Contacts of the helix formed by residues 201 - 220 (chain A) in PDB entry 1RC7
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 SER 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A PHE* 3.4 11.0 - - - -
199A GLY 3.2 1.7 - - - -
200A LYS* 1.3 81.1 - - - +
202A LYS* 1.3 65.9 + - - +
203A LYS* 3.6 9.2 + - - +
204A GLU* 3.0 24.7 + - - +
205A ALA* 2.9 22.3 + - - +
16C G 3.8 15.9 - - - -
17C C 3.5 16.6 - - - -
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.0 31.4 - - + +
184A PHE* 3.6 26.1 - - + -
186A VAL* 4.4 4.9 - - + +
201A SER* 1.3 70.8 - - - +
203A LYS* 1.3 64.5 + - - +
205A ALA* 3.2 5.7 + - - +
206A GLU* 2.9 37.8 + - + +
17C C 2.9 41.0 + - - +
18C G 2.9 32.8 + - - +
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 4.6 1.9 - - + +
201A SER* 3.1 9.1 + - - +
202A LYS* 1.3 79.6 - - - +
204A GLU* 1.3 58.3 + - - +
206A GLU* 3.3 14.7 + - - +
207A GLN* 2.9 37.6 + - + +
17C C 4.3 1.9 + - - +
26D G 2.8 36.3 + - - +
27D C 2.7 35.0 + - - +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY* 3.7 7.0 - - - -
200A LYS* 3.2 41.1 + - - +
201A SER* 3.0 18.3 + - - +
203A LYS* 1.3 75.7 - - - +
205A ALA* 1.3 68.1 + - - +
207A GLN* 3.0 11.7 + - + +
208A ARG* 2.8 61.7 + - + +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 3.6 26.7 - - + +
186A VAL* 3.7 18.8 - - + -
197A GLY* 3.6 12.4 - - - +
198A GLU 3.9 12.8 - - - -
199A GLY* 3.9 1.5 - - - +
201A SER 2.9 13.9 + - - +
202A LYS 3.5 7.9 - - - +
204A GLU* 1.3 73.9 - - - +
206A GLU* 1.3 64.9 + - - +
208A ARG* 3.1 4.5 + - - +
209A ALA* 2.9 22.5 + - - +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 2.8 36.4 + - + -
170A TYR* 3.8 31.4 - - + +
186A VAL* 3.9 25.5 - - + +
202A LYS* 2.9 34.3 + - + +
203A LYS* 3.5 19.0 - - - +
205A ALA* 1.3 75.0 - - - +
207A GLN* 1.3 58.2 + - - +
209A ALA* 3.2 2.1 + - - +
210A ALA* 2.8 31.9 + - - +
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Residues in contact with GLN 207 (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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151A ASP* 2.9 30.9 + - - +
152A TYR* 3.3 25.6 + - + +
153A LYS* 3.2 36.3 + - + +
203A LYS* 2.9 24.4 + - + +
204A GLU* 3.3 13.2 - - + +
206A GLU* 1.3 76.7 - - - +
208A ARG* 1.3 57.9 + - + +
210A ALA* 3.2 3.8 + - - +
211A GLU* 2.9 27.6 + - - +
26D G 4.1 9.9 + - - -
27D C 5.8 0.4 + - - -
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 5.7 0.2 - - - -
197A GLY* 4.1 12.3 - - - -
198A GLU* 3.0 35.2 + - - +
199A GLY* 4.1 1.6 - - - -
200A LYS* 6.2 0.4 - - - +
204A GLU* 2.8 42.5 + - + +
205A ALA 3.7 6.7 - - - +
207A GLN* 1.3 77.6 - - + +
209A ALA* 1.3 63.1 + - - +
211A GLU* 3.1 20.7 + - - +
212A GLU* 3.0 27.7 + - + +
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 3.5 26.0 - - + +
187A GLU 4.4 0.7 - - - -
188A ALA* 3.7 21.8 - - + +
195A THR* 2.7 21.4 + - - +
196A LEU 3.7 14.1 - - - -
197A GLY* 3.7 3.0 - - - +
205A ALA 2.9 11.0 + - - +
206A GLU* 3.5 11.0 - - - +
208A ARG* 1.3 77.4 - - - +
210A ALA* 1.3 63.8 + - - +
212A GLU* 3.4 0.7 + - - +
213A LEU* 3.0 10.2 + - - +
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Residues in contact with ALA 210 (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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152A TYR* 3.9 2.9 - - + -
153A LYS* 3.9 21.8 - - + +
156A LEU* 3.9 15.4 - - + +
170A TYR* 3.7 20.6 - - - +
188A ALA* 4.2 2.2 - - - +
206A GLU 2.8 16.6 + - - +
207A GLN 3.4 5.6 - - - +
209A ALA* 1.3 75.6 - - - +
211A GLU* 1.3 65.1 + - - +
213A LEU* 3.3 1.6 + - - +
214A ILE* 2.9 30.4 + - - +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 2.6 58.6 + - + +
207A GLN 2.9 12.7 + - - +
