Contacts of the helix formed by residues 171 - 181 (chain M) in PDB entry 6MUO
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 171 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137M TRP* 3.2 51.4 - - + +
166M SER* 5.6 4.5 + - - -
168M LEU* 5.0 10.3 - - + +
169M ARG 2.8 10.7 + - - +
170M ARG* 1.3 82.2 - - - +
172M THR* 1.3 63.4 + - - +
173M PRO* 3.7 1.8 - - - -
174M LEU* 3.3 35.9 - - - +
175M LEU* 3.4 15.5 + - - +
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Residues in contact with THR 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M PHE* 4.5 19.3 - - + -
166M SER* 5.2 8.4 - - - -
168M LEU 5.5 0.7 + - - -
169M ARG* 4.7 17.0 + - - -
170M ARG 3.5 4.1 + - - -
171M ASN* 1.3 78.9 + - - +
173M PRO* 1.4 71.7 - - + +
175M LEU* 3.4 7.8 + - - +
176M GLY* 3.4 13.9 + - - -
190M LYS* 4.0 30.3 - - - +
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Residues in contact with PRO 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M ARG 4.4 9.4 - - - +
171M ASN 4.0 0.7 - - - -
172M THR* 1.4 95.8 - - + +
174M LEU* 1.3 59.9 + - + +
176M GLY* 3.0 4.7 + - - +
177M GLN* 2.8 38.7 + - + +
188M ILE* 5.7 0.7 - - - +
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Residues in contact with LEU 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ILE* 3.8 38.1 - - + -
137M TRP* 4.5 12.3 - - + -
170M ARG 5.7 0.9 - - - +
171M ASN* 3.3 24.9 + - - +
172M THR 3.4 0.6 - - - -
173M PRO* 1.3 80.1 - - + +
175M LEU* 1.3 55.9 + - - +
177M GLN* 3.4 27.6 - - + +
178M ALA* 2.7 36.1 + - + +
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Residues in contact with LEU 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M PHE* 4.6 12.1 - - + -
135M ILE* 4.5 21.3 - - + -
137M TRP* 4.0 25.8 - - + -
150M THR* 5.1 8.3 - - + -
152M VAL* 3.8 25.6 - - + -
163M THR* 4.2 15.0 - - + +
166M SER* 5.7 1.8 - - - +
171M ASN* 3.4 19.4 + - - +
172M THR* 3.4 7.3 + - - +
173M PRO 3.2 0.2 - - - -
174M LEU* 1.3 78.6 - - - +
176M GLY* 1.3 61.7 + - - +
178M ALA* 3.6 7.0 + - + -
179M LEU* 3.3 33.5 + - + +
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Residues in contact with GLY 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M PHE* 5.0 4.9 - - - -
172M THR 3.4 6.9 + - - -
173M PRO* 3.0 9.6 + - - -
175M LEU* 1.3 81.8 - - - +
177M GLN* 1.3 58.0 + - - +
179M LEU* 3.9 0.8 - - - -
180M THR* 2.8 35.0 + - - -
188M ILE* 3.8 31.3 - - - +
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Residues in contact with GLN 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M PRO* 2.8 28.2 + - + +
174M LEU* 3.2 28.3 + - + +
176M GLY* 1.3 73.2 - - - +
178M ALA* 1.3 63.9 + - - +
179M LEU 3.1 0.4 - - - -
180M THR* 4.8 2.0 - - - -
181M ILE* 3.2 48.2 + - + +
188M ILE* 6.2 1.1 - - + -
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Residues in contact with ALA 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M PHE* 5.3 0.5 - - - -
108M PHE 4.6 5.7 - - - +
110M LYS 5.0 7.9 + - - +
111M ILE* 4.2 35.7 - - + -
137M TRP* 5.8 2.7 - - + -
174M LEU* 2.7 24.0 + - + +
175M LEU* 4.0 10.3 - - + +
177M GLN* 1.3 71.9 - - - +
179M LEU* 1.3 58.6 + - - +
181M ILE* 5.5 0.2 - - - -
182M ALA* 3.4 22.1 - - - +
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Residues in contact with LEU 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M PHE* 6.2 1.8 - - + -
88M MET* 3.7 31.2 - - + -
104M PHE* 4.1 15.0 - - + -
152M VAL* 3.7 31.2 - - + -
154M TYR* 4.9 9.6 - - + -
161M ALA* 4.6 17.0 - - + -
163M THR* 5.7 0.2 - - - +
175M LEU* 3.3 26.4 + - + +
176M GLY* 4.1 2.9 - - - +
177M GLN 3.1 0.4 - - - -
178M ALA* 1.3 79.8 - - - +
180M THR* 1.3 59.0 + - - +
181M ILE 3.6 0.4 - - - -
182M ALA* 4.1 2.5 - - - -
183M SER* 2.9 25.6 + - - -
188M ILE* 4.4 11.0 - - + -
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Residues in contact with THR 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M MET* 3.6 4.9 - - - -
176M GLY 2.8 22.1 + - - -
177M GLN* 4.5 2.5 - - - -
179M LEU* 1.3 76.4 - - - +
181M ILE* 1.3 61.1 + - + +
183M SER* 2.9 28.8 + - - +
185M HIS* 3.5 15.5 - - + +
186M HIS* 3.6 42.0 - - - +
187M GLN 3.7 6.5 - - - +
188M ILE* 3.4 25.8 - - + +
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Residues in contact with ILE 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M LYS* 6.2 0.9 - - + +
177M GLN* 3.2 36.8 + - + +
180M THR* 1.3 79.1 - - + +
182M ALA* 1.3 58.0 + - - +
183M SER 3.0 12.0 - - - +
185M HIS 5.0 3.6 - - - +
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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