Contacts of the helix formed by residues 183 - 197 (chain A) in PDB entry 4RMA
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 LEU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLY 3.3 8.2 + - - +
182A MET* 1.3 77.2 - - - +
184A LYS* 1.3 65.8 + - - +
185A ASP* 3.3 5.6 - - + +
186A ASN* 3.1 29.8 + - - +
187A ALA* 3.0 19.1 + - - +
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Residues in contact with LYS 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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100A LYS* 5.4 8.3 - - - +
103A PHE* 6.1 1.3 - - - -
131A GLN 5.0 2.4 + - - +
132A ALA* 3.2 44.9 - - + +
133A LYS* 4.8 3.3 - - - +
182A MET 3.8 1.4 + - - -
183A LEU* 1.3 72.1 - - - +
185A ASP* 1.3 66.8 + - - +
187A ALA* 3.2 3.7 + - - +
188A MET* 3.0 43.7 + - + +
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Residues in contact with ASP 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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96A ASP* 3.6 41.5 - - - +
99A GLN* 3.3 21.1 + - - +
100A LYS* 5.4 0.3 - - - +
183A LEU* 3.3 4.0 - - + +
184A LYS* 1.3 78.9 - - - +
186A ASN* 1.3 62.6 + - - +
188A MET* 3.3 22.8 + - - +
189A LEU* 3.0 23.4 + - - +
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Residues in contact with ASN 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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99A GLN* 5.6 0.9 + - - -
182A MET* 4.2 12.3 - - + -
183A LEU* 3.1 33.5 + - - +
185A ASP* 1.3 83.8 - - - +
187A ALA* 1.3 55.8 + - - +
189A LEU* 3.3 18.5 + - + +
190A GLU* 2.9 35.0 + - + +
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Residues in contact with ALA 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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128A TYR* 3.7 29.5 - - + +
131A GLN* 4.0 9.0 - - + -
132A ALA* 3.8 14.4 - - + +
182A MET* 3.6 21.4 - - - +
183A LEU 3.0 11.6 + - - +
184A LYS 3.5 8.3 - - - +
186A ASN* 1.3 71.4 - - - +
188A MET* 1.3 65.5 - - - +
190A GLU* 3.2 1.0 + - - +
191A TYR* 2.9 24.1 + - - +
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Residues in contact with MET 188 (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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99A GLN* 4.9 7.6 - - + +
100A LYS* 4.0 34.3 - - + +
103A PHE* 3.4 53.0 - - + -
132A ALA* 3.9 9.6 - - + -
184A LYS* 3.0 42.9 + - + +
185A ASP* 3.5 30.7 - - - +
187A ALA* 1.3 75.2 - - - +
189A LEU* 1.3 62.7 + - - +
191A TYR* 3.3 3.6 - - - +
192A LEU* 3.0 29.0 + - - +
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Residues in contact with LEU 189 (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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89A VAL* 4.4 9.4 - - + +
90A ALA* 3.9 25.1 - - + +
99A GLN* 3.3 29.5 - - - +
185A ASP 3.0 12.7 + - - +
186A ASN* 3.6 21.3 - - - +
188A MET* 1.3 78.3 - - - +
190A GLU* 1.3 74.5 + - - +
192A LEU* 3.2 4.6 + - - -
193A LYS* 2.9 43.7 + - + +
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Residues in contact with GLU 190 (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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128A TYR* 3.6 39.4 + - + +
182A MET* 4.3 12.8 - - + -
186A ASN* 2.9 21.8 + - + +
187A ALA 3.2 2.4 + - - +
189A LEU* 1.3 86.3 - - - +
191A TYR* 1.3 63.1 + - - +
193A LYS* 3.0 39.7 + - - +
194A ILE* 3.2 27.9 + - - +
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Residues in contact with TYR 191 (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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103A PHE* 3.5 25.8 - + + -
106A VAL* 4.5 2.0 - - + -
107A LYS* 3.3 46.2 - - + +
110A ILE* 3.5 27.5 - - + +
111A LEU* 5.2 1.6 - - - +
125A LEU* 3.2 59.3 - - + +
128A TYR* 4.0 8.6 - - + -
129A ALA* 4.0 15.9 - - + -
187A ALA 2.9 15.1 + - - +
188A MET 3.3 9.4 - - - +
190A GLU* 1.3 76.2 - - - +
192A LEU* 1.3 71.2 + - + +
194A ILE 3.2 2.3 + - - -
195A ALA* 3.0 23.4 + - + -
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Residues in contact with LEU 192 (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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89A VAL* 4.0 32.6 - - + +
99A GLN* 3.6 34.1 - - + +
102A PHE* 3.8 18.2 - - + +
103A PHE* 3.8 23.8 - - + +
106A VAL* 3.9 23.1 - - + -
188A MET 3.0 20.2 + - - +
189A LEU* 3.2 4.7 + - - +
191A TYR* 1.3 80.7 - - + +
193A LYS* 1.3 58.9 + - - +
195A ALA* 3.9 2.6 - - - +
196A GLN* 2.9 31.5 + - - +
201A TYR* 4.7 10.5 + - + +
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Residues in contact with LYS 193 (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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88A ASP* 5.4 2.7 - - - +
89A VAL* 5.8 1.3 - - + -
90A ALA* 4.1 21.9 - - + +
189A LEU* 2.9 43.3 + - + +
190A GLU* 3.0 41.6 + - - +
192A LEU* 1.3 77.1 - - - +
194A ILE* 1.3 65.3 + - + +
196A GLN* 3.5 20.1 + - - +
197A ASP* 3.5 16.3 - - - +
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Residues in contact with ILE 194 (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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121A THR* 3.5 30.0 - - + +
124A LEU* 3.8 31.4 - - + -
125A LEU* 3.7 20.9 - - + -
128A TYR* 4.5 9.6 - - + -
190A GLU* 3.2 14.3 + - - +
191A TYR 3.7 0.9 - - - +
193A LYS* 1.3 78.4 - - + +
195A ALA* 1.3 65.1 + - - +
197A ASP* 3.1 26.4 + - + +
198A LEU* 3.8 5.5 + - - +
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Residues in contact with ALA 195 (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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106A VAL* 3.6 31.0 - - + -
110A ILE* 4.0 14.4 - - + -
125A LEU* 4.5 2.9 - - + -
191A TYR* 3.0 19.5 + - + +
192A LEU* 3.3 6.5 + - - +
194A ILE* 1.3 77.7 - - - +
196A GLN* 1.3 58.3 + - - +
198A LEU* 2.9 32.6 + - - +
201A TYR* 3.2 19.2 - - + +
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Residues in contact with GLN 196 (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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86A PRO 4.6 1.9 - - - +
87A GLU 3.6 14.1 + - - +
88A ASP* 2.9 28.2 + - - +
89A VAL* 2.8 36.5 + - - +
90A ALA 5.2 0.2 - - - +
192A LEU 2.9 17.0 + - - +
193A LYS* 3.5 15.5 + - - +
195A ALA* 1.3 78.7 - - - +
197A ASP* 1.3 65.4 + - - +
198A LEU 3.4 6.6 + - - +
201A TYR* 3.7 31.9 + - + +
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Residues in contact with ASP 197 (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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193A LYS 3.5 15.0 - - - +
194A ILE* 3.1 17.8 + - + +
196A GLN* 1.3 83.7 + - - +
198A LEU* 1.3 64.0 + - - +
199A GLU* 3.5 5.4 + - - +
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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
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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