Contacts of the helix formed by residues 180 - 200 (chain B) in PDB entry 5UWS
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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154B ARG* 3.6 15.8 - - - +
178B PHE* 3.3 2.6 - - - +
179B GLY* 1.3 78.6 - - - +
181B LYS* 1.3 65.2 + - - +
182B GLU* 3.1 30.2 + - - +
183B ASN* 3.4 16.5 + - - +
184B ALA* 3.2 16.8 + - - +
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASP* 3.3 47.5 + - + +
154B ARG* 4.0 4.6 - - - +
180B SER* 1.3 74.3 - - - +
182B GLU* 1.3 62.3 + - - +
184B ALA* 3.3 2.3 + - - +
185B ASP* 2.8 54.1 + - - +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B SER* 3.1 23.2 + - - +
181B LYS* 1.3 81.4 - - - +
183B ASN* 1.3 61.8 + - - +
185B ASP* 3.1 9.1 + - - +
186B LYS* 2.6 38.4 + - - +
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Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.6 6.6 + - - -
89B VAL* 4.4 18.9 - - + +
178B PHE* 4.0 14.9 - - + -
179B GLY* 4.5 6.7 - - - +
180B SER* 3.4 25.6 + - - +
181B LYS 3.4 0.2 - - - -
182B GLU* 1.3 87.7 + - - +
184B ALA* 1.3 57.6 + - - +
186B LYS* 4.3 6.6 - - - +
187B PHE* 2.8 29.3 + - - +
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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
----------------------------------------------------------
153B ASP 4.7 1.3 - - - +
154B ARG* 3.7 28.3 - - - -
155B SER 4.3 0.2 - - - +
156B TRP* 2.7 31.9 + - + +
178B PHE* 3.4 29.3 - - + -
180B SER 3.2 7.1 + - - +
181B LYS 3.5 8.1 - - - +
182B GLU 3.2 0.4 - - - -
183B ASN* 1.3 74.7 - - - +
185B ASP* 1.3 64.4 + - - +
187B PHE* 3.3 1.4 + - - +
188B LYS 3.1 12.3 + - - -
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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
----------------------------------------------------------
153B ASP 5.4 0.7 - - - +
156B TRP* 4.0 16.0 - - - -
181B LYS* 2.8 55.5 + - - +
182B GLU* 3.1 7.0 + - - +
184B ALA* 1.3 71.2 - - - +
186B LYS* 1.3 64.4 + - - +
188B LYS* 3.3 8.4 + - - +
189B GLU* 3.0 21.6 + - - +
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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
----------------------------------------------------------
87B TYR* 4.2 16.1 - - + +
182B GLU 2.6 21.3 + - - +
183B ASN* 3.7 8.7 - - - +
185B ASP* 1.3 73.2 - - - +
187B PHE* 1.3 61.9 + - - +
189B GLU* 3.0 28.7 + - - +
190B GLU* 2.8 55.7 + - + +
193B LYS* 3.9 8.1 - - - +
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Residues in contact with PHE 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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87B TYR* 3.7 26.6 + + + -
89B VAL* 4.2 1.1 - - + -
111B CYS* 4.1 6.7 - - - -
113B PHE* 3.5 21.0 - + - -
124B ILE* 4.4 7.6 - - + -
146B LEU* 4.0 11.2 - - + -
156B TRP* 3.8 11.0 - + - -
158B TYR* 5.5 2.2 - + - -
176B ILE* 3.9 30.3 - - + -
178B PHE* 3.2 34.8 - + + -
183B ASN 2.8 18.7 + - - +
184B ALA 3.4 4.7 - - - +
185B ASP 3.3 0.2 - - - -
186B LYS* 1.3 75.6 - - - +
188B LYS* 1.3 56.1 + - - +
190B GLU* 3.2 2.3 + - - +
191B PHE* 2.6 69.3 + + - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 4.0 29.4 + - + -
156B TRP* 3.7 40.1 - - + +
184B ALA 3.1 12.9 + - - +
185B ASP* 3.3 8.3 + - - +
187B PHE* 1.3 76.8 - - - +
189B GLU* 1.3 63.6 + - - +
191B PHE* 3.6 6.9 - - - +
192B GLU* 3.0 48.2 + - - +
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Residues in contact with GLU 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 ASP 3.0 12.4 + - - +
186B LYS* 3.2 40.3 + - - +
188B LYS* 1.3 77.3 - - - +
190B GLU* 1.3 63.5 + - - +
192B GLU* 3.2 6.2 + - - +
193B LYS* 3.0 47.5 + - + +
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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
----------------------------------------------------------
86B LEU* 4.3 11.8 - - - +
87B TYR* 3.7 37.1 - - + +
113B PHE* 3.6 16.6 - - + -
186B LYS* 2.8 47.6 + - + +
187B PHE 3.8 4.9 - - - +
189B GLU* 1.3 72.3 - - - +
191B PHE* 1.3 64.3 + - - +
