Contacts of the helix formed by residues 181 - 195 (chain O) in PDB entry 1UW9
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 181 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115M GLN* 2.9 26.4 + - - +
180O LEU* 1.3 74.2 - - - +
182O ALA* 1.3 59.6 + - - +
183O LYS* 3.7 6.1 + - - +
184O ASN* 3.2 28.1 + - - +
185O TYR* 2.8 28.8 + - - +
211O PHE 3.7 10.1 - - - -
212O MET* 3.9 1.1 - - - -
156R GLN* 3.7 28.7 - - - -
160R ASP* 4.4 3.6 + - - -
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Residues in contact with ALA 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O SER* 1.3 72.9 - - - +
183O LYS* 1.3 62.7 + - - +
185O TYR* 3.1 5.6 + - - +
186O GLY 3.1 17.7 + - - -
211O PHE 4.6 0.6 + - - -
212O MET* 3.7 23.9 - - + +
216O ASP* 3.6 17.9 - - + -
217O ARG* 3.6 28.6 - - - +
220O PHE* 3.6 18.9 - - + +
156R GLN* 5.2 1.8 - - - +
157R VAL* 5.8 4.9 - - + +
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Residues in contact with LYS 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M ARG* 5.0 6.6 + - - +
72M TYR* 2.7 50.2 + - + +
106M ARG* 5.9 0.4 - - - +
117M GLN* 5.0 1.4 + - - -
181O SER* 3.3 3.3 + - - +
182O ALA* 1.3 77.4 - - - +
184O ASN* 1.3 58.6 + - - +
187O ARG* 2.9 39.6 + - - +
220O PHE* 3.5 14.1 - - + -
160R ASP* 3.6 43.0 + - + +
163R ASN* 2.9 27.3 - - - +
165R TYR* 2.9 31.2 + - - +
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Residues in contact with ASN 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M PHE* 4.9 4.4 - - - -
115M GLN* 2.9 44.1 + - - +
116M VAL* 6.0 0.6 - - - +
180O LEU* 4.2 12.7 - - + +
181O SER* 3.2 16.7 + - - +
183O LYS* 1.3 75.8 - - - +
185O TYR* 1.3 65.1 + - - +
187O ARG* 3.0 29.2 + - - +
188O ALA* 3.0 24.9 + - - +
71V THR* 5.9 0.2 - - - +
74V LEU* 3.7 33.5 + - + +
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Residues in contact with TYR 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174O ILE* 3.6 33.9 + - + +
176O PRO 5.0 2.0 - - - -
177O LYS 4.9 4.0 - - - -
180O LEU* 4.0 19.9 - - + +
181O SER 2.8 10.0 + - - +
182O ALA* 3.2 10.3 - - - +
184O ASN* 1.3 75.6 - - - +
186O GLY* 1.3 56.6 + - - +
188O ALA* 3.3 4.9 + - - +
189O VAL* 2.9 33.9 + - + +
202O ASP* 3.3 22.0 - - - -
203O ASP 3.2 26.5 + - - -
206O VAL* 3.6 15.9 - - + +
212O MET* 3.5 31.9 - - + -
217O ARG* 3.7 16.6 - - + -
221O VAL* 4.2 8.7 - - + -
238O HIS* 3.9 13.2 - - - -
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Residues in contact with GLY 186 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M TYR* 3.1 19.9 - - - -
182O ALA 3.1 11.6 + - - -
183O LYS 3.3 0.4 + - - -
185O TYR* 1.3 72.6 - - - +
187O ARG* 1.3 59.7 + - - +
189O VAL* 4.2 5.8 - - - -
190O TYR* 2.9 27.7 + - - +
220O PHE 4.1 17.5 - - - -
221O VAL* 4.3 4.2 - - - +
224O ALA* 3.2 9.6 - - - +
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Residues in contact with ARG 187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M GLU* 3.0 28.3 + - - -
72M TYR* 3.3 20.1 + - + -
75M MET* 3.8 29.8 - - + +
106M ARG* 5.9 0.2 - - - +
110M PHE* 3.7 31.6 - - - -
117M GLN* 4.3 6.3 + - - -
183O LYS* 2.9 46.7 + - - +
184O ASN* 3.0 32.0 + - - +
186O GLY* 1.3 77.1 - - - +
188O ALA* 1.3 61.8 + - - +
190O TYR* 3.5 4.1 + - + +
191O GLU* 3.2 31.0 + - + +
70V TRP* 5.2 3.1 - - + -
74V LEU* 4.7 10.5 - - + -
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Residues in contact with ALA 188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174O ILE* 4.2 23.3 - - + -
180O LEU* 5.0 1.1 - - + -
184O ASN 3.0 17.1 + - - +
185O TYR 3.7 3.6 - - - +
187O ARG* 1.3 76.9 - - - +
189O VAL* 1.3 59.0 + - - +
191O GLU* 3.4 1.2 + - - -
