Contacts of the helix formed by residues 172 - 183 (chain A) in PDB entry 3PMM
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 THR 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ASN 4.7 0.2 - - - -
107A VAL* 2.8 41.7 + - - -
110A MSE 3.4 19.6 - - + +
138A TRP* 4.7 1.3 - - + -
139A ALA* 4.2 14.4 - - + -
143A MSE 4.1 13.4 - - + +
151A MSE 3.9 22.9 - - + -
168A THR* 3.0 10.8 + - - -
171A MSE 1.3 77.8 - - - +
173A VAL* 1.3 61.2 + - - +
175A PRO* 3.4 7.0 - - - +
176A LEU* 3.0 25.2 + - + +
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Residues in contact with VAL 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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151A MSE 3.6 28.0 - - + -
168A THR* 3.2 15.4 + - + +
169A LEU* 3.3 25.5 + - + +
172A THR* 1.3 74.6 - - - +
174A LEU* 1.3 61.7 + - - +
176A LEU* 3.2 7.1 + - + +
177A ALA* 2.9 26.7 + - - +
192A ALA* 3.5 38.6 - - + +
195A GLN* 4.0 7.0 - - + -
196A PHE* 3.7 18.2 - - + -
242A PHE* 5.2 0.2 - - + -
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Residues in contact with LEU 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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72A TYR* 4.3 1.8 - - - +
114A LEU* 3.7 29.6 - - + -
169A LEU 2.9 17.2 + - - +
170A MSE 4.0 14.8 - - + +
173A VAL* 1.3 73.6 - - - +
175A PRO* 1.4 69.2 - - + +
177A ALA* 3.2 3.1 + - - +
178A LYS* 2.9 23.0 + - - +
196A PHE* 5.3 0.4 - - - -
238A VAL* 4.0 16.6 - - + -
241A ASP* 3.8 28.0 - - + +
242A PHE* 4.0 33.7 - - + +
245A LEU* 4.0 17.9 - - + -
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Residues in contact with PRO 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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110A MSE 4.1 23.3 - - + +
113A PHE* 4.5 2.9 - - + -
114A LEU* 3.9 31.6 - - + +
170A MSE 3.4 16.4 - - - +
171A MSE 3.4 20.0 - - - +
172A THR 3.4 10.8 - - - +
174A LEU* 1.4 90.3 - - + +
176A LEU* 1.3 62.0 + - - +
178A LYS* 3.3 1.2 + - - +
179A ILE* 3.0 31.0 + - - +
388A FMT 3.7 12.8 - - - +
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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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110A MSE 4.0 9.8 - - + +
136A ALA* 3.9 26.9 - - + +
139A ALA* 4.4 7.2 - - + -
140A MSE 4.1 7.9 - - + -
151A MSE 3.8 27.6 - - + -
172A THR 3.0 16.6 + - - +
173A VAL* 3.2 7.8 + - - +
175A PRO* 1.3 75.4 - - - +
177A ALA* 1.3 57.7 + - - +
179A ILE* 3.4 3.9 + - - +
180A GLY* 2.9 24.9 + - - -
188A TYR* 3.6 44.8 - - + +
191A GLU* 4.1 12.8 - - + -
192A ALA* 4.6 5.8 - - + +
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Residues in contact with ALA 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 VAL 2.9 15.9 + - - +
174A LEU 3.7 2.5 - - - +
176A LEU* 1.3 77.0 - - - +
178A LYS* 1.3 64.7 + - - +
180A GLY* 3.2 1.9 + - - -
181A LYS* 3.0 26.3 + - - +
188A TYR 4.7 0.9 - - - -
189A VAL* 3.7 14.2 - - + +
192A ALA* 3.7 20.9 - - + -
242A PHE* 3.8 16.2 - - + -
245A LEU* 3.6 17.5 - - + -
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Residues in contact with LYS 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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114A LEU* 3.6 21.8 - - + -
117A ALA* 3.7 26.5 - - + -
118A TYR* 3.5 38.5 + - + +
121A GLU* 2.8 32.0 + - - -
174A LEU 2.9 16.7 + - - +
175A PRO 3.8 2.9 - - - +
177A ALA* 1.3 77.4 - - - +
179A ILE* 1.3 56.6 + - - +
181A LYS* 3.3 4.0 + - + +
182A LEU* 2.9 35.1 + - - +
245A LEU* 3.4 29.7 - - + +
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Residues in contact with ILE 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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110A MSE 4.3 11.7 - - + -
113A PHE* 4.4 12.6 - - + +
117A ALA* 4.2 9.9 - - + -
132A LEU* 4.0 44.4 - - + +
135A TRP* 5.7 0.7 - - + -
136A ALA* 3.8 26.7 - - + +
175A PRO 3.0 21.5 + - - +
176A LEU 3.7 3.4 - - - +
178A LYS* 1.3 76.0 - - - +
180A GLY* 1.3 57.5 + - - +
182A LEU* 4.4 5.6 - - + -
183A LEU* 2.8 55.2 + - + +
188A TYR* 4.1 3.8 - - + -
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Residues in contact with GLY 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 11.1 + - - -
177A ALA 3.2 3.5 + - - -
179A ILE* 1.3 77.2 - - - +
181A LYS* 1.3 59.2 + - - +
184A ASN* 3.1 3.1 + - - -
185A ARG 2.8 45.5 + - - +
188A TYR* 3.6 21.0 - - - -
189A VAL* 3.9 6.9 - - - +
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ALA 3.0 16.5 + - - +
178A LYS* 3.6 8.7 - - + +
180A GLY* 1.3 77.0 - - - +
182A LEU* 1.3 64.1 + - - +
184A ASN* 3.3 18.9 + - - +
189A VAL* 4.1 25.4 - - + +
245A LEU* 3.8 42.0 - - + +
246A VAL* 4.2 20.4 + - - +
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Residues in contact with LEU 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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117A ALA* 3.2 40.2 - - + +
120A PHE* 3.7 23.6 - - + -
121A GLU* 3.8 34.3 - - + +
132A LEU* 4.6 4.9 - - + -
178A LYS* 2.9 25.3 + - - +
179A ILE* 3.9 4.5 - - - +
181A LYS* 1.3 79.2 - - - +
183A LEU* 1.3 68.2 + - + +
184A ASN* 3.3 8.4 + - - -
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Residues in contact with LEU 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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120A PHE* 4.3 15.5 - - + -
129A LEU* 3.7 23.3 - - + -
132A LEU* 4.6 6.7 - - + -
133A GLU* 4.0 28.5 - - + +
179A ILE* 2.8 42.3 + - + +
182A LEU* 1.3 82.7 - - + +
184A ASN* 1.3 73.2 + - - +
185A ARG* 3.4 30.6 + - - +
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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