Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 3DBI
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 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 TRP* 4.0 25.3 - - + -
163A CYS* 1.3 70.1 - - - +
165A HIS* 1.3 55.5 + - - +
166A LYS* 3.6 11.8 + - - +
167A GLN* 3.3 33.8 + - + +
168A THR* 2.8 32.2 + - - -
198A GLU* 5.6 0.2 - - - -
322A THR* 5.8 3.6 - - + -
323A PHE 2.8 16.4 + - - +
324A SER* 4.7 4.9 - - - -
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Residues in contact with HIS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.4 18.5 + - - -
150A ASN* 3.0 28.8 + - - -
163A CYS* 2.9 42.6 + - - +
164A ASP* 1.3 72.3 + - - +
166A LYS* 1.3 58.2 + - - +
168A THR* 3.9 5.7 - - - +
169A SER* 3.1 27.9 + - - -
195A THR* 3.7 26.0 - - + +
198A GLU* 3.9 28.4 + - + +
199A ARG* 3.4 37.2 + - + +
295A ILE* 4.2 8.6 - - + +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 3.2 9.8 + - - +
165A HIS* 1.3 76.9 - - - +
167A GLN* 1.3 63.1 + - + +
169A SER 3.4 1.0 + - - -
170A PHE* 3.0 25.0 + - + +
198A GLU* 3.4 29.8 - - + +
201A ALA* 3.8 20.2 + - + +
202A GLY* 3.4 32.7 - - - +
205A ASP* 3.8 24.3 + - + -
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Residues in contact with GLN 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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164A ASP* 3.3 30.7 + - + +
166A LYS* 1.3 78.6 - - + +
168A THR* 1.3 61.4 + - - +
170A PHE* 3.3 25.9 + - - +
171A ASN* 2.8 71.3 + - - +
324A SER* 5.6 5.2 - - - -
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Residues in contact with THR 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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163A CYS* 4.3 1.9 - - - -
164A ASP 2.8 21.7 + - - -
165A HIS* 3.9 9.2 - - - +
167A GLN* 1.3 76.9 - - - +
169A SER* 1.3 61.7 + - - +
171A ASN* 3.5 5.8 + - - +
172A ALA* 3.2 23.2 + - - +
277A PHE* 4.3 7.6 - - + -
293A VAL* 3.5 31.9 - - + -
295A ILE* 4.3 8.1 - - + -
324A SER* 3.5 7.9 - - - -
325A GLY* 2.9 37.7 + - - +
326A LYS* 5.4 0.2 - - - -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A HIS 3.1 19.9 + - - -
166A LYS 3.7 4.7 - - - -
168A THR* 1.3 74.0 - - - +
170A PHE* 1.3 65.9 + - - +
172A ALA* 3.3 2.9 + - - +
173A VAL* 3.0 31.4 + - - +
186A PHE* 4.4 3.1 - - - -
199A ARG* 2.6 37.2 + - - +
202A GLY* 4.2 2.0 - - - -
203A TYR* 3.7 4.9 + - - -
277A PHE* 4.0 24.1 - - - -
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Residues in contact with PHE 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 LYS* 3.0 15.4 + - + +
167A GLN* 3.3 25.8 - - - +
169A SER* 1.3 74.5 - - - +
171A ASN* 1.3 68.0 + - - +
173A VAL* 3.1 4.5 + - - +
174A ALA* 2.7 44.6 + - + +
202A GLY* 3.5 13.6 + - - +
205A ASP* 3.8 14.1 - - + -
206A ALA* 3.6 33.6 - - - +
209A GLN* 3.4 38.8 - - + -
210A HIS* 4.5 13.9 - + - -
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Residues in contact with ASN 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 GLN* 2.8 55.5 + - - +
168A THR* 3.8 7.5 - - - +
169A SER 3.4 0.2 - - - -
170A PHE* 1.3 81.6 - - - +
172A ALA* 1.3 56.6 + - - +
174A ALA* 3.3 6.6 + - - +
175A GLU* 3.0 37.1 + - - +
324A SER* 5.5 4.2 + - - -
325A GLY 5.1 8.0 + - - +
326A LYS* 6.5 0.7 - - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR 3.2 14.2 + - - +
