Contacts of the helix formed by residues 165 - 181 (chain A) in PDB entry 5LDH
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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164A GLY* 1.3 63.5 - - - -
166A ASN* 1.3 64.6 + - - +
167A LEU 2.9 1.6 - - - -
168A ASP* 2.9 18.1 + - - +
169A SER* 2.7 27.6 + - - +
191A ILE* 3.9 23.2 - - + +
192A LEU* 5.1 2.5 - - - -
193A GLY 5.3 0.2 - - - -
194A GLU 4.8 6.8 + - - -
270A PRO* 2.3 45.8 - - + -
271A VAL 3.5 1.3 - - - +
288A SER* 3.4 32.6 + - - -
289A LEU 4.6 1.1 - - - -
290A PRO* 5.7 0.4 - - - -
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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
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163A SER* 3.3 17.7 + - - -
164A GLY 2.5 21.3 + - - +
165A CYS* 1.3 76.3 - - - +
167A LEU* 1.3 79.1 + - - +
169A SER* 3.1 7.6 + - - -
170A ALA* 2.9 23.3 + - - +
190A TRP* 5.7 0.2 - - - -
253A SER* 3.2 30.4 + - - -
256A ASP* 5.0 3.8 - - - +
257A LEU* 5.0 10.5 - - - +
269A HIS* 4.0 23.7 - - + +
270A PRO* 2.8 13.1 - - + +
271A VAL* 3.6 11.3 - - - +
71B LEU* 5.2 3.5 - - + +
72B PHE* 4.9 8.3 - - + -
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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
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163A SER* 5.7 2.2 - - - +
164A GLY* 4.2 10.8 - - - +
166A ASN* 1.3 87.4 + - - +
168A ASP* 1.3 67.7 + - - +
170A ALA* 3.0 12.6 + - + +
171A ARG* 3.0 64.9 + - - +
195A HIS* 5.4 1.6 - - + -
249A ALA* 5.1 9.6 - - + -
250A ILE* 3.9 22.2 - - + +
253A SER* 3.8 23.8 - - - +
332A LNC 3.1 30.3 - - - +
68B HIS* 5.3 2.0 - - + -
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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* 2.9 18.0 + - - +
167A LEU* 1.3 78.3 - - - +
169A SER* 1.3 50.4 + - - +
171A ARG* 3.3 16.2 + - - +
172A PHE* 2.6 36.2 + - - +
191A ILE* 2.9 26.1 - - + +
194A GLU 4.9 2.1 - - - +
195A HIS* 4.2 29.7 + - - -
196A GLY 5.1 1.7 + - - -
199A SER* 4.2 21.4 + - - -
232A VAL* 5.9 0.5 - - - +
233A VAL* 5.2 5.9 - - - +
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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
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165A CYS 2.7 27.6 + - - -
166A ASN* 3.3 10.1 - - - -
168A ASP* 1.3 67.6 - - - +
170A ALA* 1.3 58.6 + - - +
172A PHE* 2.8 6.0 + - - +
173A ARG* 2.5 51.3 + - - +
189A GLY 4.9 7.9 - - - -
190A TRP* 4.0 20.7 - - - -
191A ILE* 2.8 19.1 + - - +
71B LEU* 6.3 0.4 - - - -
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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 2.9 12.1 + - - +
167A LEU* 3.1 17.9 - - + +
169A SER* 1.3 76.6 - - - +
171A ARG* 1.3 66.4 + - + +
173A ARG* 3.1 10.3 + - - +
174A TYR* 3.0 27.1 + - - +
253A SER* 5.6 0.2 - - - +
68B HIS* 4.2 20.6 - - + +
71B LEU* 4.0 22.1 - - + +
72B PHE* 5.6 4.5 - - + -
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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* 3.0 40.8 + - + +
168A ASP* 3.4 14.3 + - - +
170A ALA* 1.3 81.6 - - - +
172A PHE* 1.3 57.4 + - - +
174A TYR* 3.7 6.1 + - - +
175A LEU* 2.4 35.6 + - + +
232A VAL* 4.3 17.0 - - + +
235A SER* 5.2 11.0 - - - -
236A ALA* 3.5 23.8 - - - +
246A THR* 4.7 2.8 + - - +
249A ALA* 5.5 3.0 - - - +
332A LNC 2.1 50.9 + - - -
68B HIS* 3.5 47.4 + - - -
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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
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168A ASP 2.6 18.1 + - - +
169A SER* 2.8 12.8 + - - +
171A ARG* 1.3 75.0 - - - +
173A ARG* 1.3 57.0 + - - +
175A LEU* 3.2 9.3 - - + +
176A MET* 3.2 34.5 - - + +
189A GLY 3.4 26.5 - - - -
