Contacts of the helix formed by residues 209 - 224 (chain A) in PDB entry 3RC0
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 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 5.7 0.7 - - - +
188A TYR* 3.4 8.7 + - - -
206A ARG 4.4 8.3 - - - -
207A VAL 3.0 10.6 + - - +
208A ARG* 1.3 75.7 - - - +
210A LEU* 1.3 59.9 + - - +
211A GLU* 3.6 9.2 + - - +
212A LEU* 3.1 30.7 + - - +
213A TYR* 2.9 28.2 + - - +
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Residues in contact with LEU 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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184A ILE* 4.9 1.6 - - + +
185A ARG* 4.8 21.3 - - + +
188A TYR* 3.6 50.6 + - + -
209A SER* 1.3 69.3 + - - +
211A GLU* 1.3 67.4 + - - +
213A TYR* 3.0 3.6 + - + +
214A HIS* 3.0 57.3 + - + +
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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
----------------------------------------------------------
151A GLY* 5.7 0.7 - - - -
209A SER* 3.3 7.6 + - - +
210A LEU* 1.3 78.6 - - - +
212A LEU* 1.3 63.0 + - - +
214A HIS* 3.3 10.9 + - - +
215A GLN* 3.2 45.3 + - - +
474A EDO 3.9 11.9 + - - +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.9 14.4 - - + -
133A LEU* 5.1 7.4 - - + -
150A LEU* 3.8 20.0 - - + -
206A ARG 4.5 3.8 - - - +
207A VAL* 3.8 36.8 - - + +
209A SER* 3.1 20.7 + - - +
211A GLU* 1.3 79.7 - - - +
213A TYR* 1.3 58.5 + - - +
215A GLN* 3.1 20.3 + - - +
216A LEU* 2.9 41.4 + - + +
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Residues in contact with TYR 213 (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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123A VAL* 4.1 2.3 - - - +
126A LEU* 3.3 37.0 - - + +
130A LEU* 4.2 19.9 - - + +
184A ILE* 3.5 39.3 - - + -
187A GLU* 2.7 31.5 + - + +
188A TYR* 4.0 24.7 - + + -
192A VAL* 3.6 33.7 - - + +
209A SER 2.9 15.6 + - - +
210A LEU* 3.0 8.7 + - + +
212A LEU* 1.3 77.1 - - - +
214A HIS* 1.3 61.0 + - - +
216A LEU* 3.5 5.2 + - + +
217A VAL* 3.1 34.2 + - + +
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Residues in contact with HIS 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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157A MET* 4.0 13.1 - - + +
158A PHE* 3.7 20.7 - + + -
181A LEU* 3.9 30.6 + - + +
184A ILE* 3.4 30.0 - - + +
185A ARG* 5.1 5.6 - - + +
210A LEU* 3.0 49.5 + - + +
211A GLU* 3.4 11.4 - - + +
213A TYR* 1.3 77.6 - - - +
215A GLN* 1.3 61.0 + - - +
217A VAL* 3.4 4.9 + - - +
218A ALA* 3.1 22.9 + - - +
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Residues in contact with GLN 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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150A LEU* 3.4 47.2 + - + +
151A GLY* 4.0 4.0 - - - -
153A LEU* 3.6 12.4 - - + +
158A PHE* 4.2 4.9 - - + -
211A GLU* 3.2 31.1 + - - +
212A LEU* 3.1 25.8 + - - +
214A HIS* 1.3 76.0 - - - +
216A LEU* 1.3 60.1 + - - +
218A ALA* 3.4 3.8 + - - +
219A LEU* 2.9 26.9 + - - +
474A EDO 2.7 30.6 + - - +
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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
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126A LEU* 3.8 13.7 - - + +
129A LEU* 4.5 10.9 - - + +
130A LEU* 3.4 43.5 - - + +
133A LEU* 3.8 29.6 - - + -
147A TRP* 4.3 2.9 - - + -
150A LEU* 4.1 13.7 - - + -
212A LEU* 2.9 23.5 + - + +
213A TYR* 4.0 6.3 - - + +
215A GLN* 1.3 75.0 - - - +
217A VAL* 1.3 59.7 + - - +
219A LEU* 3.6 24.5 - - + +
220A VAL* 2.9 32.9 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 4.1 6.9 - - + -
126A LEU* 3.9 28.0 - - + -
180A ASP* 6.2 0.9 - - + -
184A ILE* 3.7 35.7 - - + -
213A TYR* 3.1 27.7 + - + +
