Contacts of the helix formed by residues 180 - 192 (chain B) in PDB entry 3K9S
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 ARG 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 5.9 0.8 - - - +
176B LYS 3.3 19.0 + - - -
177B PHE* 2.6 35.1 + - - +
178B GLN* 2.9 30.9 + - - +
179B ASN* 1.3 91.8 - - - +
181B ARG* 1.3 63.6 + - - +
182B PRO* 3.2 7.6 - - + -
183B ASP* 2.9 39.8 + - + +
184B TYR 3.2 8.7 + - - -
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 5.8 3.6 - - - -
120B ALA 2.7 37.7 + - - -
121B ALA* 3.4 15.0 + - - +
123B ARG 2.9 27.7 + - - -
125B GLY 3.4 17.6 + - - +
168B VAL* 3.5 23.3 + - - +
170B GLU* 5.3 3.0 + - - +
173B TYR* 3.0 50.9 + - + +
179B ASN 2.8 12.6 + - - +
180B ARG* 1.3 72.4 - - - +
182B PRO* 1.3 64.6 - - + +
184B TYR* 3.1 9.8 + - + +
185B ILE* 2.8 46.5 + - + +
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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
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121B ALA* 5.3 11.0 - - + -
179B ASN 4.4 2.0 - - - +
180B ARG* 3.3 7.4 - - - -
181B ARG* 1.3 94.7 - - + +
183B ASP* 1.3 58.6 + - - +
185B ILE* 3.5 10.8 + - + +
186B LYS* 2.6 54.2 + - - +
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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
----------------------------------------------------------
177B PHE* 3.7 15.0 - - + -
180B ARG* 2.9 40.4 + - + +
182B PRO* 1.3 78.3 - - - +
184B TYR* 1.3 65.9 + - - +
186B LYS* 3.4 17.2 + - - +
187B GLU* 3.1 26.3 + - - +
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Residues in contact with TYR 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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18B PHE* 3.5 25.9 - + - -
84B PHE* 3.9 10.4 - - - -
166B LEU* 3.1 28.4 - - + +
167B ASP 2.8 28.7 + - - -
168B VAL* 4.5 1.8 - - + -
172B ALA* 3.5 25.0 + - + +
173B TYR* 3.2 39.0 - + + -
177B PHE* 3.4 36.4 - + + -
180B ARG 3.2 7.1 + - - +
181B ARG* 3.1 13.4 + - + +
183B ASP* 1.3 74.6 - - - +
185B ILE* 1.3 67.8 - - + +
187B GLU* 3.1 5.0 + - - +
188B PHE* 3.1 19.6 + - - +
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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
----------------------------------------------------------
116B PHE* 5.3 3.6 - - + -
117B GLU* 3.8 36.8 - - + +
120B ALA* 3.5 29.4 - - + -
121B ALA* 3.7 23.6 - - + +
166B LEU* 4.1 19.3 - - + -
181B ARG* 2.8 45.4 + - + +
182B PRO* 3.7 9.6 - - + +
184B TYR* 1.3 73.2 - - + +
186B LYS* 1.3 66.6 + - - +
188B PHE* 3.3 14.9 + - - +
189B TRP* 3.7 10.9 + - + +
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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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117B GLU* 4.8 18.3 + - - +
182B PRO* 2.6 51.2 + - - +
183B ASP* 3.6 16.8 - - - +
184B TYR 3.2 0.2 - - - -
185B ILE* 1.3 81.6 - - - +
187B GLU* 1.3 63.5 + - + +
189B TRP* 3.2 27.3 + - + +
190B ASN* 4.2 3.8 + - - +
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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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16B PRO 4.8 2.8 - - - +
17B HIS* 2.9 51.7 + - + +
18B PHE* 4.1 6.1 - - + -
176B LYS* 4.8 3.8 + - - +
177B PHE* 3.8 22.2 - - + -
183B ASP 3.1 15.2 + - - +
184B TYR 3.1 10.1 + - - +
186B LYS* 1.3 74.8 - - + +
188B PHE* 1.3 64.2 + - - +
189B TRP 3.0 2.7 - - - -
190B ASN* 2.8 25.7 + - - +
191B VAL* 3.5 7.6 + - - +
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Residues in contact with PHE 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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18B PHE* 3.9 8.5 - + + -
84B PHE* 4.5 0.2 - + - -
87B GLY 4.9 1.3 - - - -
88B LEU* 4.0 24.7 - - + -
116B PHE* 3.6 34.3 - + - -
164B MET* 3.9 13.7 - - + -
165B GLY 3.8 25.1 - - - -
166B LEU* 3.7 27.1 - - + -
184B TYR 3.1 11.2 + - - +
185B ILE* 3.4 12.1 - - + +
186B LYS 3.3 0.6 - - - -
187B GLU* 1.3 76.4 - - - +
189B TRP* 1.3 69.2 + + - +
191B VAL* 2.9 9.2 + - - -
192B VAL* 2.7 63.1 + - + +
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Residues in contact with TRP 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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112B PHE* 3.9 22.2 - + - -
113B LYS* 3.6 63.4 - - + +
116B PHE* 3.7 34.3 - + + -
117B GLU* 2.8 30.8 + - + +
164B MET* 4.5 1.6 - - + -
185B ILE* 3.7 10.9 + - + -
186B LYS* 3.2 22.4 + - + +
187B GLU 3.0 0.8 - - - -
188B PHE* 1.3 93.4 - + - +
190B ASN* 1.3 64.4 + - - +
191B VAL 3.6 0.2 + - - -
192B VAL* 3.6 24.3 + - + +
194B TRP* 4.1 19.4 + + - -
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Residues in contact with ASN 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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17B HIS* 2.9 44.3 + - + +
89B LYS 4.2 0.9 - - - +
90B LYS* 4.1 13.5 - - - +
91B GLY 4.7 3.1 + - - -
186B LYS 5.1 3.2 - - - +
187B GLU* 2.8 17.5 + - - +
189B TRP* 1.3 82.9 - - - +
191B VAL* 1.3 62.7 + - - +
192B VAL 5.3 0.4 - - - -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.9 26.0 - - + +
17B HIS* 3.7 28.0 - - + -
18B PHE* 3.7 40.4 - - + -
88B LEU* 3.2 11.6 - - + -
89B LYS 2.9 31.6 + - - -
90B LYS* 4.0 11.0 - - + -
187B GLU 3.7 6.5 - - - +
188B PHE* 2.9 11.3 + - - +
190B ASN* 1.3 85.8 - - - +
192B VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 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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87B GLY 3.8 5.4 - - - +
89B LYS 3.9 2.3 - - - +
92B THR* 3.3 9.5 + - - -
164B MET* 3.4 38.4 - - + -
188B PHE* 2.7 42.1 + - + +
189B TRP* 3.6 20.5 - - + +
190B ASN 3.8 0.7 - - - -
191B VAL* 1.3 73.2 - - - +
193B ASN* 1.3 63.8 + - - +
194B TRP* 3.1 45.9 + - + +
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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