190A TRP 4.1 10.5 - - - -
191A ILE* 4.1 11.2 - - + -
201A ALA* 3.9 24.9 - - + -
202A VAL 4.4 4.9 - - - -
203A TRP* 6.1 2.7 - + + -
206A VAL* 4.3 24.0 - - + -
228A VAL* 4.3 23.8 - - + -
229A HIS* 4.4 16.2 - - + -
232A VAL* 4.2 10.4 - - + +
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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* 2.5 36.9 + - - +
170A ALA* 3.1 6.8 + - - +
172A PHE* 1.3 71.7 - - + +
174A TYR* 1.3 58.0 + - - +
176A MET* 3.9 12.1 - - + +
177A GLY* 2.8 32.7 + - - -
184A PRO 3.9 11.0 + - - -
185A SER* 3.5 12.3 + - - +
186A SER 3.2 25.1 + - - -
187A CYS* 3.6 26.2 + - - -
188A HIS* 5.1 2.2 - - - +
189A GLY 4.5 17.7 - - - +
333A CIT 3.7 23.8 + - - -
71B LEU* 3.1 44.2 - - - +
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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 3.0 15.5 + - - +
171A ARG* 4.8 4.5 - - - -
173A ARG* 1.3 74.0 - - - +
175A LEU* 1.3 90.5 + - + +
177A GLY* 3.4 0.6 - - - -
178A GLU* 2.6 62.1 + - + +
67B GLN* 2.3 49.0 + - + +
68B HIS* 5.0 17.9 - + - +
70B SER* 4.7 22.4 - - - -
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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* 2.4 33.9 - - + +
172A PHE* 3.2 11.7 - - + +
174A TYR* 1.3 100.6 - - + +
176A MET* 1.3 81.4 + - + +
178A GLU* 2.8 6.8 + - - +
179A LYS* 2.6 25.5 + - + +
228A VAL* 4.2 27.1 - - + +
231A MET* 5.3 10.5 - - + -
232A VAL* 3.3 28.9 - - + -
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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* 3.2 33.9 - - + +
173A ARG* 3.9 8.3 - - + +
174A TYR 3.3 0.4 - - - -
175A LEU* 1.3 86.3 - - + +
177A GLY* 1.3 58.9 + - - +
179A LYS* 2.8 17.7 + - + +
180A LEU* 2.5 51.6 + - + +
187A CYS* 4.3 24.2 - - + -
188A HIS 4.9 5.2 - - - +
206A VAL* 4.2 27.8 - - + -
207A ASN 4.5 11.2 - - - +
210A GLN* 5.0 5.6 - - - +
228A VAL* 5.4 7.4 - - + -
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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 2.8 18.7 + - - -
174A TYR* 3.4 0.7 - - - -
176A MET* 1.3 85.2 - - - +
178A GLU* 1.3 51.6 + - - +
180A LEU* 2.8 8.0 + - - +
181A GLY 2.5 34.3 + - - -
182A VAL* 3.4 26.4 + - - -
183A HIS 5.7 0.4 - - - -
187A CYS* 5.5 2.7 - - - -
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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* 2.6 51.8 + - + +
175A LEU* 2.8 13.1 + - - +
177A GLY* 1.3 71.2 - - - -
179A LYS* 1.3 64.2 + - - +
181A GLY* 3.2 12.5 + - - +
182A VAL 4.8 4.3 - - - +
67B GLN* 5.5 0.2 + - - -
77B LYS* 5.4 16.0 + - - +
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Residues in contact with LYS 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* 2.6 16.8 + - + +
176A MET* 3.2 13.7 - - + +
178A GLU* 1.3 71.7 - - - +
180A LEU* 1.3 76.1 + - - +
181A GLY* 4.0 0.7 - - - -
223A GLU* 4.5 9.5 + - - +
224A ASN 5.0 0.8 + - - -
225A TRP* 3.3 37.9 - - - -
228A VAL* 4.0 25.8 - - + +
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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* 2.5 36.8 + - + +
177A GLY* 2.8 10.1 + - - +
179A LYS* 1.3 81.8 - - + +
181A GLY* 1.3 52.3 - - - +
182A VAL* 4.4 10.5 - - + -
208A VAL* 3.5 41.3 - - + -
210A GLN* 4.4 23.3 - - + +
4B LYS* 2.5 64.9 + - + +
5B GLU* 6.3 1.3 - - + -
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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 2.5 11.7 + - - -
178A GLU 3.5 10.5 - - - -
179A LYS 3.2 2.1 + - - -
180A LEU* 1.3 75.6 - - - +
182A VAL* 1.3 67.7 + - - +
4B LYS* 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
------------------------------------------------------------
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