214A HIS 3.6 4.9 - - - +
215A GLN 3.3 0.2 - - - -
216A LEU* 1.3 76.6 - - - +
218A ALA* 1.3 58.2 + - - +
220A VAL* 3.2 5.2 + - - +
221A MET* 2.9 40.2 + - + +
475A EDO 4.0 19.1 - - - -
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Residues in contact with ALA 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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153A LEU* 3.8 7.2 - - + -
155A HIS* 3.4 22.3 + - + +
157A MET* 4.3 1.1 - - - -
158A PHE* 3.7 27.1 - - + -
214A HIS 3.1 14.1 + - - +
215A GLN 3.4 9.2 - - - +
217A VAL* 1.3 77.2 - - - +
219A LEU* 1.3 56.7 - - - +
221A MET* 3.3 18.8 - - + +
222A ALA* 2.9 24.6 + - - +
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Residues in contact with LEU 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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129A LEU* 5.1 1.3 - - + -
147A TRP* 3.2 51.8 - - + -
148A PRO* 3.9 22.2 - - + -
150A LEU* 4.5 10.3 - - + -
153A LEU* 4.7 5.3 - - + +
155A HIS* 5.7 0.4 - - - -
215A GLN 2.9 17.6 + - - +
216A LEU* 3.6 17.5 - - + +
217A VAL 3.2 0.2 - - - -
218A ALA* 1.3 73.1 - - - +
220A VAL* 1.3 56.7 + - + +
222A ALA* 4.8 0.2 - - - -
223A TYR* 2.7 77.7 + - + +
243A MET* 4.5 3.6 - - + -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 3.6 34.1 - - + -
125A LEU* 3.8 20.2 - - + -
126A LEU* 3.6 19.1 - - + -
129A LEU* 3.7 20.6 - - + -
216A LEU 2.9 21.3 + - - +
217A VAL 3.6 4.7 - - - +
219A LEU* 1.3 74.4 - - - +
221A MET* 1.3 63.4 - - - +
224A SER* 2.6 48.7 + - - +
241A PRO* 4.2 1.6 - - + -
243A MET* 4.6 4.0 - - - -
308P THR 4.5 0.2 - - - +
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Residues in contact with MET 221 (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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122A TRP* 3.6 26.5 - - + -
155A HIS* 4.1 10.3 - - + -
157A MET* 3.5 26.2 - - - -
180A ASP* 4.2 18.4 - - - +
217A VAL* 2.9 19.9 + - + +
218A ALA* 3.3 32.8 - - - +
220A VAL* 1.3 78.9 - - - +
222A ALA* 1.3 60.4 + - - +
295A HIS* 4.4 8.5 - - + +
296A MET* 3.7 37.9 - - + +
297A TYR* 3.7 16.1 + - - -
309P PHE* 4.0 13.5 - - - +
310P LYS* 4.2 2.3 + - - -
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Residues in contact with ALA 222 (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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155A HIS* 3.7 8.5 - - + +
218A ALA 2.9 17.6 + - - +
221A MET* 1.3 76.2 - - - +
223A TYR* 1.3 71.0 + - + +
296A MET 3.5 12.3 - - - +
297A TYR* 3.1 27.3 - - + -
484A SAM 3.5 36.9 - - - +
310P LYS* 3.3 4.0 + - - -
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Residues in contact with TYR 223 (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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147A TRP* 4.9 8.7 - + - -
148A PRO* 3.4 29.9 - - + +
153A LEU* 5.6 3.4 - - + -
155A HIS* 6.4 0.2 - + - -
219A LEU* 2.7 44.2 + - + +
222A ALA* 1.3 89.6 - - + +
224A SER* 1.3 64.4 + - - +
225A PHE* 3.6 18.9 - - - -
243A MET* 3.8 17.2 - - + +
244A VAL 5.1 1.0 + - - -
248A ASP* 3.6 38.8 - - - +
484A SAM 2.6 63.9 + - + -
310P LYS* 3.7 2.5 + - - -
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Residues in contact with SER 224 (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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219A LEU 3.9 0.8 + - - -
220A VAL* 2.6 29.3 + - - +
222A ALA 3.9 0.2 - - - -
223A TYR* 1.3 79.2 - - - +
225A PHE* 1.3 60.3 + - - +
241A PRO* 3.3 19.3 - - - +
242A VAL 3.4 12.6 - - - -
243A MET* 3.8 18.5 - - - +
308P THR 2.9 19.8 + - - +
310P LYS* 2.9 28.1 + - - +
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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