192O CYS* 3.0 27.4 + - - -
407O LEU* 4.3 6.3 - - + -
413O ASN* 3.1 27.0 + - - +
70V TRP* 5.2 3.1 - - + -
71V THR* 4.5 12.1 - - + -
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Residues in contact with VAL 189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174O ILE* 3.8 16.8 - - + -
185O TYR* 2.9 24.4 + - + +
186O GLY* 3.6 5.6 - - - +
187O ARG 3.3 0.2 - - - -
188O ALA* 1.3 73.8 - - - +
190O TYR* 1.3 67.1 + - - +
192O CYS* 3.2 3.5 + - - +
193O LEU* 2.9 39.2 + - + +
200O THR* 3.4 17.5 - - - +
221O VAL* 4.2 15.5 - - + +
224O ALA* 3.8 12.8 - - + -
238O HIS* 3.3 33.7 - - + +
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Residues in contact with TYR 190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M TYR* 4.9 8.5 - + + -
73M TRP 3.5 19.3 - - - -
74M THR* 2.7 21.0 + - - -
186O GLY 2.9 21.1 + - - +
187O ARG* 3.9 5.4 - - - +
189O VAL* 1.3 72.9 - - - +
191O GLU* 1.3 90.1 + - + +
193O LEU* 4.0 0.9 - - - +
194O ARG* 3.0 44.0 + - + +
224O ALA* 3.7 20.2 - - + -
227O LYS* 3.4 37.2 - - + -
228O ALA* 3.9 14.8 - - + -
231O GLU* 2.5 30.0 + - - -
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Residues in contact with GLU 191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M TRP 4.2 1.2 - - - +
74M THR* 3.9 0.3 - - - -
75M MET* 2.9 54.4 + - + +
187O ARG* 3.2 20.6 + - + +
188O ALA* 3.9 1.8 - - - +
189O VAL 3.3 0.2 - - - -
190O TYR* 1.3 92.2 - - + +
192O CYS* 1.3 62.6 + - - +
194O ARG* 2.9 38.0 + - - +
195O GLY 3.7 0.2 + - - -
413O ASN* 3.6 21.8 - - + +
414O ALA* 3.1 33.4 + - - +
70V TRP* 5.8 2.2 - - + -
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Residues in contact with CYS 192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O CYS* 3.7 25.4 - - - -
174O ILE* 4.1 10.1 - - - -
188O ALA 3.0 23.5 + - - +
189O VAL 3.5 0.9 - - - +
191O GLU* 1.3 74.6 - - - +
193O LEU* 1.3 65.7 + - - +
195O GLY 3.3 1.7 + - - -
197O LEU* 3.7 12.1 + - + +
200O THR* 3.5 19.3 - - + -
406O THR* 3.9 7.0 - - - -
407O LEU* 4.1 2.5 - - - -
413O ASN* 3.5 28.9 - - - -
417O ALA* 3.1 24.6 - - - +
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Residues in contact with LEU 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189O VAL* 2.9 39.7 + - + +
192O CYS* 1.3 73.8 - - - +
194O ARG* 1.3 61.2 + - - +
195O GLY 3.2 0.9 + - - -
196O GLY 3.3 4.0 + - - -
197O LEU* 3.4 15.1 - - + +
198O ASP 3.7 6.1 - - - +
199O PHE 3.5 32.5 - - - +
200O THR* 3.6 7.4 - - + +
224O ALA 4.4 1.1 - - - +
225O ILE* 3.9 26.2 - - + -
228O ALA* 3.5 15.9 - - + -
236O LYS* 2.8 39.6 + - + -
237O GLY 3.6 14.6 - - - +
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Residues in contact with ARG 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M THR* 3.5 18.6 - - - +
75M MET 4.6 5.1 + - - -
190O TYR* 3.0 48.6 + - + +
191O GLU* 2.9 34.0 + - - +
193O LEU* 1.3 77.6 - - - +
195O GLY* 1.3 61.1 + - - +
196O GLY 3.3 0.6 + - - -
228O ALA* 3.8 5.8 - - + +
231O GLU* 3.0 30.4 + - - +
232O THR* 3.5 23.8 - - + +
414O ALA* 3.6 17.3 - - + +
415O PRO* 5.7 0.2 - - - +
3T VAL* 4.7 2.2 - - - +
4T TRP* 2.7 56.3 + - - +
6T PRO* 3.7 11.9 - - - +
17T TYR* 4.3 1.6 + - - -
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Residues in contact with GLY 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O GLU 3.7 1.2 + - - -
192O CYS 3.3 3.6 + - - -
193O LEU 3.2 1.4 - - - -
194O ARG* 1.3 79.8 - - - +
196O GLY* 1.3 55.5 + - - +
414O ALA* 3.4 23.8 - - - -
417O ALA* 3.6 10.5 - - - -
418O ALA* 3.0 27.9 - - - +
4T TRP* 4.2 10.1 - - - -
17T TYR* 3.4 12.5 - - - -
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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