Contacts of the helix formed by residues 165 - 181 (chain A) in PDB entry 3LDH
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 CYS 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A SER 3.5 0.8 + - - -
164A GLY* 1.3 70.1 - - - -
166A ASN* 1.3 65.6 + - - +
167A LEU 3.5 1.1 - - - -
168A ASP* 2.2 55.3 - - - +
169A SER* 3.6 4.0 + - - -
191A VAL 4.0 8.5 - - - +
192A ILE* 4.9 0.9 - - - -
193A GLY* 3.4 23.6 - - - +
194A GLN 3.9 5.6 - - - -
195A HIS 3.9 0.7 - - - -
199A VAL* 4.1 3.1 - - - -
270A PRO* 3.5 22.0 - - + +
271A VAL 4.8 3.6 - - - +
288A SER* 2.3 35.1 + - - +
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Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A SER* 3.1 20.5 + - - +
164A GLY 3.3 2.2 + - - -
165A CYS* 1.3 77.3 - - - +
167A LEU* 1.3 88.5 + - - +
169A SER* 3.4 16.1 + - - -
170A ALA* 3.8 3.8 + - - +
250A LYS* 3.2 19.2 + - - -
253A SER* 2.0 49.5 + - - -
257A LEU* 3.1 34.4 - - + +
269A HIS* 6.0 0.2 - - - -
270A PRO* 3.4 17.5 - - + +
271A VAL 5.1 0.8 - - - +
332A NAD 4.4 0.7 - - - +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY 3.7 0.7 - - - +
166A ASN* 1.3 103.6 - - - +
168A ASP* 1.3 74.6 + - - +
170A ALA* 3.0 16.6 + - + +
171A ARG* 2.4 49.1 + - + +
195A HIS* 2.7 15.9 - - + +
250A LYS* 4.2 16.6 - - + +
253A SER* 3.4 10.3 - - - +
333A PYR 1.2 77.8 - - + +
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Residues in contact with ASP 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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165A CYS* 2.2 52.9 + - - +
166A ASN 3.1 0.4 - - - -
167A LEU* 1.3 90.2 - - - +
169A SER* 1.3 64.0 + - - +
171A ARG* 3.3 16.3 + - - +
172A PHE* 3.1 15.2 + - - +
191A VAL* 3.7 10.9 - - + +
195A HIS* 3.6 23.0 + - - -
199A VAL* 3.9 6.8 - - - +
231A TRP* 4.1 22.0 - - - -
234A GLY* 4.8 6.2 - - - +
235A LEU* 5.7 0.3 - - - -
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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 CYS 3.8 4.5 + - - -
166A ASN 3.4 10.8 + - - -
167A LEU 3.1 0.6 + - - -
168A ASP* 1.3 77.2 - - - +
170A ALA* 1.3 51.6 + - - +
172A PHE* 2.6 8.9 + - - +
173A ARG* 2.3 42.5 + - - -
189A GLY 4.3 10.9 - - - +
190A TRP* 4.4 12.0 - - - -
191A VAL* 3.4 28.9 + - - +
270A PRO* 4.1 10.7 - - - +
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Residues in contact with ALA 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 ASN 3.8 1.9 + - - +
167A LEU* 3.0 21.1 + - + +
169A SER* 1.3 75.3 - - - +
171A ARG* 1.3 52.1 + - + +
173A ARG* 3.7 8.6 - - - +
174A TYR* 2.3 44.2 + - - +
184A SER* 5.0 2.2 - - - -
253A SER* 5.0 4.7 - - - +
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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 LEU* 2.4 50.8 + - + +
168A ASP* 3.9 14.3 + - - +
170A ALA* 1.3 78.7 - - + +
172A PHE* 1.3 55.4 + - - +
174A TYR* 3.9 16.4 - - + -
175A LEU* 2.6 48.3 + - + +
195A HIS* 5.3 0.6 - - - -
234A GLY* 3.8 14.4 + - - -
237A VAL* 2.8 51.4 - - + +
238A SER* 4.9 2.8 + - - +
247A VAL* 5.9 2.2 - - - +
250A LYS* 5.2 3.8 - - - +
333A PYR 2.7 7.9 + - - -
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP 3.1 4.1 + - - +
169A SER 2.6 15.8 + - - +
171A ARG* 1.3 72.1 - - - +
173A ARG* 1.3 60.4 + - - -
175A LEU* 4.1 7.0 - - + +
176A MET* 2.7 54.5 + - + +
189A GLY 4.4 2.5 - - - -
190A TRP 3.8 15.9 - - - -
191A VAL* 3.2 40.4 - - + -
201A SER* 4.4 11.0 - - - -
203A TRP* 4.4 14.6 - + - -
206A MET* 3.9 24.9 - - + -
230A SER* 4.0 18.1 + - - -
231A TRP* 3.7 36.8 - + + -
234A GLY* 6.0 2.0 - - - -
