Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 1RFV
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ILE* 3.5 5.2 - - - +
163A HIS* 1.3 84.0 - - - +
165A GLN* 1.3 65.0 + - - +
166A GLU* 3.0 24.1 + - - +
167A GLU* 3.1 30.5 + - - +
168A ALA 3.1 9.5 + - - -
190A LEU* 3.1 16.0 - - - +
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Residues in contact with GLN 165 (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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164A SER* 1.3 75.7 - - - +
166A GLU* 1.3 75.6 + - + +
168A ALA* 3.3 6.3 + - - +
169A LEU* 3.2 33.8 + - + +
190A LEU* 3.1 15.2 - - + +
193A PRO* 5.5 0.8 - - - +
200A MET* 2.9 27.8 - - + +
202A LEU* 4.3 11.9 - - + -
220A ARG* 2.7 35.6 + - - +
312A LEU* 3.8 24.0 - - + +
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 3.0 22.9 + - - +
165A GLN* 1.3 92.8 + - - +
167A GLU* 1.3 65.3 + - + +
169A LEU* 3.5 14.4 + - + +
170A GLU* 3.3 29.0 + - - +
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Residues in contact with GLU 167 (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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160A ARG* 3.7 21.2 + - - +
161A LYS 3.1 8.6 - - - +
162A ILE* 4.3 5.2 - - - -
163A HIS* 2.6 57.4 + - - +
164A SER* 3.1 19.5 + - - +
166A GLU* 1.3 76.7 - - + +
168A ALA* 1.3 59.6 + - - +
170A GLU* 3.0 11.2 + - - +
171A VAL* 2.9 32.4 + - - +
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Residues in contact with ALA 168 (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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162A ILE* 3.8 27.3 - - + +
164A SER 3.1 11.1 + - - +
165A GLN* 3.4 7.6 - - - +
167A GLU* 1.3 76.9 - - - +
169A LEU* 1.3 58.4 + - - +
171A VAL* 3.0 3.8 + - - +
172A MET* 2.8 34.3 + - - +
185A ILE* 4.6 4.6 - - + +
190A LEU* 4.9 2.7 - - + -
202A LEU* 3.4 31.6 - - + -
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Residues in contact with LEU 169 (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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165A GLN* 3.2 22.8 + - + +
166A GLU* 3.7 16.2 - - + +
167A GLU 3.3 0.2 - - - -
168A ALA* 1.3 77.4 - - - +
170A GLU* 1.3 61.5 + - + +
172A MET* 3.3 28.9 + - + +
173A ASP* 3.1 28.8 + - - +
202A LEU* 4.8 3.6 - - + -
218A ARG* 3.7 35.5 + - + +
312A LEU* 4.2 29.4 - - + -
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Residues in contact with GLU 170 (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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160A ARG* 2.5 48.2 + - - +
166A GLU* 3.3 17.5 + - - +
167A GLU* 3.0 12.2 + - - +
169A LEU* 1.3 76.9 - - + +
171A VAL* 1.3 65.1 + - - +
173A ASP* 3.2 10.6 + - - +
174A MET* 3.1 26.3 + - - +
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Residues in contact with VAL 171 (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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154A ALA* 3.8 24.9 - - + +
158A THR* 3.4 31.6 - - + +
160A ARG* 4.2 25.4 - - + +
161A LYS 5.0 0.9 - - - +
162A ILE* 3.8 25.1 - - + -
167A GLU 2.9 17.2 + - - +
168A ALA 3.5 6.7 - - - +
170A GLU* 1.3 75.3 - - - +
172A MET* 1.3 63.1 + - - +
174A MET* 3.1 11.1 + - - +
175A LEU* 3.0 24.2 + - + +
185A ILE* 5.4 1.3 - - + -
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Residues in contact with MET 172 (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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168A ALA 2.8 15.6 + - - +
169A LEU* 3.3 43.7 - - + +
171A VAL* 1.3 77.0 - - - +
173A ASP* 1.3 56.5 + - - +
