 51.3 + - - +
173D VAL* 3.1 9.4 + - + +
174D TYR* 2.7 65.7 + - + +
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Residues in contact with ALA 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D CYS* 3.0 14.8 + - + +
170D PRO* 1.3 79.2 - - - +
172D TYR* 1.3 64.5 + - + +
174D TYR* 3.9 10.2 - - - +
175D LEU* 3.1 28.8 + - - +
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Residues in contact with TYR 172 (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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164D ALA 3.0 28.1 + - - -
165D ILE* 4.9 1.3 - - - -
168D CYS* 3.3 21.1 - - + +
169D GLY* 2.9 24.9 + - - +
171D ALA* 1.3 79.9 - - + +
173D VAL* 1.3 61.7 + - + +
175D LEU* 3.5 8.7 + - + +
176D PHE* 2.9 27.6 + - - +
246D VAL* 6.0 7.2 - - + -
249D ALA* 3.9 22.7 + - + -
250D VAL* 3.9 21.3 - - + -
253D ALA* 3.5 19.1 - - - +
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Residues in contact with VAL 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D GLY 3.1 18.8 + - - +
170D PRO* 3.6 8.5 - - + +
172D TYR* 1.3 77.0 - - + +
174D TYR* 1.3 62.1 + - + +
176D PHE* 3.2 12.4 + - + +
177D ILE* 2.8 50.3 + - + +
202D ILE* 5.4 10.1 - - + -
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Residues in contact with TYR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D THR* 3.9 17.2 + - - -
117D PRO* 4.4 10.3 - - + +
170D PRO* 2.7 49.7 + - + +
171D ALA* 3.9 9.0 - - - +
173D VAL* 1.3 76.2 - - + +
175D LEU* 1.3 50.5 + - - +
177D ILE* 3.3 17.3 + - + +
178D GLU* 2.7 38.0 + - - +
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Residues in contact with LEU 175 (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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171D ALA 3.1 18.8 + - - +
172D TYR* 3.8 7.0 - - + +
173D VAL 3.3 0.2 - - - -
174D TYR* 1.3 73.1 - - - +
176D PHE* 1.3 56.5 + - - +
178D GLU* 3.4 30.5 - - - +
179D SER* 2.7 46.4 + - - +
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Residues in contact with PHE 176 (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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172D TYR 2.9 18.8 + - - +
173D VAL* 3.3 13.7 - - + +
175D LEU* 1.3 73.3 - - - +
177D ILE* 1.3 64.3 + - - +
179D SER* 3.3 6.1 + - - -
180D LEU* 3.1 56.9 + - + +
202D ILE* 4.2 20.4 - - + -
242D PHE* 3.7 35.7 - + - -
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Residues in contact with ILE 177 (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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173D VAL* 2.8 39.4 + - + +
174D TYR* 3.6 17.9 - - + +
176D PHE* 1.3 70.3 - - - +
178D GLU* 1.3 64.8 + - - +
180D LEU* 3.3 3.1 + - - +
181D ILE* 3.0 43.0 + - + +
195D LYS* 5.4 0.7 - - + -
198D VAL* 4.0 17.0 - - + -
199D LEU* 4.0 26.0 - - + -
202D ILE* 3.7 23.6 - - + -
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Residues in contact with GLU 178 (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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178A GLU* 4.8 4.5 - - - +
174D TYR 2.7 21.3 + - - +
175D LEU* 3.4 33.3 - - + +
176D PHE 3.3 0.2 - - - -
177D ILE* 1.3 74.1 - - - +
179D SER* 1.3 57.5 + - - +
181D ILE* 3.5 8.3 + - - +
182D ASP* 3.1 45.2 + - - +
217E GLN* 5.8 4.8 - - - +
220E LYS* 4.3 16.3 + - - -
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LEU* 2.7 36.3 + - - +
176D PHE* 3.8 7.1 - - - -
177D ILE 3.3 0.2 - - - -
178D GLU* 1.3 70.4 - - - +
180D LEU* 1.3 60.8 + - - +
182D ASP* 3.5 8.9 + - - +
183D ALA* 3.1 27.5 + - - +
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Residues in contact with LEU 180 (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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176D PHE* 3.1 58.7 + - + +
