Contacts of the helix formed by residues 175 - 187 (chain A) in PDB entry 3MDY
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 SER 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLU* 1.3 73.6 - - - +
176A LEU* 1.3 51.8 + - - +
177A ARG* 4.3 4.5 + - - +
178A ASP* 2.6 59.3 + - - +
179A LEU* 2.9 15.3 + - - +
226A GLU* 4.3 5.5 + - - -
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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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174A GLU 2.9 18.4 + - - +
175A SER* 1.3 69.4 + - - +
177A ARG* 1.3 58.9 + - - +
179A LEU* 3.6 7.0 - - + +
180A ILE* 2.9 41.0 + - + +
192A LEU* 4.3 7.2 - - + -
223A TRP* 3.2 55.4 - - + +
224A ARG* 4.5 3.8 - - + -
226A GLU* 3.4 34.6 + - + +
228A VAL* 5.0 9.0 - - + -
262A ILE* 4.2 26.2 - - + -
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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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175A SER* 3.0 5.1 + - - +
176A LEU* 1.3 78.3 - - - +
178A ASP* 1.3 56.6 + - - +
180A ILE* 3.1 9.6 + - - +
181A GLU* 2.7 51.6 + - - +
226A GLU* 4.5 3.8 + - - +
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Residues in contact with ASP 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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175A SER* 2.6 38.9 + - - +
177A ARG* 1.3 75.5 - - - +
179A LEU* 1.3 51.1 + - + +
181A GLU* 3.7 16.2 - - - +
182A GLN* 2.7 52.1 + - + +
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Residues in contact with LEU 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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174A GLU* 3.2 43.1 - - - +
175A SER 2.9 19.9 + - - +
176A LEU* 3.6 9.0 - - + +
178A ASP* 1.3 76.2 - - + +
180A ILE* 1.3 60.0 + - - +
182A GLN* 3.6 13.4 + - - +
183A SER* 3.0 27.0 + - - -
192A LEU* 3.8 21.1 - - + +
193A PRO* 5.0 0.7 - - - +
196A VAL* 4.8 12.3 - - + -
223A TRP* 4.9 5.8 - - + -
224A ARG* 4.0 27.8 - - - +
45B LYS* 4.5 17.7 - - - +
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Residues in contact with ILE 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 LEU* 2.9 31.5 + - + +
177A ARG* 3.5 7.0 - - - +
179A LEU* 1.3 74.1 - - - +
181A GLU* 1.3 65.5 + - + +
183A SER* 2.9 18.7 + - - -
184A GLN* 3.0 43.7 + - + +
191A GLY* 4.5 7.2 - - - +
192A LEU* 3.7 19.3 - - + +
254A ARG* 4.1 17.3 - - - +
261A PHE 4.8 1.8 - - - +
262A ILE* 3.9 35.0 - - + -
280A ASP* 5.2 2.7 - - - +
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Residues in contact with GLU 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 ARG* 2.7 43.1 + - - +
178A ASP* 3.7 15.1 + - - +
180A ILE* 1.3 76.2 - - + +
182A GLN* 1.3 55.7 + - + +
184A GLN* 4.1 6.0 - - - +
185A SER* 2.7 36.1 + - - +
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Residues in contact with GLN 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 ASP* 2.7 39.3 + - + +
179A LEU* 3.7 13.4 - - - +
181A GLU* 1.3 73.7 - - + +
183A SER* 1.3 61.8 + - - +
185A SER* 3.7 14.4 - - - -
186A SER 3.8 1.9 + - - -
43B ARG* 3.6 28.3 - - + +
45B LYS* 3.1 42.0 + - - +
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Residues in contact with SER 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 LEU 3.0 11.0 + - - -
180A ILE* 2.9 17.2 + - - -
182A GLN* 1.3 78.3 - - - +
184A GLN* 1.3 61.6 + - - +
185A SER 3.3 0.2 - - - -
186A SER* 3.4 17.3 - - - -
187A GLY 3.4 8.7 + - - +
189A GLY 5.0 1.9 - - - +
191A GLY 3.4 15.7 + - - -
193A PRO* 3.4 34.7 - - - +
43B ARG* 3.9 15.3 - - - +
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Residues in contact with GLN 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 ILE* 3.0 32.6 + - - +
181A GLU* 4.4 6.0 - - - +
183A SER* 1.3 74.2 - - - +
185A SER* 1.3 64.1 + - - +
186A SER 3.3 0.4 - - - -
187A GLY* 3.7 13.6 + - - +
189A GLY 3.4 22.0 - - - +
190A SER* 3.4 4.1 - - - -
191A GLY 2.6 31.9 + - - +
254A ARG* 3.1 42.0 + - - +
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Residues in contact with SER 185 (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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181A GLU* 2.7 23.8 + - - +
182A GLN* 3.7 9.5 - - - -
184A GLN* 1.3 74.4 - - - +
186A SER* 1.3 67.3 + - - +
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Residues in contact with SER 186 (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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182A GLN 3.8 2.6 + - - -
183A SER* 3.4 13.8 + - - -
185A SER* 1.3 82.2 - - - +
187A GLY* 1.3 62.4 + - - -
39B SER 4.8 1.7 + - - -
42B ASP* 3.4 46.0 + - - +
43B ARG* 4.3 11.8 + - - +
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Residues in contact with GLY 187 (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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183A SER 3.4 9.8 + - - +
184A GLN* 3.8 12.6 - - - -
185A SER 4.5 0.2 - - - -
186A SER* 1.3 84.8 + - - +
188A SER* 1.3 67.4 + - - -
189A GLY 3.1 11.3 + - - +
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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