Contacts of the helix formed by residues 148 - 161 (chain B) in PDB entry 2RGZ
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 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B ARG* 5.6 0.4 - - - +
141B ILE* 3.9 17.9 - - + -
145B GLU* 3.0 43.9 + - + +
146B PRO 2.8 1.6 - - - -
147B GLU* 1.3 90.8 - - + +
149B LEU* 1.3 63.7 + - - +
150B VAL 3.0 3.6 - - - -
151B ALA* 2.9 23.3 + - + +
152B HIS* 3.8 5.9 + - - -
215B THR* 4.5 1.1 - - + +
218B ARG* 4.1 21.3 - - + +
219B ILE* 3.6 41.1 - - + +
222B GLU* 4.5 18.2 - - + +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.7 25.8 - - + -
84B GLU* 3.6 36.6 - - + +
85B MET* 3.8 17.7 - - + -
88B ASN* 3.8 17.3 - - + +
94B PHE* 3.8 22.7 - - + -
138B ILE* 4.9 3.8 - - + -
141B ILE* 3.6 20.7 - - + +
142B GLY* 4.6 2.5 - - - +
146B PRO* 2.8 15.5 + - + +
148B LEU* 1.3 78.1 - - - +
150B VAL* 1.3 61.4 + - - +
152B HIS* 3.2 6.8 + - + +
153B ALA* 3.2 18.9 + - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.8 8.7 - - + -
37B LEU* 5.3 1.3 - - + -
93B ALA 5.2 4.7 + - - +
94B PHE* 4.2 6.2 - - + -
97B LEU* 3.2 35.9 - - + -
146B PRO 4.4 0.8 + - - -
147B GLU 3.5 11.2 - - - +
148B LEU 4.1 0.2 - - - -
149B LEU* 1.3 79.4 - - - +
151B ALA* 1.3 66.3 + - - +
153B ALA* 3.2 3.8 + - - +
154B TYR* 2.9 24.1 + - + +
206B MET* 4.2 22.9 - - + -
209B LEU* 4.8 8.5 - - + -
211B LEU* 5.9 0.2 - - + -
219B ILE* 3.5 35.9 - - + -
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Residues in contact with ALA 151 (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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37B LEU* 4.9 1.1 - - - -
148B LEU 2.9 13.5 + - - +
150B VAL* 1.3 82.1 - - - +
152B HIS* 1.3 53.0 + - - +
154B TYR* 3.9 5.2 - - - +
155B THR* 2.6 37.3 + - - -
219B ILE* 3.2 39.5 - - + +
222B GLU* 4.2 11.7 - - + -
223B ALA* 4.0 15.6 - - + +
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Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.7 31.3 - - + +
134B TYR* 3.3 40.3 + + - +
137B ARG* 4.5 10.7 - - + +
138B ILE* 4.6 8.7 - - + -
141B ILE* 4.1 19.3 - - + +
148B LEU 4.2 11.0 - - - -
149B LEU* 3.2 8.3 + - + +
151B ALA* 1.3 74.4 - - - +
153B ALA* 1.3 64.9 + - - +
155B THR* 3.3 5.5 + - - -
156B ARG* 3.2 18.2 + - - +
222B GLU* 3.0 36.3 + - + +
225B LYS* 6.1 0.2 - - + -
226B ALA* 3.6 18.0 - - + +
229B TYR* 4.9 2.5 - + - -
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Residues in contact with ALA 153 (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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81B LEU* 4.5 1.7 - - - +
85B MET* 3.2 32.1 - - + -
94B PHE* 4.3 2.0 - - + -
149B LEU 3.2 11.0 + - - +
150B VAL* 3.2 10.5 + - - +
152B HIS* 1.3 78.3 - - - +
154B TYR* 1.3 61.4 + - - +
157B TYR* 3.1 41.6 + - + +
158B MET* 3.7 0.7 + - - +
202B TYR* 3.2 20.6 + - - +
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Residues in contact with TYR 154 (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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34B SER 5.2 3.4 - - - -
37B LEU* 3.6 55.0 - - + -
38B LYS* 4.1 15.8 + - - +
41B THR* 4.9 5.7 + - - -
150B VAL 2.9 16.2 + - - +
151B ALA 3.9 3.1 - - - +
153B ALA* 1.3 77.5 - - - +
155B THR* 1.3 65.3 + - - +
158B MET* 3.2 39.2 - - + +
202B TYR* 4.2 2.4 + - + -
203B ARG* 4.9 1.3 - - - -
206B MET* 4.3 21.5 - - + -
223B ALA* 4.9 2.0 - - + -
227B PHE* 5.5 4.3 - + - -
265B HEM 2.7 78.5 + - + +
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Residues in contact with THR 155 (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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134B TYR* 4.3 4.0 - - - +
