Contacts of the helix formed by residues 222 - 238 (chain X) in PDB entry 1UNF
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 222 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100X GLU 4.3 0.7 - - - -
101X CYS 2.7 18.1 + - - +
102X MET 3.8 10.8 - - - -
103X LYS* 3.7 30.4 - - - +
220X LEU 3.3 0.4 + - - -
221X VAL* 1.3 72.7 - - - +
223X TRP* 1.3 62.3 + - - +
224X ASP* 3.7 9.0 + - - +
225X ALA* 3.1 32.5 + - - +
226X VAL* 3.2 15.8 + - - +
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Residues in contact with TRP 223 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X LYS* 5.5 1.8 - - - +
107X GLY 3.5 20.4 + - - -
108X GLY 2.8 18.2 + - - -
109X LYS 3.5 16.5 - - - +
110X PRO* 3.7 26.2 - - + -
114X LEU* 3.7 20.9 - - + +
118X ILE* 4.7 3.8 - - + -
125X PHE* 3.6 22.0 - + - -
128X PHE* 3.8 18.2 - + - -
147X LEU* 4.9 1.3 - - + -
192X LEU* 4.1 10.8 - - + -
217X MET* 3.8 27.8 - - + -
221X VAL* 3.5 20.8 + - + +
222X SER* 1.3 70.2 - - - +
224X ASP* 1.3 62.2 + - - +
226X VAL* 3.2 27.1 + - + +
227X SER* 2.8 34.2 + - - +
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Residues in contact with ASP 224 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103X LYS* 3.4 25.1 + - + +
222X SER* 3.2 7.8 - - - +
223X TRP* 1.3 78.2 - - - +
225X ALA* 1.3 62.0 + - - +
227X SER* 3.4 6.3 + - - -
228X SER* 3.1 26.0 + - - -
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Residues in contact with ALA 225 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X GLU* 3.1 32.1 - - + +
101X CYS* 4.6 4.3 - - - -
191X LEU 4.9 0.4 - - - -
222X SER* 3.1 18.6 + - - +
224X ASP* 1.3 81.3 - - - +
226X VAL* 1.3 61.5 + - + +
228X SER* 3.2 8.7 + - - -
229X ARG* 3.1 26.6 + - + +
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Residues in contact with VAL 226 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X CYS* 5.4 2.0 - - - +
114X LEU* 3.8 22.4 - - + -
147X LEU* 4.3 6.1 - - + -
191X LEU* 3.6 40.4 - - + +
192X LEU* 4.0 22.7 - - + -
221X VAL* 4.3 0.7 - - + -
222X SER 3.2 16.6 - - - +
223X TRP* 3.2 29.3 + - + +
225X ALA* 1.3 76.5 - - + +
227X SER* 1.3 57.7 + - - +
229X ARG* 3.2 3.7 + - - +
230X LEU* 2.9 27.2 + - - +
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Residues in contact with SER 227 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X PRO* 5.3 0.7 - - - +
111X SER 4.4 6.9 + - - -
114X LEU* 3.5 24.1 + - - +
223X TRP* 2.8 19.6 + - - +
224X ASP* 3.7 7.6 - - - -
225X ALA 3.3 0.2 - - - -
226X VAL* 1.3 74.2 - - - +
228X SER* 1.3 64.6 + - - +
230X LEU* 3.3 9.3 + - - +
231X GLU* 3.1 32.5 + - - +
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Residues in contact with SER 228 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224X ASP 3.1 14.7 + - - -
225X ALA* 3.2 10.9 + - - -
227X SER* 1.3 75.8 - - - +
229X ARG* 1.3 63.9 + - - +
231X GLU* 3.3 15.4 + - - +
232X GLN* 3.2 37.7 + - - +
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Residues in contact with ARG 229 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X TRP* 4.7 12.1 - - - +
97X PHE* 3.6 24.7 - - + -
100X GLU* 3.0 30.1 + - - -
189X TYR* 3.4 23.1 + - + -
190X PRO* 3.8 15.6 + - - +
191X LEU* 3.6 26.0 - - + +
225X ALA* 3.1 13.9 + - + +
226X VAL 3.2 7.6 + - - +
228X SER* 1.3 80.1 - - - +
230X LEU* 1.3 53.2 + - - +
232X GLN* 3.1 21.4 + - - +
233X ALA* 2.7 35.7 + - - +
