Contacts of the helix formed by residues 164 - 179 (chain D) in PDB entry 1RFU
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 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ILE* 3.2 7.5 - - - +
163D HIS* 1.3 85.5 - - - +
165D GLN* 1.3 66.6 + - - +
166D GLU* 3.5 10.4 + - - +
167D GLU* 2.7 34.4 + - - +
168D ALA* 3.0 16.6 + - - +
190D LEU* 3.8 11.9 - - - +
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Residues in contact with GLN 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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164D SER* 1.3 72.3 - - - +
166D GLU* 1.3 64.1 + - - +
168D ALA* 2.8 8.0 - - - +
169D LEU* 2.7 30.4 + - + +
190D LEU* 3.2 21.9 - - + +
200D MET* 3.9 4.9 - - - +
202D LEU* 4.0 17.0 - - + -
220D ARG* 2.4 42.7 + - - +
312D LEU* 3.4 33.1 - - - +
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Residues in contact with GLU 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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164D SER* 3.5 9.3 + - - +
165D GLN* 1.3 77.8 - - - +
167D GLU* 1.3 71.1 + - - +
168D ALA 2.6 2.1 + - - -
169D LEU* 2.6 28.3 + - + +
170D GLU* 2.8 32.7 + - + +
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Residues in contact with GLU 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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160D ARG* 2.9 32.2 + - - -
161D LYS 4.0 1.9 - - - +
162D ILE* 3.5 16.8 - - + +
163D HIS* 2.6 46.7 + - + +
164D SER* 2.7 37.2 + - - +
166D GLU* 1.3 75.1 + - - +
168D ALA* 1.3 65.1 + - - +
170D GLU* 3.5 13.0 + - - +
171D VAL* 3.2 23.6 + - - +
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Residues in contact with ALA 168 (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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162D ILE* 3.3 18.8 - - + +
164D SER 3.0 10.4 + - - +
165D GLN 2.8 15.0 + - - +
166D GLU 2.6 3.8 + - - -
167D GLU* 1.3 73.9 - - - +
169D LEU* 1.3 61.1 + - - +
170D GLU 2.7 2.3 + - - -
171D VAL* 2.8 17.6 + - - +
172D MET* 3.2 15.8 + - + +
185D ILE* 5.8 6.2 - - + +
188D SER* 5.9 0.9 - - - +
190D LEU* 4.0 5.6 - - + -
202D LEU* 3.5 22.2 - - + -
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Residues in contact with LEU 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 GLN* 2.7 25.8 + - + +
166D GLU* 2.6 20.7 + - + +
168D ALA* 1.3 70.6 - - - +
170D GLU* 1.3 59.6 + - + +
172D MET* 3.5 21.5 + - + +
173D ASP* 2.8 31.4 + - - +
202D LEU* 4.9 3.6 - - + -
218D ARG* 3.4 48.4 + - - +
219D ILE 6.0 0.2 - - - +
312D LEU* 4.2 26.9 - - + -
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Residues in contact with GLU 170 (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 ARG* 3.0 33.0 + - - +
166D GLU* 2.8 37.8 + - + +
167D GLU* 3.6 16.1 - - - +
168D ALA 2.7 4.6 + - - -
169D LEU* 1.3 70.8 - - + +
171D VAL* 1.3 52.8 + - - +
173D ASP* 2.6 35.8 + - - +
174D MET* 2.7 22.9 + - + +
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Residues in contact with VAL 171 (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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154D ALA* 3.7 16.6 - - + +
158D THR* 3.0 34.5 - - + +
160D ARG* 5.0 11.0 - - + +
162D ILE* 3.2 26.0 - - + -
167D GLU 3.2 16.4 - - - +
168D ALA* 2.8 11.5 + - - +
170D GLU* 1.3 72.1 - - + +
172D MET* 1.3 51.1 + - + +
174D MET* 3.1 12.6 + - - +
175D LEU* 2.6 53.6 + - + +
185D ILE* 5.4 2.0 - - + -
