Contacts of the helix formed by residues 164 - 177 (chain A) in PDB entry 8LDH
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 ASN 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A SER* 3.4 16.2 + - - +
162A GLY 3.6 0.4 - - - -
163A CYS* 1.3 73.3 - - - +
165A LEU* 1.3 60.8 - - - +
167A SER* 3.0 6.6 + - - -
168A ALA* 2.9 28.3 + - - +
252A SER* 2.9 41.4 + - - +
255A ASP* 5.1 4.2 + - - +
256A LEU* 3.7 16.4 - - + +
268A HIS* 3.2 24.3 + - - +
269A PRO* 3.0 25.7 + - - +
270A VAL* 4.2 2.2 - - + -
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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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161A SER* 4.9 4.3 + - - +
162A GLY 5.0 2.5 + - - +
163A CYS 3.5 0.4 - - - -
164A ASN* 1.3 79.2 - - - +
166A ASP* 1.3 52.6 + - - +
168A ALA* 3.0 18.5 - - + +
169A ARG* 2.8 72.4 + - + +
248A ALA* 3.7 26.5 - - + +
249A ILE* 3.4 43.7 - - + +
252A SER* 3.9 15.0 + - - +
330A CIT 4.4 7.0 - - - +
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Residues in contact with ASP 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 GLY 5.1 0.7 - - - -
163A CYS* 3.6 22.9 - - - +
165A LEU* 1.3 79.0 - - - +
167A SER* 1.3 55.8 + - - +
169A ARG* 3.2 16.6 + - - -
170A PHE* 2.9 24.1 + - - +
189A VAL* 4.0 18.1 - - + +
193A HIS* 3.1 36.0 + - - -
194A GLY* 5.2 1.3 - - - -
197A VAL* 4.2 7.4 - - - +
231A VAL* 3.3 25.8 - - + +
232A VAL* 5.4 3.3 - - - +
330A CIT 4.4 6.9 - - - +
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Residues in contact with SER 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 CYS 3.1 12.7 + - - -
164A ASN 3.0 9.9 + - - -
166A ASP* 1.3 74.2 - - - +
168A ALA* 1.3 57.1 + - - +
169A ARG 3.0 1.6 - - - -
170A PHE* 3.5 7.2 - - - +
171A ARG* 2.7 45.4 + - - +
187A GLY 4.6 9.6 - - - -
188A TRP* 4.2 1.5 - - - -
189A VAL* 3.1 31.9 + - - +
269A PRO* 3.9 15.8 - - - +
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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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164A ASN* 2.9 13.5 + - - +
165A LEU* 3.0 27.8 - - + +
167A SER* 1.3 76.5 - - - +
169A ARG* 1.4 54.1 - - - -
171A ARG* 4.0 8.1 + - - +
172A TYR* 3.3 23.2 + - - +
182A SER* 5.0 2.9 + - - -
252A SER* 6.0 1.6 - - - -
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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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165A LEU* 2.8 55.1 + - + +
166A ASP* 3.6 13.5 + - - +
167A SER 3.0 0.2 - - - -
168A ALA* 1.4 75.6 - - - +
170A PHE* 1.3 61.6 + - - +
172A TYR* 3.2 7.9 + - + +
173A LEU* 2.9 36.2 + - + +
231A VAL* 4.0 28.9 + - + +
234A SER* 6.2 1.8 - - - -
235A ALA* 3.5 22.5 - - - +
238A VAL* 5.4 6.3 - - - +
245A THR* 4.7 13.3 - - - +
248A ALA* 4.2 13.4 - - - +
330A CIT 2.8 39.4 + - - +
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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 ASP 2.9 16.9 + - - +
167A SER* 3.1 7.4 + - - +
169A ARG* 1.3 74.9 - - - +
171A ARG* 1.3 65.4 + - - +
173A LEU* 3.1 3.9 + - - +
174A MET* 2.9 30.0 + - - +
187A GLY* 4.3 20.6 - - - -
188A TRP 4.5 3.8 - - - -
189A VAL* 4.0 20.2 - - + -