169A SER* 3.7 6.3 - - - +
170A PHE 3.3 0.2 - - - -
171A ASN* 1.3 77.8 - - - +
173A VAL* 1.3 62.3 + - + +
175A GLU* 3.3 12.3 + - - +
176A LEU* 3.4 19.0 + - - +
275A ILE* 4.1 14.6 - - + -
277A PHE* 4.9 2.5 - - + -
293A VAL* 3.8 26.0 - - + -
327A LEU* 4.1 20.8 - - + +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.0 26.1 + - - +
170A PHE 3.7 2.9 - - - +
172A ALA* 1.3 74.0 - - + +
174A ALA* 1.3 63.2 + - - +
176A LEU* 3.3 8.7 + - + +
177A ILE* 3.1 26.4 + - + +
184A ILE* 4.2 17.9 - - + -
203A TYR* 4.1 41.7 - - + +
206A ALA* 3.7 21.5 - - + -
207A LEU* 4.4 2.5 - - + -
247A VAL* 4.3 20.9 - - + -
277A PHE* 6.1 0.2 - - + -
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Residues in contact with ALA 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 PHE* 2.7 29.5 + - + +
171A ASN* 3.4 11.4 - - - +
173A VAL* 1.3 74.7 - - - +
175A GLU* 1.3 57.1 + - - +
177A ILE* 3.3 9.7 + - - +
178A ASN* 2.9 41.0 + - - +
206A ALA* 4.4 1.5 - - + +
210A HIS* 4.1 21.5 + - + +
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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 ASN* 3.0 20.5 + - - +
172A ALA 3.3 8.7 + - - +
173A VAL 3.3 0.4 - - - -
174A ALA* 1.3 76.2 - - + +
176A LEU* 1.3 57.7 + - - +
178A ASN* 3.9 8.8 - - - +
179A ALA* 3.1 28.4 + - - +
326A LYS* 5.8 1.6 - - - +
327A LEU* 3.9 40.2 + - + +
329A ARG* 4.1 19.2 + - - +
333A LEU* 5.7 4.5 - - + +
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Residues in contact with LEU 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 ALA 3.4 17.0 + - - +
173A VAL* 3.3 13.2 + - - +
174A ALA 3.3 0.6 - - - -
175A GLU* 1.3 76.6 - - - +
177A ILE* 1.3 62.6 + - - +
179A ALA* 3.4 3.0 + - - -
180A GLY 3.4 3.8 + - - -
181A HIS* 3.0 36.3 + - + +
184A ILE* 4.0 13.9 - - + -
245A ALA* 3.7 26.2 - - + -
246A LEU 5.5 0.9 - - - +
247A VAL* 3.8 29.6 - - + -
273A SER* 4.8 2.2 - - - +
275A ILE* 3.8 22.2 - - + -
327A LEU* 5.5 0.4 - - + -
333A LEU* 3.6 31.2 - - + -
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Residues in contact with ILE 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 VAL* 3.1 20.4 + - + +
174A ALA* 3.3 6.9 + - - +
176A LEU* 1.3 76.2 - - - +
178A ASN* 1.3 56.2 + - - +
180A GLY* 2.8 22.3 + - - -
181A HIS 3.5 16.7 + - - +
182A GLN* 4.3 10.7 + - - +
184A ILE* 3.8 10.1 - - + -
206A ALA* 3.6 30.1 - - + +
207A LEU* 4.2 7.4 - - + -
210A HIS* 3.6 38.6 - - + +
212A ILE* 3.9 19.7 - - + -
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Residues in contact with ASN 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 ALA* 2.9 29.2 + - - +
175A GLU* 4.0 9.0 - - - +
176A LEU 3.4 0.2 - - - -
177A ILE* 1.3 75.8 - - - +
179A ALA* 1.3 58.1 + - - +
180A GLY 3.2 1.5 + - - -
210A HIS* 3.9 20.3 + - - -
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Residues in contact with ALA 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 GLU 3.1 17.6 + - - +
176A LEU* 3.7 7.6 - - - +
177A ILE 3.2 0.8 - - - -
178A ASN* 1.3 76.5 - - - +
180A GLY* 1.3 56.0 + - - +
181A HIS* 3.7 10.8 - - + -
329A ARG* 4.8 15.5 - - - +
333A LEU* 5.2 3.4 - - + -
334A ILE 4.4 8.3 - - - +
335A ALA* 3.2 28.7 - - + +
336A PRO* 3.4 5.8 - - - +
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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