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Residues in contact with ARG 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 SER* 2.3 35.6 + - - +
170A ALA* 3.7 7.4 - - - +
172A PHE* 1.3 66.3 - - - +
174A TYR* 1.3 58.4 + - - +
176A MET* 2.5 36.9 - - - +
177A GLY 3.3 0.3 + - - -
184A SER* 2.6 23.2 + - - +
185A CYS* 2.5 32.5 + - - +
187A VAL* 2.6 37.6 + - + +
188A ILE* 2.8 28.3 - - - +
189A GLY 2.9 28.2 + - - +
190A TRP* 5.6 5.1 - - - +
269A HIS* 6.3 1.4 - - - -
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Residues in contact with TYR 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 ALA 2.3 35.6 + - - +
171A ARG* 3.5 19.3 - - + -
173A ARG* 1.3 64.5 - - - +
175A LEU* 1.3 101.1 + - + +
176A MET 2.8 2.1 + - - -
177A GLY* 3.0 11.7 + - - +
178A GLU* 3.8 20.7 + - + +
183A HIS* 4.1 23.6 + + + +
184A SER* 4.2 16.3 + - - +
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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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171A ARG* 2.6 35.0 + - + +
172A PHE* 4.1 6.3 - - + +
174A TYR* 1.3 99.7 - - + +
176A MET* 1.3 64.8 + - - +
178A GLU* 3.1 23.3 + - + +
179A ARG* 4.1 2.8 + - - +
230A SER* 4.8 24.0 - - - +
233A ILE* 4.9 18.8 - - + +
234A GLY* 5.3 2.7 - - - -
237A VAL* 5.0 4.9 - - + -
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Residues in contact with MET 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 PHE* 2.7 79.2 + - + +
173A ARG* 2.5 27.8 - - - +
174A TYR 2.8 0.4 - - - -
175A LEU* 1.3 78.7 - - - +
177A GLY* 1.3 59.5 + - - +
178A GLU 3.2 1.2 + - - -
179A ARG* 3.4 12.2 + - - +
180A LEU* 3.4 23.2 - - + +
187A VAL* 3.6 12.1 - - + -
188A ILE 5.1 0.4 - - - -
189A GLY* 3.6 26.9 - - - -
206A MET* 4.5 11.4 - - + +
213A LYS* 6.0 7.2 - - - -
230A SER* 5.6 5.5 + - - +
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Residues in contact with GLY 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 ARG 3.3 3.2 + - - -
174A TYR 3.0 11.2 + - - -
176A MET* 1.3 74.1 - - - +
178A GLU* 1.3 66.3 + - - +
180A LEU* 3.6 7.9 - - - -
181A GLY* 2.9 24.4 + - - -
182A VAL 2.9 22.9 - - - +
183A HIS* 4.3 11.4 - - - -
184A SER 4.7 0.4 - - - -
187A VAL* 4.0 6.5 - - - +
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Residues in contact with GLU 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 TYR* 3.8 22.8 + - + +
175A LEU* 3.1 17.3 + - + +
177A GLY* 1.3 79.5 - - - +
179A ARG* 1.3 64.4 + - + +
181A GLY* 4.0 5.4 + - - -
183A HIS* 5.9 2.8 - - - -
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Residues in contact with ARG 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 LEU 4.1 2.0 + - - +
176A MET* 3.4 8.3 + - - +
177A GLY 3.3 0.4 - - - -
178A GLU* 1.3 82.6 - - + +
180A LEU* 1.3 66.1 + - + +
225A LEU* 4.2 31.9 + - - +
226A LYS 5.9 0.2 - - - -
227A GLY* 5.8 4.6 - - - +
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Residues in contact with LEU 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 MET* 3.4 21.8 - - + +
177A GLY* 3.1 12.0 + - - +
178A GLU 4.5 0.2 - - - -
179A ARG* 1.3 87.6 - - + +
181A GLY* 1.3 63.0 + - - +
182A VAL* 4.1 13.5 - - + +
187A VAL* 3.9 21.3 - - + -
208A ASP* 4.6 12.3 - - - +
213A LYS* 5.6 13.5 - - + +
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Residues in contact with GLY 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 GLY 2.9 10.7 + - - -
178A GLU 4.0 3.3 + - - -
179A ARG 3.8 1.0 - - - -
180A LEU* 1.3 71.4 - - - +
182A VAL* 1.3 77.5 + - - +
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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