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Residues in contact with LEU 230 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X GLU* 4.2 8.7 - - + +
114X LEU* 3.6 44.2 - - + +
117X LEU* 3.8 30.3 - - + -
149X TYR* 4.1 15.9 - - + -
191X LEU* 3.4 20.1 - - + +
226X VAL 2.9 13.8 + - - +
227X SER* 3.5 10.3 - - - +
228X SER 3.3 0.2 - - - -
229X ARG* 1.3 77.8 - - - +
231X GLU* 1.3 56.3 + - - +
233X ALA* 3.3 0.6 + - + -
234X LYS* 2.8 50.5 + - + +
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Residues in contact with GLU 231 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X GLU* 6.4 2.0 - - + -
227X SER* 3.1 27.1 + - - +
228X SER* 3.6 13.8 + - - +
229X ARG 3.2 0.2 - - - -
230X LEU* 1.3 73.4 - - + +
232X GLN* 1.3 61.6 + - + +
234X LYS* 3.5 6.0 + - - +
235X ALA* 3.0 29.3 + - - +
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Residues in contact with GLN 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X TYR* 2.7 32.4 + - + +
228X SER* 3.2 28.9 + - - +
229X ARG* 3.1 28.8 + - - +
231X GLU* 1.3 75.4 - - + +
233X ALA* 1.3 58.2 + - - +
235X ALA* 3.2 6.6 + - - +
236X LEU* 2.9 40.3 + - + +
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Residues in contact with ALA 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X TYR* 4.0 22.5 - - + -
154X LEU* 4.2 1.9 - - - +
189X TYR* 3.4 38.3 - - + -
191X LEU* 4.1 0.7 - - + -
229X ARG 2.7 20.4 + - - +
230X LEU* 3.6 9.0 - - - +
232X GLN* 1.3 74.9 - - - +
234X LYS* 1.3 59.9 + - - +
236X LEU* 3.4 3.2 + - - +
237X SER* 2.9 28.3 + - - -
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Residues in contact with LYS 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X GLU* 4.8 12.7 + - - +
117X LEU* 4.8 9.5 - - + +
149X TYR* 3.5 35.0 - - + +
230X LEU* 2.8 41.6 + - + +
231X GLU* 3.9 5.8 - - - +
233X ALA* 1.3 72.8 - - - +
235X ALA* 1.3 67.0 + - - +
237X SER* 3.3 5.3 + - - -
238X ALA* 3.1 24.8 + - - +
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Residues in contact with ALA 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X GLU 3.0 18.5 + - - +
232X GLN* 3.6 7.4 - - - +
234X LYS* 1.3 78.4 - - - +
236X LEU* 1.3 62.6 + - + +
237X SER 3.4 0.9 + - - -
238X ALA* 3.6 15.1 + - - +
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Residues in contact with LEU 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LYS 4.1 9.2 - - - +
154X LEU* 3.6 21.6 - - + +
189X TYR* 3.4 36.8 - - + +
232X GLN* 2.9 19.7 + - + +
233X ALA 3.9 0.9 - - - +
234X LYS 3.2 0.2 - - - -
235X ALA* 1.3 80.1 - - + +
237X SER* 1.3 58.8 + - - +
238X ALA* 3.5 2.6 - - - +
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Residues in contact with SER 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X TYR* 3.4 17.2 + - - -
151X ALA* 3.4 27.8 - - - -
153X LYS* 3.2 26.0 - - - +
154X LEU* 3.8 9.6 - - - -
169X ASN* 4.5 6.8 + - - +
233X ALA 2.9 17.2 + - - -
234X LYS* 3.3 5.8 + - - -
236X LEU* 1.3 76.3 - - - +
238X ALA* 1.3 67.4 + - - +
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Residues in contact with ALA 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LYS* 3.4 30.5 + - - +
234X LYS 3.1 14.6 + - - +
235X ALA* 3.7 11.3 - - - +
236X LEU 3.5 3.8 - - - +
237X SER* 1.3 83.6 - - - +
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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