175A LEU* 3.3 11.9 + - + +
176A HIS* 3.0 32.9 + - - -
183A VAL* 4.2 14.3 - - + +
185A ILE* 3.9 22.0 - - + -
202A LEU* 3.5 37.0 - - + +
203A GLY 4.2 10.3 - - - +
204A SER* 3.9 30.5 - - - -
218A ARG* 5.5 0.9 - - - +
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Residues in contact with ASP 173 (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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169A LEU* 3.1 16.2 + - - +
170A GLU* 3.4 12.7 - - - +
171A VAL 3.2 0.2 - - - -
172A MET* 1.3 74.1 - - - +
174A MET* 1.3 67.3 + - + +
176A HIS* 3.1 15.2 + - - +
177A SER* 3.1 22.3 + - - -
204A SER* 4.8 0.7 + - - -
206A ARG* 3.3 24.3 + - - +
216A THR* 4.9 0.7 - - - +
218A ARG* 3.0 33.5 + - - -
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Residues in contact with MET 174 (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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158A THR* 3.7 38.1 - - + +
160A ARG* 4.0 30.7 - - + -
170A GLU 3.1 17.7 + - - +
171A VAL* 3.3 13.7 - - - +
173A ASP* 1.3 76.8 - - + +
175A LEU* 1.3 60.7 + - - +
177A SER* 2.6 21.4 + - - -
178A MET* 3.2 19.3 + - - +
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Residues in contact with LEU 175 (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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141A VAL* 4.9 3.6 - - + -
147A ILE* 4.2 13.9 - - + -
149A PRO* 4.5 4.3 - - + -
154A ALA* 4.5 15.3 - - + -
157A LEU* 4.1 23.6 - - + -
158A THR* 3.7 19.5 - - + -
171A VAL* 3.0 27.4 + - + +
172A MET* 3.5 11.4 - - + +
173A ASP 3.2 0.2 - - - -
174A MET* 1.3 74.5 - - - +
176A HIS* 1.3 65.5 + - - +
178A MET* 3.0 28.7 + - + +
179A GLY 3.3 7.6 + - - -
180A PRO* 3.5 10.3 - - - +
183A VAL* 3.8 32.5 - - + -
185A ILE* 5.7 0.4 - - + -
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Residues in contact with HIS 176 (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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172A MET 3.0 29.8 + - - -
173A ASP* 3.1 17.9 + - - +
175A LEU* 1.3 77.2 - - - +
177A SER* 1.3 57.1 + - - +
179A GLY* 3.0 24.4 + - - +
180A PRO 2.9 22.2 + - - +
181A ASP* 3.1 31.1 + - - +
183A VAL* 4.0 9.0 - - + +
204A SER* 2.7 43.6 + - - -
206A ARG* 3.5 40.5 + - + +
216A THR* 5.2 0.2 - - + -
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP 3.1 12.6 + - - -
174A MET* 2.6 26.2 + - - -
176A HIS* 1.3 75.4 - - - +
178A MET* 1.3 59.8 + - - +
179A GLY* 3.2 0.9 + - - -
206A ARG* 4.2 9.8 - - - +
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Residues in contact with MET 178 (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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137A ARG* 3.6 43.5 - - + +
141A VAL* 3.9 21.5 - - + -
142A PRO* 3.3 27.6 - - + +
157A LEU* 3.9 13.2 - - + +
158A THR* 4.4 5.6 - - - -
174A MET* 3.2 17.4 + - - +
175A LEU* 3.0 28.7 + - + +
177A SER* 1.3 77.4 - - - +
179A GLY* 1.3 56.0 + - - +
180A PRO* 3.9 2.2 - - - -
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Residues in contact with GLY 179 (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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141A VAL 4.2 3.1 - - - -
142A PRO 4.4 8.3 - - - -
144A ALA 3.8 5.2 - - - +
176A HIS 3.0 11.9 + - - +
177A SER 3.2 1.4 - - - -
178A MET* 1.3 81.8 - - - +
180A PRO* 1.3 70.5 - - - +
181A ASP* 3.4 9.2 + - - +
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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
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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