Contacts of the helix formed by residues 165 - 179 (chain G) in PDB entry 2R9R
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 PRO 165 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163G ASN 4.3 4.0 - - - +
164G THR* 1.4 90.9 - - + +
166G MET* 1.3 67.0 + - - +
167G GLU* 4.5 7.6 - - + +
168G GLU* 3.0 35.4 + - + +
169G THR* 3.2 9.0 + - - -
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Residues in contact with MET 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G THR 3.4 3.9 + - - +
165G PRO* 1.3 70.3 - - - +
167G GLU* 1.3 56.3 + - - +
169G THR* 3.1 10.2 + - - +
170G VAL* 2.9 33.3 + - + +
190G TRP* 3.5 42.0 - - + -
194G GLU* 3.8 17.0 - - + +
197G GLU* 3.3 37.9 + - + +
198G ALA* 3.7 28.9 - - - +
201G VAL* 4.0 12.3 - - + -
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Residues in contact with GLU 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G PRO* 3.2 6.6 - - + +
166G MET* 1.3 78.9 - - - +
168G GLU* 1.3 54.1 + - - +
170G VAL* 3.9 0.7 - - - +
171G ARG* 2.7 73.3 + - + +
201G VAL* 3.7 17.0 - - + +
205G PHE* 3.7 34.3 - - + -
207G LEU* 4.7 0.2 - - - +
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Residues in contact with GLU 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G SER* 3.3 13.5 - - - -
133G ARG* 2.9 39.7 + - + +
134G LYS 4.8 0.2 + - - -
164G THR* 3.7 14.4 - - + +
165G PRO* 3.0 27.8 + - + +
167G GLU* 1.3 79.7 - - - +
169G THR* 1.3 65.0 + - - +
171G ARG* 3.8 5.6 - - - +
172G ALA* 3.0 25.7 + - - +
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Residues in contact with THR 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 3.0 50.8 + - + +
136G ILE* 4.1 10.5 - - + +
161G ASP* 5.6 0.3 - - - +
164G THR* 3.7 11.8 + - - +
165G PRO 3.2 3.9 + - - -
166G MET* 3.1 15.4 + - - -
168G GLU* 1.3 78.1 - - - +
170G VAL* 1.3 63.5 + - - +
172G ALA* 3.1 3.6 + - - +
173G MET* 2.9 33.1 + - + +
185G TRP* 4.7 4.3 - - + -
190G TRP* 4.5 15.9 - - + -
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Residues in contact with VAL 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G MET* 2.9 40.8 + - + +
167G GLU 4.1 2.5 - - - +
169G THR* 1.3 72.8 - - - +
171G ARG* 1.3 62.1 + - - +
173G MET* 3.4 0.7 + - - +
174G THR* 2.9 28.8 + - - -
185G TRP* 3.9 22.2 - - + -
198G ALA* 3.9 16.6 - - - +
201G VAL* 4.1 7.0 - - + -
202G ALA* 4.0 19.7 - - + +
207G LEU* 3.7 27.4 - - + -
208G ILE 4.0 10.1 - - - +
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Residues in contact with ARG 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ARG* 4.1 14.6 + - - +
167G GLU* 2.7 48.7 + - + +
168G GLU* 3.8 6.1 - - - +
170G VAL* 1.3 73.6 - - - +
172G ALA* 1.3 57.2 + - - +
174G THR* 3.4 4.9 + - - -
175G HIS* 2.8 29.1 + - - +
205G PHE* 3.2 39.8 + - - +
207G LEU* 3.6 29.2 - - + +
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Residues in contact with ALA 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ARG* 3.8 36.7 - - + +
136G ILE* 3.8 21.1 - - + -
137G ILE* 5.1 1.3 - - + -
168G GLU 3.0 17.8 + - - +
169G THR 3.1 4.0 + - - +
171G ARG* 1.3 73.1 - - - +
173G MET* 1.3 65.5 + - - +
175G HIS* 3.3 7.0 + - - +
176G VAL* 3.0 30.3 + - - +
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Residues in contact with MET 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G ILE* 5.5 1.8 - - + -
131G LEU* 4.9 0.9 - - + -
136G ILE* 4.2 31.2 - - + -
155G VAL* 4.1 20.4 - - + +
156G PHE 4.1 5.8 - - - +
157G ALA* 3.8 36.3 - - + +
169G THR* 2.9 22.2 + - + +
170G VAL 3.8 2.5 - - - +
172G ALA* 1.3 74.4 - - - +
174G THR* 1.3 66.8 + - - +
175G HIS 3.3 0.2 + - - -
176G VAL* 3.3 7.9 + - - +
177G ILE* 3.1 27.4 + - - +
185G TRP* 3.4 59.2 - - + -
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Residues in contact with THR 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G VAL 2.9 19.1 + - - -
171G ARG 3.7 4.3 - - - -
173G MET* 1.3 78.1 - - - +
175G HIS* 1.3 57.1 + - - +
177G ILE* 3.3 7.9 + - - +
178G ASN* 2.8 51.5 + - - +
185G TRP* 4.8 0.2 + - - -
206G ASN 5.5 0.4 - - - +
207G LEU* 3.4 25.0 - - + +
208G ILE* 3.0 45.5 + - + +
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Residues in contact with HIS 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ARG* 3.3 33.2 + - - +
137G ILE* 3.6 27.1 - - + +
171G ARG 2.8 17.7 + - - +
172G ALA* 3.5 6.3 - - - +
173G MET 3.1 0.2 - - - -
174G THR* 1.3 78.0 - - - +
176G VAL* 1.3 65.8 + - + +
178G ASN* 3.1 8.6 + - - +
179G GLN* 2.9 54.7 + - + +
181G MET* 5.8 1.3 - - - -
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Residues in contact with VAL 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ILE* 4.1 13.5 - - + -
137G ILE* 4.1 24.7 - - + -
140G LEU* 3.7 27.1 - - + -
155G VAL* 4.2 15.0 - - + -
172G ALA 3.0 14.9 + - - +
173G MET* 3.4 18.4 - - - +
175G HIS* 1.3 77.7 - - + +
177G ILE* 1.3 60.6 + - + +
179G GLN* 3.5 6.1 + - - -
180G GLY 3.4 2.4 + - - -
181G MET* 2.9 49.0 + - + +
182G ALA* 3.4 3.7 + - + -
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Residues in contact with ILE 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G MET 3.1 17.4 + - - +
174G THR 3.7 6.5 - - - +
176G VAL* 1.3 75.9 - - + +
178G ASN* 1.3 68.6 + - - +
180G GLY* 3.0 15.1 + - - -
182G ALA* 3.3 32.0 - - + +
183G MET* 3.8 14.4 - - - +
184G TYR* 3.8 19.1 - - - +
185G TRP* 3.7 28.9 - - + +
208G ILE* 3.8 31.9 - - + -
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Residues in contact with ASN 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G THR* 2.8 42.2 + - - +
175G HIS* 3.8 8.5 - - - +
177G ILE* 1.3 77.1 - - - +
179G GLN* 1.3 64.8 + - - +
180G GLY 3.6 0.3 + - - -
208G ILE* 4.4 11.2 - - - +
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Residues in contact with GLN 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G GLU* 5.5 0.7 - - - +
175G HIS* 2.9 49.9 + - + +
176G VAL 3.9 5.2 - - - +
177G ILE 3.1 0.4 - - - -
178G ASN* 1.3 79.6 - - - +
180G GLY* 1.3 61.3 + - - +
181G MET* 3.4 21.9 + - + +
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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