Contacts of the helix formed by residues 167 - 184 (chain A) in PDB entry 6B3I
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 ASP 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASP 4.1 1.2 - - - -
166A VAL* 1.3 68.8 - - - +
168A LYS* 1.3 58.4 + - - +
169A ASP* 2.9 27.4 + - - +
170A LEU* 3.0 30.4 + - + +
171A ALA* 2.9 25.5 + - - +
204A GLN* 2.9 17.3 + - - +
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Residues in contact with LYS 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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166A VAL* 3.4 21.4 + - + +
167A ASP* 1.3 71.6 + - - +
169A ASP* 1.3 68.2 + - - +
171A ALA* 3.9 7.9 - - - +
172A GLY* 3.2 18.4 + - - -
207A ALA* 5.9 3.1 - - + -
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Residues in contact with ASP 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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167A ASP* 2.9 13.0 + - - +
168A LYS* 1.3 81.3 + - - +
170A LEU* 1.3 56.7 + - - +
172A GLY* 3.5 1.4 + - - -
173A GLN* 3.0 28.4 + - - +
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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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167A ASP* 3.0 31.4 + - + +
169A ASP* 1.3 74.7 - - - +
171A ALA* 1.3 59.2 + - - +
173A GLN* 4.3 8.7 - - + -
174A ASP* 2.7 61.5 + - - +
200A ARG* 3.6 30.5 - - - +
204A GLN* 3.9 9.9 - - + +
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Residues in contact with ALA 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 ASP 2.9 17.6 + - - +
168A LYS* 3.9 7.4 - - - +
170A LEU* 1.3 76.7 - - - +
172A GLY* 1.3 60.4 + - - +
175A ALA* 3.1 23.4 + - - +
204A GLN* 3.4 8.2 - - - +
207A ALA* 3.7 17.7 - - + +
208A THR* 3.5 40.8 - - - +
211A ALA* 4.0 3.0 - - + +
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Residues in contact with GLY 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 LYS 3.2 12.9 + - - -
169A ASP* 4.0 2.2 - - - -
170A LEU 3.2 0.2 - - - -
171A ALA* 1.3 77.4 - - - +
173A GLN* 1.3 61.5 + - - +
175A ALA* 3.4 3.5 + - - +
176A LYS* 3.2 35.0 + - - +
211A ALA* 4.1 15.8 - - - +
215A LEU* 4.0 4.6 - - - +
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Residues in contact with GLN 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 ASP 3.0 18.8 + - - +
170A LEU* 3.8 11.0 - - + +
172A GLY* 1.3 74.6 - - - +
174A ASP* 1.3 62.1 + - - +
176A LYS* 3.1 30.3 + - - +
177A ASP* 2.9 57.9 + - - +
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Residues in contact with ASP 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* 2.7 37.0 + - - +
173A GLN* 1.3 72.9 - - - +
175A ALA* 1.3 56.6 + - - +
177A ASP* 3.2 14.5 + - - +
178A LEU* 2.8 34.0 + - - +
196A VAL* 3.9 19.4 - - + +
200A ARG* 2.7 47.3 + - - +
204A GLN* 4.8 0.5 + - - -
208A THR* 3.8 20.5 + - + -
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Residues in contact with ALA 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 ALA 3.1 20.3 + - - +
172A GLY 3.5 6.3 - - - +
173A GLN 3.2 0.2 - - - -
174A ASP* 1.3 77.2 - - - +
176A LYS* 1.3 61.4 + - - +
178A LEU* 3.4 2.0 + - - -
179A TYR* 3.1 19.1 + - - +
208A THR* 3.8 11.4 - - - +
211A ALA* 4.1 1.8 - - + -
212A TYR* 3.4 47.7 - - - +
215A LEU* 4.0 10.8 - - + -
216A ILE* 5.3 1.0 - - - +
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Residues in contact with LYS 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 GLY* 3.2 20.3 + - - +
173A GLN* 3.1 32.8 + - - +
175A ALA* 1.3 76.1 - - - +
177A ASP* 1.3 58.4 + - - +
179A TYR* 3.3 6.8 + - - +
180A ASP* 2.9 40.6 + - - +
215A LEU* 4.0 25.1 - - + -
216A ILE* 6.0 1.3 - - - -
