Contacts of the helix formed by residues 187 - 202 (chain U) in PDB entry 5K0Y
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 187 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176U GLU* 3.3 26.7 - - - +
179U ASN* 3.6 21.1 + - - +
180U ALA* 3.5 11.6 + - - -
185U SER 3.6 2.1 + - - -
186U ASN* 1.4 80.9 + - - +
188U TYR* 1.4 64.1 + - - +
189U ALA 3.5 1.3 + - - -
190U ILE* 3.2 30.2 + - - +
191U LYS* 3.3 25.9 + - - +
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Residues in contact with TYR 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153U LEU* 3.4 43.0 - - + +
156U THR* 4.4 19.0 - - + +
157U GLY* 4.1 12.3 - - - -
160U GLU* 4.3 25.5 + - - +
176U GLU* 3.3 17.2 + - - +
186U ASN 4.1 1.4 + - - -
187U SER* 1.4 67.7 - - - +
189U ALA* 1.4 59.7 + - - +
191U LYS* 3.3 21.8 + - + +
192U LYS* 3.0 62.5 + - + +
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Residues in contact with ALA 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119U SER* 3.3 28.2 - - - +
153U LEU* 3.7 35.1 - - + +
154U LEU* 3.7 20.4 - - + +
176U GLU* 3.5 3.2 + - - +
180U ALA* 5.3 0.7 - - + -
187U SER 3.3 1.0 - - - -
188U TYR* 1.4 78.9 - - - +
190U ILE* 1.4 57.0 + - + +
192U LYS* 3.6 2.1 + - - +
193U LYS* 3.1 29.6 + - - +
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Residues in contact with ILE 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P LYS* 3.5 30.1 - - - +
118U ASN* 3.4 44.2 - - + +
119U SER* 4.0 7.0 - - - +
179U ASN 4.8 1.6 - - - +
180U ALA* 3.8 17.3 - - + +
183U GLY* 5.5 8.7 - - - -
185U SER* 5.3 8.1 - - - +
187U SER* 3.2 26.7 + - - +
188U TYR 3.4 0.4 - - - -
189U ALA* 1.4 71.8 - - - +
191U LYS* 1.4 63.4 + - + +
193U LYS* 3.4 9.0 + - - +
194U ASP* 2.8 34.1 + - - +
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Residues in contact with LYS 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P LYS* 4.8 16.2 - - + +
82P TYR* 3.4 44.4 - - + +
185U SER* 4.7 15.9 - - - +
186U ASN* 4.8 3.3 - - - +
187U SER 3.3 26.9 + - - +
188U TYR* 3.3 21.2 + - + +
190U ILE* 1.4 77.2 - - - +
192U LYS* 1.4 61.6 + - + +
194U ASP* 3.7 3.6 + - - +
195U GLU* 3.5 27.5 + - - +
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Residues in contact with LYS 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P GLU* 4.2 20.6 + - - -
30P MET* 5.5 2.2 - - - -
33P TYR* 3.4 23.6 + - - -
82P TYR* 6.0 1.3 - - - -
153U LEU* 4.1 21.1 - - + -
188U TYR* 3.0 56.8 + - + +
189U ALA 3.9 4.0 - - - +
191U LYS* 1.4 75.7 - - + +
193U LYS* 1.4 63.0 + - - +
195U GLU* 3.4 22.1 + - + +
196U LEU* 3.2 30.3 + - + +
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Residues in contact with LYS 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P LYS* 5.9 0.4 - - - +
118U ASN* 3.1 31.5 + - - +
119U SER 3.5 13.0 - - - +
120U GLY 3.4 15.0 + - - +
121U PRO* 3.8 11.2 - - + -
153U LEU* 5.1 1.3 - - - +
189U ALA 3.1 18.8 + - - +
190U ILE* 3.4 11.1 + - - +
192U LYS* 1.4 71.7 - - - +
194U ASP* 1.4 81.1 + - - +
196U LEU* 3.1 13.0 + - - +
197U GLU* 3.0 56.6 + - - +
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Residues in contact with ASP 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P ARG* 5.7 2.4 + - - -
77P ASP* 6.1 0.9 - - - -
80P LYS* 3.1 40.5 + - + +
190U ILE* 2.8 23.9 + - - +
191U LYS 3.9 5.8 - - - +
193U LYS* 1.4 98.1 + - - +
195U GLU* 1.4 58.8 + - + +
197U GLU* 4.4 5.2 - - - +
198U ARG* 3.2 28.2 + - - +
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Residues in contact with GLU 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P MET* 5.2 5.5 - - - +