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Residues in contact with MET 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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168D ALA 3.2 5.8 + - - +
169D LEU* 3.6 37.7 - - + +
170D GLU 3.0 0.4 - - - -
171D VAL* 1.3 76.1 - - - +
173D ASP* 1.3 61.8 + - - +
175D LEU* 3.5 6.8 - - - +
176D HIS* 2.7 37.1 + - - -
183D VAL* 3.5 21.8 - - + +
185D ILE* 4.1 17.5 - - + -
202D LEU* 3.2 54.7 - - + +
203D GLY 4.2 0.9 - - - -
204D SER* 3.8 33.4 - - - -
218D ARG* 5.4 0.2 - - - +
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Residues in contact with ASP 173 (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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169D LEU 2.8 20.4 - - - +
170D GLU* 2.6 23.9 + - - +
172D MET* 1.3 72.3 - - - +
174D MET* 1.3 54.2 + - + +
176D HIS* 3.2 15.4 - - - +
177D SER* 2.9 27.8 + - - -
204D SER* 4.7 0.2 + - - -
206D ARG* 5.9 4.2 + - - +
218D ARG* 2.9 32.3 + - - -
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Residues in contact with MET 174 (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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158D THR* 3.5 41.5 - - + +
160D ARG* 3.8 34.5 - - + -
170D GLU* 2.7 17.8 + - + +
171D VAL* 3.3 11.9 - - - +
173D ASP* 1.3 74.7 - - + +
175D LEU* 1.3 65.6 + - - +
177D SER* 2.9 24.5 - - - -
178D MET* 3.0 15.6 + - + +
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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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141D VAL* 4.4 3.1 - - + +
147D ILE* 3.7 26.5 - - + -
149D PRO* 4.4 2.5 - - + -
154D ALA* 4.6 2.9 - - + +
157D LEU* 4.1 27.8 - - + -
158D THR* 3.5 16.8 - - + +
171D VAL* 2.6 45.3 + - + +
172D MET* 3.5 4.3 - - - +
174D MET* 1.3 70.4 - - - +
176D HIS* 1.3 68.2 + - - +
178D MET* 2.7 29.5 + - - +
179D GLY 3.3 3.1 + - - -
180D PRO* 3.3 8.1 - - - +
183D VAL* 3.6 23.8 - - + -
185D ILE* 4.2 13.9 - - + -
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Residues in contact with HIS 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 MET 2.7 29.9 + - - -
173D ASP* 3.2 14.8 - - - +
175D LEU* 1.3 69.6 - - - +
177D SER* 1.3 53.9 + - - +
179D GLY* 2.6 29.5 + - - +
180D PRO* 2.9 34.8 + - - +
181D ASP* 2.6 33.2 + - - -
183D VAL* 3.6 9.8 - - + +
204D SER* 2.6 43.4 + - - -
205D GLN* 3.8 3.8 + - - -
206D ARG* 3.9 29.7 + - + +
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Residues in contact with SER 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 ASP 2.9 13.9 + - - -
174D MET* 2.9 18.0 + - - -
176D HIS* 1.3 75.4 - - - +
178D MET* 1.3 61.5 + - - +
179D GLY* 3.6 0.3 + - - -
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Residues in contact with MET 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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137D ARG* 3.2 44.2 - - + +
141D VAL* 3.8 22.7 - - + -
142D PRO* 3.0 29.0 - - + +
157D LEU* 4.6 11.7 - - + +
158D THR* 4.6 11.4 - - - -
174D MET* 3.1 16.6 - - - +
175D LEU* 2.7 28.1 + - - +
177D SER* 1.3 75.2 - - - +
179D GLY* 1.3 54.5 + - - -
180D PRO* 3.9 1.8 - - - -
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Residues in contact with GLY 179 (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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142D PRO 3.5 15.3 - - - -
144D ALA 3.6 6.1 - - - +
176D HIS 2.6 15.7 + - - +
177D SER 3.3 0.8 - - - -
178D MET* 1.3 74.6 - - - +
180D PRO* 1.3 70.7 - - - +
181D ASP* 3.5 13.3 + - - +
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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