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Residues in contact with ASP 177 (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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173A GLN* 2.9 45.7 + - - +
174A ASP* 3.6 18.3 - - - +
176A LYS* 1.3 77.9 - - - +
178A LEU* 1.3 59.3 + - + +
180A ASP* 3.3 8.2 + - - +
181A ALA* 2.9 32.5 + - - +
192A ALA* 4.8 7.2 - - + +
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Residues in contact with LEU 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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174A ASP 2.8 23.7 + - - +
175A ALA* 3.9 5.4 - - - +
176A LYS 3.4 0.2 - - - -
177A ASP* 1.3 74.4 - - - +
179A TYR* 1.3 60.6 + - - +
181A ALA* 4.4 0.2 - - - -
182A GLY* 3.7 6.1 + - - -
192A ALA* 4.1 3.4 - - + +
193A PHE* 3.2 73.2 - - + +
196A VAL* 4.0 34.1 - - + -
197A LEU* 4.7 12.1 - - + -
208A THR* 4.4 12.6 - - + -
209A PHE* 5.1 2.7 - - + -
212A TYR* 4.2 12.0 + - + -
220A ILE* 4.3 17.5 - - + -
227A GLU* 4.7 1.0 - - - +
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Residues in contact with TYR 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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175A ALA 3.1 12.7 + - - +
176A LYS* 3.7 5.2 - - - +
177A ASP 3.2 0.2 - - - -
178A LEU* 1.3 75.7 - - - +
180A ASP* 1.3 75.4 + - - +
181A ALA 3.2 0.2 - - - -
182A GLY* 3.2 2.3 + - - -
183A GLU* 3.0 61.9 + - + +
212A TYR* 3.6 29.4 - - + -
216A ILE* 3.5 38.6 - - + -
218A LYS* 5.9 2.2 - - - -
227A GLU* 5.2 3.8 - - - +
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Residues in contact with ASP 180 (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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176A LYS* 2.9 30.2 + - - +
177A ASP* 3.9 7.9 - - - +
179A TYR* 1.3 93.5 - - - +
181A ALA* 1.3 58.4 + - - +
182A GLY 3.2 1.3 + - - -
183A GLU* 4.5 4.1 - - - +
184A GLY* 3.5 18.7 + - - -
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Residues in contact with ALA 181 (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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177A ASP 2.9 18.2 + - - +
178A LEU 4.2 0.4 - - - -
179A TYR 3.2 0.6 - - - -
180A ASP* 1.3 76.4 - - - +
182A GLY* 1.3 55.4 + - - +
184A GLY* 4.7 1.6 - - - -
187A GLY 5.3 0.4 - - - -
188A THR* 3.3 8.1 - - - +
189A ASP* 2.6 56.8 + - + +
192A ALA* 3.6 18.4 - - + -
193A PHE* 3.9 14.1 - - + -
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Residues in contact with GLY 182 (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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178A LEU 3.7 4.7 + - - -
179A TYR 3.2 5.2 + - - -
180A ASP 3.2 0.2 - - - -
181A ALA* 1.3 76.8 - - - +
183A GLU* 1.3 62.7 + - - +
184A GLY 3.4 5.2 - - - +
188A THR* 4.1 14.9 + - - -
193A PHE* 4.7 0.4 - - - -
227A GLU* 3.3 44.9 - - - +
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Residues in contact with GLU 183 (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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179A TYR* 3.0 52.3 + - + +
180A ASP* 3.7 4.9 + - - +
182A GLY* 1.3 81.7 - - - +
184A GLY* 1.3 62.7 + - - +
185A ARG* 3.2 34.2 + - - +
227A GLU* 4.5 6.1 - - - +
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Residues in contact with GLY 184 (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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180A ASP 3.5 13.5 + - - -
181A ALA 4.7 1.2 - - - -
182A GLY 3.4 5.7 - - - +
183A GLU* 1.3 74.7 - - - +
185A ARG* 1.3 64.7 + - - -
186A TRP* 3.1 5.3 + - - -
187A GLY* 3.3 23.3 + - - -
188A THR* 4.4 1.0 + - - -
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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