193B LYS* 2.9 34.1 + - - +
194B ALA* 2.9 25.8 + - - +
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.4 14.5 - + + -
124B ILE* 3.9 17.0 - - + -
138B HIS* 6.3 0.2 - + - -
140B ILE* 3.7 25.0 - - + +
144B TYR* 4.3 21.5 - + + -
146B LEU* 3.6 42.0 - - + -
158B TYR* 4.4 12.6 - + - -
187B PHE* 2.6 45.8 + + + +
188B LYS 3.6 4.5 - - - +
190B GLU* 1.3 73.5 - - - +
192B GLU* 1.3 60.3 + - + +
194B ALA* 3.7 1.2 + - - +
195B GLN* 3.3 50.4 + - - +
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 5.8 0.2 - - + -
188B LYS* 3.0 53.4 + - + +
189B GLU* 3.8 4.9 - - - +
190B GLU 3.1 0.2 - - - -
191B PHE* 1.3 79.4 - - + +
193B LYS* 1.3 66.2 + - - +
194B ALA 3.2 1.3 - - - -
195B GLN* 3.0 30.3 + - - +
196B GLU* 3.1 17.7 + - + +
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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
----------------------------------------------------------
186B LYS* 3.9 5.5 - - - +
189B GLU* 3.0 40.2 + - + +
190B GLU* 2.9 40.9 + - - +
192B GLU* 1.3 74.8 - - - +
194B ALA* 1.3 62.7 + - - +
196B GLU* 3.1 19.5 + - - +
197B ILE* 3.3 21.0 + - + +
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Residues in contact with ALA 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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86B LEU* 5.2 2.7 - - + -
113B PHE* 4.4 4.9 - - + -
122B VAL* 4.0 16.2 - - + -
140B ILE* 3.7 30.3 - - + -
190B GLU 2.9 16.1 + - - +
191B PHE 3.8 2.7 - - - +
193B LYS* 1.3 76.6 - - - +
195B GLN* 1.3 58.4 + - - +
197B ILE* 3.1 14.8 + - - +
198B ASN* 2.4 34.0 + - - -
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Residues in contact with GLN 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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140B ILE* 3.8 11.2 - - + -
141B ALA 3.1 25.2 + - - +
142B PRO* 3.4 17.8 + - + +
144B TYR 2.9 28.7 + - - -
191B PHE* 3.3 25.8 + - - +
192B GLU* 3.0 32.7 + - - +
194B ALA* 1.3 78.3 - - - +
196B GLU* 1.3 57.8 + - + +
198B ASN* 3.2 8.9 + - - +
199B LYS* 2.9 40.2 + - - +
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Residues in contact with GLU 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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192B GLU* 3.1 14.7 + - + +
193B LYS* 3.1 10.9 + - - +
195B GLN* 1.3 75.0 - - + +
197B ILE* 1.3 58.7 + - + +
199B LYS* 3.1 42.7 + - - +
200B LYS* 2.9 45.1 + - - +
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Residues in contact with ILE 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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86B LEU* 4.2 21.8 - - + -
115B LYS* 4.6 11.2 - - + +
120B ASN* 3.0 33.1 - - + +
121B LYS* 5.5 0.2 - - - -
122B VAL* 4.2 7.0 - - + -
193B LYS* 3.4 18.2 - - + +
194B ALA* 3.1 16.0 + - - +
196B GLU* 1.3 77.3 - - + +
198B ASN* 1.3 62.2 + - - +
200B LYS* 3.1 23.1 + - + +
201B ALA* 3.6 12.3 + - - +
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Residues in contact with ASN 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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186A GLU* 4.2 14.1 - - - +
121B LYS* 3.4 14.5 - - - +
122B VAL* 2.9 44.5 + - - +
139B ILE* 3.7 8.0 - - + +
140B ILE* 3.4 23.5 + - - +
142B PRO* 4.2 16.2 - - + +
194B ALA 2.4 38.0 + - - -
195B GLN 3.2 4.5 + - - +
197B ILE* 1.3 74.5 - - - +
199B LYS* 1.3 61.0 + - - +
201B ALA* 3.8 14.8 + - - +
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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
----------------------------------------------------------
142B PRO* 3.8 34.9 + - + -
195B GLN* 2.9 23.5 + - - +
196B GLU* 3.2 37.0 + - - +
197B ILE 3.0 0.4 - - - -
198B ASN* 1.3 73.7 - - - +
200B LYS* 1.3 58.7 + - + +
201B ALA 2.9 20.6 + - - +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 2.9 32.4 + - - +
197B ILE* 3.1 13.4 + - + +
199B LYS* 1.3 75.1 - - + +
201B ALA* 1.3 56.3 + - - +
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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