Contacts of the helix formed by residues 183 - 197 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B GLY 3.2 10.5 + - - +
182B MET* 1.3 79.6 - - - +
184B LYS* 1.3 67.3 + - - +
185B ASP* 3.5 5.2 - - + +
186B ASN* 3.2 25.5 + - - +
187B ALA* 3.0 19.2 + - - +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS* 5.5 8.2 - - - +
103B PHE* 6.1 0.9 - - - -
131B GLN 5.0 2.4 + - - +
132B ALA* 3.3 40.7 + - - +
133B LYS* 5.1 3.2 - - - +
182B MET 3.9 0.8 + - - -
183B LEU* 1.3 72.2 - - - +
185B ASP* 1.3 67.2 + - - +
187B ALA* 3.1 5.1 + - - +
188B MET* 3.0 47.3 + - + +
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Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASP* 3.7 42.2 - - - +
99B GLN* 3.1 22.2 + - - +
100B LYS* 5.5 0.5 - - - +
183B LEU* 3.5 3.4 - - + +
184B LYS* 1.3 78.2 - - - +
186B ASN* 1.3 66.6 + - - +
188B MET* 3.2 23.4 + - - +
189B LEU 3.0 17.7 + - - -
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Residues in contact with ASN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 5.6 0.5 + - - -
182B MET* 4.2 13.5 - - + -
183B LEU* 3.2 30.9 + - - +
184B LYS 3.2 0.8 - - - -
185B ASP* 1.3 78.8 - - - +
187B ALA* 1.3 64.5 + - - +
189B LEU* 3.1 16.6 + - + +
190B GLU* 3.0 30.2 + - + +
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 3.6 30.0 - - + +
131B GLN* 4.0 8.1 - - + -
132B ALA* 3.7 15.0 - - + +
182B MET* 3.6 22.1 - - - +
183B LEU 3.0 13.3 + - - +
184B LYS 3.4 9.0 - - - +
186B ASN* 1.3 74.4 - - - +
188B MET* 1.3 57.5 + - - +
190B GLU* 3.3 1.4 + - - +
191B TYR* 3.0 29.0 + - - +
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Residues in contact with MET 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 4.7 7.6 - - + +
100B LYS* 3.9 33.9 - - + +
103B PHE* 3.4 51.6 - - + -
104B LEU* 5.8 0.2 - - - -
132B ALA* 3.9 9.2 - - + -
184B LYS* 3.0 35.2 + - + +
185B ASP* 3.4 39.3 - - - +
186B ASN 3.2 0.2 - - - -
187B ALA* 1.3 77.2 - - - +
189B LEU* 1.3 61.7 + - - +
191B TYR* 3.3 4.0 - - - +
192B LEU* 3.1 27.2 + - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 4.5 9.2 - - + +
90B ALA* 3.8 33.9 - - + +
99B GLN* 3.3 30.0 - - + +
185B ASP 3.0 10.7 + - - +
186B ASN* 3.1 19.9 + - + +
188B MET* 1.3 73.7 - - - +
190B GLU* 1.3 71.5 + - - +
192B LEU* 3.2 4.8 + - + +
193B LYS* 2.9 47.6 + - + +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 3.6 39.7 + - + +
182B MET* 4.4 11.0 - - + -
186B ASN* 3.0 23.6 + - + +
187B ALA 3.7 2.5 - - - +
189B LEU* 1.3 81.1 - - - +
191B TYR* 1.3 66.5 + - - +
193B LYS* 3.1 40.0 + - - +
194B ILE* 3.2 30.1 + - - +
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Residues in contact with TYR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.5 26.2 - + + -
106B VAL* 4.3 4.0 - - + -
107B LYS* 3.3 52.7 - - + +
110B ILE* 3.4 33.6 - - + +
111B LEU* 5.2 1.6 - - - +
125B LEU* 3.2 57.3 - - + +
126B GLY* 5.2 0.2 - - - -
128B TYR* 4.1 7.9 - - + -
129B ALA* 4.1 6.5 - - + -
187B ALA 3.0 14.5 + - - +
188B MET 3.3 10.3 - - - +
190B GLU* 1.3 76.2 - - - +
192B LEU* 1.3 70.6 + - + +
194B ILE 3.2 2.9 + - - -
195B ALA* 3.0 19.0 + - + +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.8 26.3 - - + +
93B LEU* 4.7 1.1 - - + -
99B GLN* 3.6 37.5 - - + +
102B PHE* 3.9 12.6 - - + +
103B PHE* 3.8 18.6 - - - +
106B VAL* 3.8 36.3 - - + -
188B MET 3.1 13.9 + - - +
189B LEU* 3.2 8.7 + - + +
191B TYR* 1.3 79.3 - - + +
193B LYS* 1.3 56.9 + - - +
195B ALA* 3.9 1.7 - - - +
196B GLN* 2.9 31.9 + - - +
201B TYR* 4.6 8.7 - - + +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ASP* 5.3 1.8 - - - +
89B VAL* 4.3 6.3 - - + -
90B ALA* 3.8 30.1 - - + -
189B LEU* 2.9 32.6 + - + +
190B GLU* 3.1 44.1 + - - +
191B TYR 3.3 0.6 - - - -
192B LEU* 1.3 73.5 - - - +
194B ILE* 1.3 62.8 + - + +
196B GLN* 3.4 19.7 + - - +
197B ASP* 3.5 15.0 - - - +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 3.5 29.5 - - + +
124B LEU* 3.4 28.3 - - + -
125B LEU* 3.6 11.2 - - + -
128B TYR* 3.4 36.6 - - + +
190B GLU* 3.2 13.1 + - - +
191B TYR 3.2 6.7 + - - +
192B LEU 3.2 0.6 - - - -
193B LYS* 1.3 76.1 - - + +
195B ALA* 1.3 66.2 + - - +
196B GLN 3.1 1.1 - - - -
197B ASP* 3.1 22.4 + - + +
198B LEU* 3.8 5.5 + - - +
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.6 31.2 - - + -
110B ILE* 3.9 15.0 - - + -
125B LEU* 4.0 5.4 - - + +
191B TYR* 3.0 17.8 + - + +
192B LEU* 3.9 6.1 - - - +
194B ILE* 1.3 77.8 - - - +
196B GLN* 1.3 62.3 + - - +
198B LEU* 3.0 32.4 + - + +
201B TYR* 3.3 13.4 - - + +
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO 4.8 1.2 - - - +
87B GLU 3.7 10.2 + - - +
88B ASP* 2.6 34.8 + - - +
89B VAL* 2.9 37.8 + - - +
192B LEU 2.9 17.8 + - - +
193B LYS* 3.4 13.1 + - - +
195B ALA* 1.3 77.5 - - - +
197B ASP* 1.3 65.8 + - - +
198B LEU 3.5 6.4 + - - +
201B TYR* 3.7 33.3 + - + -
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LYS 3.5 14.8 - - - +
194B ILE* 3.1 12.0 + - - +
195B ALA 3.1 1.2 - - - -
196B GLN* 1.3 83.6 + - - +
198B LEU* 1.3 64.2 + - - +
199B GLU* 3.5 5.7 + - - +
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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