33P TYR* 4.8 8.8 + - - -
45P MET* 3.8 28.2 - - + +
82P TYR* 3.5 37.5 + - + -
191U LYS 3.5 15.7 + - - +
192U LYS* 3.4 34.2 + - + +
193U LYS 3.2 0.4 - - - -
194U ASP* 1.4 77.9 - - + +
196U LEU* 1.4 62.1 + - + +
198U ARG* 3.6 4.1 + - - +
199U VAL* 3.1 34.1 + - + +
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Residues in contact with LEU 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121U PRO* 4.5 12.1 - - + -
123U GLU 3.9 3.5 - - - +
124U ASP* 3.6 32.9 - - + +
125U SER* 4.9 1.3 + - - +
149U GLN* 6.5 1.6 - - + -
153U LEU* 5.4 7.9 - - + -
192U LYS* 3.2 21.9 + - + +
193U LYS* 3.1 13.7 + - - +
195U GLU* 1.4 77.1 - - + +
197U GLU* 1.4 60.5 + - - +
199U VAL* 4.0 4.3 - - - +
200U ALA* 3.2 22.5 + - - +
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Residues in contact with GLU 197 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120U GLY 4.1 0.5 - - - +
121U PRO* 3.5 11.8 - - + +
122U ARG* 3.2 35.7 + - + +
123U GLU* 3.7 22.8 - - - +
193U LYS* 3.0 41.2 + - - +
194U ASP* 4.4 5.2 - - - +
196U LEU* 1.4 73.4 - - - +
198U ARG* 1.4 64.3 + - - +
200U ALA* 3.4 4.5 + - - +
201U LYS* 3.2 22.5 + - - +
59l LEU* 5.2 12.7 - - + +
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Residues in contact with ARG 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P MET* 5.9 1.1 - - - -
49P SER* 6.3 1.2 - - - -
50P GLU* 5.8 1.8 + - - -
74P ILE* 3.3 43.8 - - - +
75P ARG* 3.8 33.4 - - + +
84P ASP* 3.4 34.3 + - - -
194U ASP 3.2 21.8 + - - +
195U GLU* 3.8 5.6 - - - +
197U GLU* 1.4 76.6 - - - +
199U VAL* 1.4 68.4 + - - +
201U LYS* 3.4 13.8 + - - +
202U SER* 3.2 41.0 + - - -
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Residues in contact with VAL 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P MET* 6.5 0.2 - - + -
48P LEU* 3.6 39.7 - - + -
49P SER* 5.0 5.8 - - - -
84P ASP* 4.8 7.2 - - - +
125U SER* 4.1 12.1 - - - +
136U ARG* 5.5 3.8 - - - +
195U GLU* 3.1 21.9 + - + +
196U LEU* 4.0 4.7 - - - +
198U ARG* 1.4 86.9 - - - +
200U ALA* 1.4 65.1 + - - +
202U SER* 3.4 11.7 + - - -
203U ASN* 3.0 35.0 + - - +
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Residues in contact with ALA 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123U GLU* 3.6 24.0 - - + +
124U ASP 3.2 24.5 - - - +
125U SER* 3.6 11.4 + - - -
138U ALA* 3.3 23.8 - - + +
196U LEU 3.2 15.0 + - - +
197U GLU 3.4 10.3 - - - +
198U ARG 3.3 0.2 - - - -
199U VAL* 1.4 76.9 - - - +
201U LYS* 1.4 62.9 + - - +
202U SER 3.4 2.8 + - - +
203U ASN* 3.5 6.2 + - - +
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Residues in contact with LYS 201 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123U GLU* 3.7 7.8 + - - -
197U GLU 3.2 11.2 + - - +
198U ARG* 3.6 11.2 - - - +
199U VAL 3.3 0.2 - - - -
200U ALA* 1.4 78.4 - - - +
202U SER* 1.4 66.0 + - - +
5l ARG 5.6 5.6 - - - +
59l LEU* 3.2 46.1 + - - +
60l GLU* 3.2 25.8 + - - +
63l ARG* 3.4 34.8 + - - +
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Residues in contact with SER 202 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P SER* 5.9 2.9 - - - -
50P GLU* 5.1 9.2 - - - -
198U ARG* 3.2 37.1 + - - -
199U VAL* 3.4 9.8 + - - -
200U ALA 3.3 2.0 - - - +
201U LYS* 1.4 83.9 - - - +
203U ASN* 1.4 76.1 + - - +
204U ARG 3.8 6.6 - - - +
72j TYR* 4.4 5.6 - - - -
63l ARG* 3.9 6.8 + - - -
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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