Contacts of the helix formed by residues 194 - 208 (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 ASN 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B VAL* 3.8 3.3 - - - +
193B ASP* 1.3 79.0 - - + +
195B ALA* 1.3 59.1 + - - +
196B GLN* 2.7 39.5 + - - +
197B GLN* 2.7 47.6 + - + +
198B PHE* 3.0 28.2 + - - +
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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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161B LEU* 4.0 19.5 - - + +
165B GLN* 5.1 10.1 - - - +
192B VAL* 4.4 9.6 - - + +
193B ASP 3.6 4.0 + - - +
194B ASN* 1.3 71.1 + - - +
196B GLN* 1.3 70.0 + - + +
197B GLN 3.1 1.6 - - - -
198B PHE* 3.0 3.2 + - - +
199B LYS* 2.9 47.2 + - - +
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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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161B LEU 5.1 0.4 + - - -
162B SER* 5.0 3.4 + - - +
163B GLY 5.8 0.4 - - - +
194B ASN* 2.7 15.2 + - - +
195B ALA* 1.3 77.2 - - + +
197B GLN* 1.3 56.1 + - + +
199B LYS* 3.1 33.1 - - - +
200B GLN* 3.0 30.5 + - - +
203B ARG* 5.6 3.3 + - - -
265B HEM 4.9 12.4 + - - +
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Residues in contact with GLN 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 ASP* 5.7 0.9 - - - +
194B ASN* 2.7 48.8 + - + +
196B GLN* 1.3 76.8 - - + +
198B PHE* 1.3 60.4 + - - +
200B GLN* 3.5 6.2 + - - +
201B LEU* 3.0 26.5 + - - +
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Residues in contact with PHE 198 (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 PHE* 3.5 50.0 - + + -
102B GLU* 4.3 13.2 - - + -
103B LEU* 3.5 31.0 - - + -
158B MET* 4.4 0.4 - - + -
161B LEU* 3.6 20.6 - - + -
192B VAL* 4.0 22.7 - - + -
194B ASN 3.0 17.9 + - - +
195B ALA* 3.0 4.5 + - - +
197B GLN* 1.3 73.6 - - - +
199B LYS* 1.3 62.2 + - - +
201B LEU* 2.8 22.1 - - + +
202B TYR* 2.8 35.3 + + - -
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Residues in contact with LYS 199 (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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158B MET* 3.4 31.1 - - - +
161B LEU* 3.1 55.1 + - + -
162B SER* 3.2 22.6 + - - +
195B ALA* 2.9 32.9 + - - +
196B GLN* 3.1 31.5 - - - +
198B PHE* 1.3 76.0 - - - +
200B GLN* 1.3 64.2 + - - +
202B TYR* 2.9 10.2 + - - +
203B ARG* 2.9 40.4 + - - +
265B HEM 5.3 4.9 + - + +
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Residues in contact with GLN 200 (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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196B GLN 3.0 20.2 + - - +
197B GLN* 3.7 6.5 - - - +
199B LYS* 1.3 75.5 - - - +
201B LEU* 1.3 64.1 + - - +
203B ARG* 3.5 21.7 + - + +
204B ALA* 3.4 17.0 + - - +
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Residues in contact with LEU 201 (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 PHE* 4.3 13.5 - - + -
197B GLN 3.0 14.0 + - - +
198B PHE* 2.8 41.0 + - + +
200B GLN* 1.3 76.8 - - - +
202B TYR* 1.3 62.5 + - - +
204B ALA* 2.9 21.4 + - + +
205B ARG* 3.1 30.1 + - + +
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Residues in contact with TYR 202 (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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85B MET* 4.9 0.5 - - - +
97B LEU* 3.4 40.9 + - + +
99B PHE* 4.2 15.0 - + - -
103B LEU* 4.1 18.7 - - + +
153B ALA* 3.2 31.2 - - + +
154B TYR* 4.2 6.2 + - + -
157B TYR* 5.6 1.4 - - + +
158B MET* 3.1 48.0 - - + -
198B PHE* 2.8 20.0 + + + +
199B LYS 2.9 9.2 + - - +
201B LEU* 1.3 74.3 - - - +
203B ARG* 1.3 62.6 + - - +
205B ARG* 2.9 18.1 + - - +
206B MET* 3.0 44.2 + - + +
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Residues in contact with ARG 203 (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* 3.7 24.7 + - - +
38B LYS* 5.8 1.0 - - - +
154B TYR* 4.9 2.8 - - - -
158B MET* 5.4 5.4 - - - -
196B GLN* 5.6 3.2 + - - -
199B LYS* 2.9 35.7 + - - +
200B GLN* 3.8 19.4 + - + +
201B LEU 3.3 0.2 - - - -
202B TYR* 1.3 73.5 - - + +
204B ALA* 1.3 63.0 + - - +
206B MET* 3.3 17.9 + - + +
207B ASN* 2.8 30.8 + - - +
265B HEM 2.5 62.2 + - - +
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Residues in contact with ALA 204 (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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200B GLN 3.4 8.7 + - - +
201B LEU* 2.9 14.1 + - + +
203B ARG* 1.3 78.7 - - - +
205B ARG* 1.3 62.6 + - + +
207B ASN* 3.6 9.1 + - - +
208B ALA* 3.2 21.8 + - - +
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Residues in contact with ARG 205 (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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95B ALA 5.1 1.0 + - - -
96B PRO* 3.0 51.1 + - + +
97B LEU* 3.9 8.7 - - + -
99B PHE* 4.0 22.9 - - + -
201B LEU* 3.1 29.3 + - + +
202B TYR* 2.9 11.4 + - - +
204B ALA* 1.3 76.5 - - + +
206B MET* 1.3 65.0 + - - +
208B ALA* 3.2 18.7 + - - +
209B LEU* 3.6 9.5 + - - +
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Residues in contact with MET 206 (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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33B LEU* 3.9 21.7 - - + +
34B SER* 3.9 20.2 - - - -
37B LEU* 4.4 8.5 - - + -
97B LEU* 3.4 24.7 - - + -
150B VAL* 4.2 12.6 - - + -
154B TYR* 4.3 22.4 - - + -
158B MET* 5.3 0.2 - - + -
202B TYR* 3.0 30.4 + - + +
203B ARG* 3.3 34.1 - - + +
205B ARG* 1.3 76.0 - - - +
207B ASN* 1.3 59.6 + - - +
209B LEU* 3.1 36.8 + - + +
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Residues in contact with ASN 207 (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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32B ASP* 3.5 25.5 + - + +
33B LEU* 2.8 17.5 + - - +
34B SER* 2.6 48.5 + - - -
203B ARG* 2.8 22.9 + - - +
204B ALA* 4.0 7.5 - - - +
205B ARG 3.2 0.2 - - - -
206B MET* 1.3 72.5 - - - +
208B ALA* 1.3 61.6 + - - +
209B LEU 3.0 13.4 + - - +
216B LYS* 5.8 1.9 + - - -
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Residues in contact with ALA 208 (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 PRO* 6.2 2.5 - - + -
204B ALA 3.2 12.7 + - - +
205B ARG* 3.2 13.8 + - - +
207B ASN* 1.3 77.7 - - - +
209B LEU* 1.3 52.4 + - - +
210B ASP* 2.7 25.5 - - - +
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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