Contacts of the helix formed by residues 180 - 190 (chain B) in PDB entry 6RLR
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 SER 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B CYS 4.0 4.7 - - - -
154B GLY 3.6 7.4 - - - -
155B LEU 3.8 4.5 - - - -
156B ALA* 3.7 30.4 + - - +
178B VAL 3.6 3.8 + - - -
179B LYS* 1.3 75.8 - - - +
181B CYS* 1.3 59.2 + - - +
182B PRO* 3.8 6.5 - - - +
183B ASP* 3.3 32.9 + - - +
184B ALA* 3.0 22.5 + - - +
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Residues in contact with CYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.6 0.9 - - + -
147B HIS* 3.5 26.9 - - - -
152B CYS* 2.1 48.2 - - - -
153B CYS 3.5 5.2 - - - -
154B GLY 2.9 8.8 + - - -
180B SER* 1.3 68.4 - - - +
182B PRO* 1.4 63.0 - - + +
184B ALA* 3.7 0.2 - - - +
185B ILE* 2.7 44.8 + - + +
125C TYR* 3.6 30.5 - - + -
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Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY 3.5 10.5 - - - +
155B LEU* 4.0 13.7 - - + -
156B ALA* 5.0 4.9 - - + +
180B SER* 3.7 8.1 - - - +
181B CYS* 1.4 93.2 - - + +
183B ASP* 1.3 63.6 + - - +
185B ILE* 3.5 2.1 + - + +
186B LYS* 3.2 10.6 + - - +
122C GLN* 2.7 42.7 + - + +
125C TYR* 4.2 9.2 - - + -
126C LYS* 4.0 31.2 - - + +
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Residues in contact with ASP 183 (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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179B LYS* 4.2 15.2 + - + +
180B SER* 3.3 25.4 + - - +
181B CYS 3.2 0.6 - - - -
182B PRO* 1.3 77.2 - - - +
184B ALA* 1.3 65.9 + - - +
186B LYS* 3.1 10.7 + - - +
187B GLU* 3.1 35.6 + - - +
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Residues in contact with ALA 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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150B LEU* 3.9 23.3 - - + +
152B CYS* 3.7 31.0 - - + -
179B LYS* 4.2 16.7 - - + +
180B SER 3.0 8.4 + - - +
181B CYS 3.1 2.7 + - - +
183B ASP* 1.3 76.1 - - - +
185B ILE* 1.3 62.9 + - - +
187B GLU* 3.2 6.9 + - - +
188B VAL* 3.1 26.6 + - - +
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Residues in contact with ILE 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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146B ILE* 5.0 3.4 - - + -
150B LEU* 3.7 19.7 - - + -
181B CYS* 2.7 34.6 + - + +
182B PRO 3.7 5.6 - - - +
184B ALA* 1.3 71.5 - - - +
186B LYS* 1.3 61.9 + - - +
188B VAL* 3.3 16.6 + - - +
189B PHE* 3.3 21.5 - - + -
118C ILE* 3.9 5.6 - - + +
121C VAL* 3.4 42.6 - - + +
122C GLN* 3.7 20.9 - - + -
125C TYR* 3.9 28.7 - - + -
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Residues in contact with LYS 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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182B PRO 3.2 13.2 + - - +
183B ASP* 3.1 14.2 + - - +
185B ILE* 1.3 76.6 - - - +
187B GLU* 1.3 70.4 + - + +
189B PHE* 3.1 19.8 + - - +
190B ASP* 3.2 53.7 + - - +
118C ILE* 4.2 23.8 - - + +
122C GLN* 4.0 8.9 - - - +
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Residues in contact with GLU 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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179B LYS* 3.2 41.0 + - - +
183B ASP* 3.1 21.4 + - - +
184B ALA* 3.2 6.3 + - - +
186B LYS* 1.3 86.8 - - + +
188B VAL* 1.3 64.1 + - - +
189B PHE 3.2 0.4 + - - -
190B ASP 3.6 22.0 - - - +
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Residues in contact with VAL 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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150B LEU* 3.7 29.6 - - + -
184B ALA 3.1 19.0 + - - +
185B ILE* 3.4 14.6 - - - +
186B LYS 3.2 0.6 - - - -
187B GLU* 1.3 78.1 - - - +
189B PHE* 1.3 82.8 + - + +
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Residues in contact with PHE 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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185B ILE* 3.3 27.1 - - + -
186B LYS 3.1 3.4 + - - +
188B VAL* 1.3 93.3 - - + +
190B ASP* 1.3 53.7 + - - +
114C LYS* 2.8 41.7 + - + +
117C VAL* 3.8 31.6 - - + -
118C ILE* 3.7 39.3 - - + -
121C VAL* 4.6 10.3 - - + -
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Residues in contact with ASP 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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186B LYS* 3.2 48.8 + - + +
187B GLU* 3.6 17.4 - - - +
188B VAL 3.6 2.0 - - - -
189B PHE* 1.3 81.4 - - + +
114C LYS* 4.4 13.8 + - - +
118C ILE* 4.9 5.2 - - + +
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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