151B ALA 2.6 21.5 + - - -
152B HIS* 3.6 5.8 - - - -
153B ALA 3.2 0.4 - - - -
154B TYR* 1.3 82.6 - - - +
156B ARG* 1.3 61.2 + - + +
223B ALA* 3.7 14.9 + - - +
226B ALA* 3.7 31.2 - - + +
227B PHE* 3.9 15.3 - - + -
230B ASN* 3.9 10.1 - - - +
265B HEM 2.9 53.1 - - + +
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Residues in contact with ARG 156 (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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74B LEU* 3.8 20.7 - - - +
77B THR* 4.8 7.0 - - + -
78B TYR* 2.9 40.2 + - + +
81B LEU* 4.5 11.2 - - + -
134B TYR* 4.2 22.0 - - + +
152B HIS 3.2 9.7 + - - +
155B THR* 1.3 80.3 - - + +
157B TYR* 1.3 55.3 + - - +
158B MET 3.5 0.2 - - - -
159B GLY* 2.9 6.9 + - - -
160B ASP* 2.6 48.4 + - - +
186B PHE* 4.9 2.8 - - - -
230B ASN* 3.8 16.7 + - - -
234B PHE* 4.8 6.3 - - - -
265B HEM 3.0 44.6 - - - +
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Residues in contact with TYR 157 (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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78B TYR* 3.3 31.1 + + - -
81B LEU* 3.6 24.8 - - + +
82B GLU* 3.2 30.2 + - + +
85B MET* 4.0 20.6 - - + -
103B LEU* 3.2 60.6 - - + -
104B HIS* 4.2 4.0 - + - -
105B ARG* 4.1 1.6 - - + -
153B ALA* 3.1 23.3 + - + +
156B ARG* 1.3 72.8 - - + +
158B MET* 1.3 61.5 + - + +
159B GLY 2.7 14.6 + - - -
160B ASP* 2.8 23.2 + - - +
161B LEU* 3.1 16.8 + - - +
189B PHE* 5.0 1.6 - + - -
202B TYR* 5.6 1.8 - - - +
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Residues in contact with MET 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.9 3.1 - - + -
153B ALA 3.7 2.6 + - - -
154B TYR* 3.2 46.9 - - + +
156B ARG 3.5 0.4 - - - -
157B TYR* 1.3 78.1 - - + +
159B GLY* 1.3 57.4 + - - +
161B LEU* 3.9 13.0 - - + -
162B SER* 3.5 11.4 + - - -
198B PHE* 4.4 3.8 - - + -
199B LYS* 3.4 41.5 - - + +
202B TYR* 3.1 61.5 - - + -
203B ARG* 5.2 7.6 - - - -
265B HEM 3.4 20.0 - - + +
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Residues in contact with GLY 159 (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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156B ARG* 2.9 9.8 + - - -
157B TYR 2.7 2.2 + - - -
158B MET* 1.3 79.1 - - - +
160B ASP* 1.3 65.3 + - - +
161B LEU 3.2 1.1 - - - -
162B SER* 3.1 21.8 + - - +
265B HEM 3.4 39.5 + - - +
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Residues in contact with ASP 160 (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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78B TYR* 2.6 39.6 + - - -
105B ARG* 4.5 0.5 - - - +
156B ARG* 2.6 32.5 + - - +
157B TYR* 2.8 18.5 + - - +
159B GLY* 1.3 73.6 - - - +
161B LEU* 1.3 62.2 + - - +
162B SER 3.1 2.1 + - - +
164B GLY* 3.7 22.0 + - - -
167B LEU* 5.7 1.2 - - - +
186B PHE* 3.8 17.1 - - + +
189B PHE* 3.4 26.5 - - + -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.6 18.2 - - + -
157B TYR 3.1 9.1 + - - +
158B MET* 3.9 7.6 - - + -
160B ASP* 1.3 78.7 - - - +
162B SER* 1.3 56.6 + - - +
163B GLY 3.4 5.9 + - - -
164B GLY* 4.2 3.0 + - - -
165B GLN* 5.1 4.2 + - - +
189B PHE* 3.8 35.7 - - + -
192B VAL* 4.7 16.6 - - + -
195B ALA* 4.0 17.9 - - + +
196B GLN* 5.1 0.3 + - - -
198B PHE* 3.6 25.6 - - + -
199B LYS* 3.1 49.1 + - + -
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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
------------------------------------------------------------
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