177D ILE 3.8 1.8 - - - +
179D SER* 1.3 74.5 - - - +
181D ILE* 1.3 64.0 + - - +
183D ALA* 3.4 8.6 + - + +
184D GLY* 3.1 18.4 + - - -
194D SER* 5.1 0.3 - - - -
198D VAL* 3.6 38.8 - - + +
202D ILE* 4.3 4.9 - - + -
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Residues in contact with ILE 181 (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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177D ILE* 3.0 40.7 + - + +
178D GLU* 3.8 7.2 - - - +
180D LEU* 1.3 76.9 - - - +
182D ASP* 1.3 60.9 - - - +
184D GLY* 3.1 3.5 + - - -
185D VAL* 2.9 30.3 + - + +
191D ARG* 3.8 34.1 - - + +
194D SER* 3.8 17.2 - - - -
195D LYS* 3.8 41.3 - - + +
198D VAL* 4.2 5.8 - - + -
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Residues in contact with ASP 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D GLU* 3.1 36.1 + - - +
179D SER* 3.7 8.6 - - - +
180D LEU 3.4 0.2 - - - -
181D ILE* 1.3 76.9 - - - +
183D ALA* 1.3 57.2 + - - +
185D VAL* 3.8 5.9 - - - +
186D LYS* 2.9 30.7 + - - +
191D ARG* 3.8 20.1 + - - +
220E LYS* 5.5 5.5 + - - -
221E ASP* 4.2 9.2 - - - +
224E VAL* 5.8 1.2 - - - +
231E ALA* 5.7 0.2 - - - +
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Residues in contact with ALA 183 (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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179D SER 3.1 17.7 + - - +
180D LEU* 3.6 9.6 - - + +
181D ILE 3.2 0.4 - - - -
182D ASP* 1.3 72.1 - - - +
184D GLY* 1.3 64.9 + - - +
186D LYS* 3.5 6.3 + - - +
187D ASN* 2.8 36.7 + - - +
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Residues in contact with GLY 184 (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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180D LEU 3.1 13.4 + - - -
181D ILE 3.1 3.8 + - - -
183D ALA* 1.3 75.1 - - - +
185D VAL* 1.3 61.3 + - - +
187D ASN* 3.3 11.5 + - - -
188D GLY 3.3 0.5 + - - -
189D LEU* 2.9 37.0 + - - +
194D SER* 3.8 15.7 - - - -
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Residues in contact with VAL 185 (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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181D ILE* 2.9 23.0 + - + +
182D ASP 3.8 4.9 - - - +
184D GLY* 1.3 73.9 - - - +
186D LYS* 1.3 59.4 + - - +
187D ASN 3.2 0.5 + - - -
188D GLY 3.3 2.6 + - - -
189D LEU 3.2 10.8 - - - +
191D ARG* 3.7 55.2 - - - +
194D SER* 4.1 1.3 - - - +
224E VAL* 3.7 39.9 - - + +
226E PRO* 3.0 18.2 - - + +
227E GLY 2.8 24.6 + - - -
231E ALA* 5.1 0.2 - - - -
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Residues in contact with LYS 186 (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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256A LYS* 5.8 0.9 + - - -
182D ASP 2.9 18.7 + - - +
183D ALA* 3.7 9.2 - - - +
184D GLY 3.3 0.2 - - - -
185D VAL* 1.3 75.7 - - - +
187D ASN* 1.3 73.8 + - - +
188D GLY 3.4 0.2 - - - -
224E VAL* 5.2 0.2 - - - +
227E GLY* 3.1 20.8 - - - -
228E GLY 4.2 0.7 + - - +
231E ALA* 3.6 32.2 - - + +
232E VAL* 3.9 23.0 - - + +
235E TYR* 3.5 56.9 - - + -
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Residues in contact with ASN 187 (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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183D ALA* 2.8 29.0 + - - +
184D GLY* 3.3 6.9 + - - +
185D VAL 3.2 0.4 - - - -
186D LYS* 1.3 98.4 + - - +
188D GLY* 1.3 56.4 + - - +
189D LEU* 3.7 3.2 + - - +
227E GLY* 4.3 2.2 - - - -
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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
------------------------------------------------------------
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