Contacts of the helix formed by residues 161 - 175 (chain A) in PDB entry 6O81
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 ILE 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 6.3 0.7 - - + -
82A PHE* 5.0 4.5 - - + -
86A THR* 3.7 19.6 - - + +
149A LEU* 3.7 28.5 - - + -
159A ILE* 3.7 27.1 - - + +
160A ASN* 1.3 76.6 + - - +
162A THR* 1.3 53.2 + - - +
163A ARG* 3.2 2.5 - - - +
164A ALA* 3.8 14.6 - - + +
165A LEU* 2.8 35.9 + - + +
184A ILE* 3.7 25.6 - - + -
249A ILE* 4.7 9.0 - - + -
251A ILE* 3.8 20.9 - - + -
290A HIS* 5.3 4.0 - - + +
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Residues in contact with THR 162 (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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43A LEU* 6.3 2.2 - - + -
86A THR* 4.3 11.7 - - + +
160A ASN* 3.3 34.8 + - - +
161A ILE* 1.3 76.7 - - - +
163A ARG* 1.3 59.6 + - - +
165A LEU* 3.7 13.0 - - + +
166A GLU* 2.9 37.2 + - - +
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Residues in contact with ARG 163 (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 ASN 4.8 4.8 + - - +
161A ILE* 3.2 1.0 - - - +
162A THR* 1.3 82.7 + - - +
164A ALA* 1.3 56.0 + - - +
166A GLU* 3.4 6.7 + - - +
167A GLU* 2.9 49.6 + - + +
290A HIS* 4.4 20.4 + - + +
295A GLU* 5.9 0.6 + - - -
468E GLY* 4.8 9.7 - - - -
469E GLU* 3.1 43.7 + - - +
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Residues in contact with ALA 164 (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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161A ILE* 3.3 19.4 + - + +
163A ARG* 1.3 76.0 - - - +
165A LEU* 1.3 60.2 + - - +
167A GLU* 3.6 12.4 - - - +
168A HIS* 2.9 29.8 + - - +
171A ARG* 4.7 2.1 + - - -
182A THR* 4.7 3.4 - - + +
184A ILE* 4.9 3.4 - - + -
251A ILE* 4.0 12.3 - - + +
290A HIS* 3.6 39.9 + - + +
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Residues in contact with LEU 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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43A LEU* 3.8 34.5 - - + -
147A ASP* 4.3 20.9 - - + +
161A ILE* 2.8 23.0 + - + +
162A THR* 3.7 13.0 - - + +
164A ALA* 1.3 73.2 - - - +
166A GLU* 1.3 59.3 + - - +
168A HIS* 3.4 3.3 + - + +
169A ARG* 2.9 73.7 + - + +
251A ILE* 4.1 21.9 - - + +
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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
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162A THR* 2.9 23.5 + - - +
163A ARG* 3.8 5.8 - - - +
165A LEU* 1.3 75.2 - - - +
167A GLU* 1.3 60.9 + - - +
169A ARG* 2.9 41.0 + - - +
170A LEU* 2.9 37.2 + - + +
173A LYS* 5.5 3.1 + - - -
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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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163A ARG* 2.9 37.2 + - + +
164A ALA* 3.6 6.8 - - - +
166A GLU* 1.3 76.3 - - - +
168A HIS* 1.3 57.2 + - - +
170A LEU* 3.3 18.9 - - + +
171A ARG* 2.9 53.4 + - - +
182A THR* 6.1 0.3 - - - +
210A ASN* 5.3 7.2 + - - -
289A MET 5.5 0.7 - - - +
290A HIS* 3.5 27.6 - - - +
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Residues in contact with HIS 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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147A ASP* 3.2 35.4 + - + -
164A ALA 2.9 18.0 + - - +
165A LEU* 3.7 7.2 - - + +
167A GLU* 1.3 75.7 - - - +
169A ARG* 1.3 57.6 + - - +
171A ARG* 3.4 7.7 + - - +
172A ARG* 2.9 34.1 + - + +
179A SER* 3.6 36.1 + - - -
180A VAL 3.7 19.3 + - - -
181A MET 4.1 0.9 - - - -
182A THR* 2.8 29.7 + - - +
251A ILE* 4.5 8.7 - - + -
252A CYS* 4.1 9.3 - - - -
253A SER* 3.6 11.5 + - - -
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Residues in contact with ARG 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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41A PRO* 4.2 31.8 + - - +
42A PRO 4.4 9.1 + - - -
43A LEU* 4.6 6.5 - - - +
146A SER 5.5 1.2 + - - -
147A ASP* 3.4 29.6 + - - +
165A LEU* 2.9 51.6 + - + +
166A GLU* 2.9 36.3 + - - +
167A GLU 3.3 0.2 - - - -
168A HIS* 1.3 77.0 - - - +
170A LEU* 1.3 57.6 + - - +
172A ARG* 3.3 5.2 + - - +
173A LYS* 2.9 50.2 + - - +
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Residues in contact with LEU 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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166A GLU* 2.9 22.7 + - + +
167A GLU* 3.3 27.4 - - + +
169A ARG* 1.3 74.3 - - - +
171A ARG* 1.3 72.3 + - + +
173A LYS* 3.7 9.6 - - + +
174A LEU* 2.9 50.4 + - + +
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Residues in contact with ARG 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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167A GLU* 2.9 47.5 + - - +
168A HIS* 3.6 15.5 - - - +
170A LEU* 1.3 86.6 - - + +
172A ARG* 1.3 60.9 + - - +
174A LEU* 5.1 3.4 - - - -
175A GLU* 3.4 30.9 + - + +
179A SER* 3.9 16.4 + - - -
182A THR* 3.1 41.4 + - - +
209A THR* 4.9 6.3 + - - -
210A ASN* 3.8 16.0 + - - +
288A HIS* 3.3 48.1 + - + +
289A MET 5.0 1.6 + - - +
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Residues in contact with ARG 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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147A ASP* 3.3 25.7 + - - -
168A HIS* 2.9 25.4 + - + +
169A ARG* 3.7 5.6 - - - +
171A ARG* 1.3 78.2 - - - +
173A LYS* 1.3 61.8 + - + +
176A LYS* 3.3 4.7 + - - -
177A ASN* 3.1 44.9 + - - +
179A SER* 3.3 30.8 + - - +
180A VAL* 4.6 0.2 - - - +
253A SER* 2.5 36.7 + - - -
254A PRO* 5.7 3.3 - - - +
255A GLN* 3.2 31.1 - - - +
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Residues in contact with LYS 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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166A GLU* 5.5 3.2 + - - -
169A ARG* 2.9 38.7 + - - +
170A LEU* 3.2 8.9 + - + +
172A ARG* 1.3 76.6 - - + +
174A LEU* 1.3 69.6 + - + +
176A LYS* 4.1 4.2 + - - -
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Residues in contact with LEU 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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170A LEU* 2.9 37.3 + - + +
171A ARG* 4.8 1.6 - - - +
173A LYS* 1.3 83.9 - - + +
175A GLU* 1.3 64.6 + - + +
176A LYS* 3.3 6.7 + - - +
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Residues in contact with GLU 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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171A ARG* 3.4 21.8 + - - +
174A LEU* 1.3 81.0 - - + +
176A LYS* 1.3 69.4 + - - +
177A ASN 3.6 1.8 - - - -
178A VAL* 3.4 21.8 - - + +
179A SER 5.0 1.1 + - - +
286A GLN* 2.6 32.4 + - - -
288A HIS* 4.2 11.4 + - - -
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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