208A ARG* 3.3 23.1 - - - +
210A ALA* 1.3 78.9 - - - +
212A GLU* 1.3 76.1 + - - +
214A ILE* 3.3 5.5 + - - +
215A LYS* 3.3 27.6 + - + +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 3.8 16.8 - - + -
196A LEU 3.9 13.0 - - - +
208A ARG* 3.0 16.6 + - + +
209A ALA 3.8 6.5 - - - +
211A GLU* 1.3 87.7 - - - +
213A LEU* 1.3 65.8 + - - +
215A LYS* 2.9 33.3 + - - +
216A LEU* 2.9 22.7 + - - +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.9 23.8 - - + -
168A PRO* 4.8 0.2 - - + -
188A ALA* 3.6 33.7 - - + +
189A LYS* 4.0 5.2 - - - +
190A ILE* 4.0 17.5 - - + -
193A TYR* 3.7 31.9 - - + -
195A THR* 3.3 27.0 + - + +
209A ALA 3.0 11.8 + - - +
210A ALA 3.8 4.7 - - - +
212A GLU* 1.3 76.2 - - - +
214A ILE* 1.3 56.9 + - - +
216A LEU* 4.0 4.3 - - + -
217A LEU* 2.9 41.5 + - + +
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Residues in contact with ILE 214 (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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152A TYR* 3.7 45.8 - - + +
155A ILE* 3.8 20.2 - - + -
156A LEU* 4.1 17.7 - - + +
159A ILE* 4.1 19.3 - - + +
210A ALA 2.9 21.2 + - - +
211A GLU 3.4 5.8 - - - +
212A GLU 3.1 0.2 - - - -
213A LEU* 1.3 73.0 - - - +
215A LYS* 1.3 69.5 + - + +
217A LEU* 3.7 8.9 - - - +
218A GLU* 2.9 32.8 + - + +
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Residues in contact with LYS 215 (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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211A GLU* 3.3 20.8 + - + +
212A GLU* 2.9 33.9 + - - +
214A ILE* 1.3 76.0 - - + +
216A LEU* 1.3 67.9 + - - +
218A GLU* 2.9 14.4 + - - +
219A GLU* 2.9 36.1 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 4.2 16.8 - - + -
194A ARG 3.6 19.1 - - - +
195A THR* 3.6 25.1 - - + -
212A GLU 2.9 12.5 + - - +
213A LEU* 3.6 18.4 - - + +
215A LYS* 1.3 77.0 - - - +
217A LEU* 1.3 63.8 + - - +
219A GLU* 3.1 14.1 + - + +
220A SER* 3.1 32.6 + - - +
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Residues in contact with LEU 217 (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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156A LEU* 4.0 19.5 - - + -
159A ILE* 4.0 29.8 - - + -
160A THR* 4.4 2.5 - - + -
163A ARG* 4.6 13.3 + - - +
164A TRP* 3.9 10.3 - - + -
190A ILE* 3.9 14.8 - - + -
193A TYR* 3.3 46.7 - - + -
213A LEU* 2.9 28.8 + - + +
214A ILE* 3.7 4.9 - - - +
216A LEU* 1.3 74.9 - - - +
218A GLU* 1.3 65.0 + - - +
220A SER* 2.9 27.2 + - - +
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Residues in contact with GLU 218 (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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214A ILE* 2.9 27.7 + - + +
215A LYS* 3.3 11.8 - - - +
217A LEU* 1.3 75.4 - - - +
219A GLU* 1.3 61.2 + - + +
220A SER* 4.3 3.3 - - - +
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Residues in contact with GLU 219 (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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215A LYS* 2.9 31.3 + - - +
216A LEU* 3.4 15.0 + - + +
217A LEU 3.0 0.2 - - - -
218A GLU* 1.3 78.1 - - + +
220A SER* 1.3 67.1 + - - +
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Residues in contact with SER 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 4.2 14.5 + - - -
193A TYR* 4.0 36.4 + - - -
216A LEU* 3.1 20.9 + - - +
217A LEU 2.9 14.2 + - - +
218A GLU 4.3 3.1 - - - +
219A GLU* 1.3 83.6 - - - +
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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
------------------------------------------------------------
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