199A SER* 4.4 9.6 - - - -
200A VAL 5.5 0.2 - - - -
201A TRP* 3.9 14.1 - + - -
204A MET* 3.5 45.1 - - + -
227A LEU* 3.7 45.1 - - + -
228A HIS* 4.2 9.2 - - + -
231A VAL* 3.6 10.0 - - + +
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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 SER* 2.7 28.3 + - - +
168A ALA* 4.1 7.8 - - - +
170A PHE* 1.3 74.8 - - - +
172A TYR* 1.3 60.3 + - - +
174A MET* 3.5 9.7 + - - +
175A GLY 3.2 16.5 + - - -
182A SER* 3.5 32.3 + - - +
183A CYS* 3.7 19.2 + - - +
185A CYS* 2.7 41.8 + - - +
186A HIS* 3.7 7.4 + - - +
187A GLY* 4.1 21.4 + - - +
188A TRP* 6.0 1.8 - - - -
331A CIT 2.5 45.8 + - - -
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Residues in contact with TYR 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 3.3 14.3 + - - +
169A ARG* 3.2 12.3 + - + +
170A PHE 3.2 0.4 - - - -
171A ARG* 1.3 73.7 - - - +
173A LEU* 1.3 88.1 + - + +
175A GLY* 3.2 3.6 + - - -
176A GLU* 3.0 57.2 + - + +
182A SER* 3.7 17.6 - - - +
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Residues in contact with LEU 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 ARG* 2.9 16.5 + - + +
170A PHE 3.9 2.5 - - - +
172A TYR* 1.3 97.7 - - + +
174A MET* 1.3 62.9 + - - +
176A GLU* 3.2 7.6 + - + +
177A ARG* 3.1 25.5 + - - +
227A LEU* 3.6 23.1 - - + +
230A ASP* 3.1 31.2 - - - +
231A VAL* 3.2 32.3 - - + +
234A SER* 5.7 4.9 - - - +
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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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170A PHE* 2.9 21.8 + - + +
171A ARG* 3.5 12.1 - - - +
173A LEU* 1.3 75.4 - - - +
175A GLY* 1.3 53.2 - - - +
177A ARG* 3.2 5.2 + - - +
178A LEU* 2.4 54.7 + - + +
185A CYS* 4.0 23.1 - - + -
186A HIS 4.3 22.0 - - - +
187A GLY* 4.5 5.2 - - - -
204A MET* 3.7 18.2 - - + -
205A ASN 4.5 7.2 - - - +
206A VAL* 4.6 0.2 - - + -
211A LEU* 3.7 30.5 - - + -
224A TRP* 4.5 3.6 - - + -
227A LEU* 3.7 23.2 - - + +
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Residues in contact with GLY 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 3.2 4.8 + - - -
172A TYR 3.2 7.7 + - - -
174A MET* 1.3 81.1 - - - +
176A GLU* 1.3 60.8 + - - +
178A LEU 4.2 0.7 - - - -
179A GLY* 2.6 30.3 + - - -
180A VAL 3.2 24.3 - - - +
181A HIS 4.9 2.2 - - - -
182A SER* 5.0 1.1 - - - -
185A CYS* 3.6 13.0 - - - -
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Residues in contact with GLU 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 TYR* 3.0 53.1 + - + +
173A LEU* 3.6 11.2 - - + +
174A MET 3.2 0.6 - - - -
175A GLY* 1.3 83.3 - - - +
177A ARG* 1.3 59.3 + - + +
179A GLY* 4.1 5.2 + - - -
180A VAL 5.4 0.2 - - - +
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Residues in contact with ARG 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 LEU 3.1 11.8 + - - +
174A MET 3.4 7.9 - - - +
176A GLU* 1.3 79.5 - - - +
178A LEU* 1.3 65.3 + - - +
223A ASP* 2.7 32.3 + - - +
224A TRP* 3.4 59.5 + - + +
226A LYS* 3.8 21.8 - - - +
227A LEU* 4.2 16.1 - - + +
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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