Contacts of the helix formed by residues 181 - 195 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K GLN* 3.7 29.2 - - - -
160K ASP* 4.4 4.7 + - - -
115P GLN* 2.9 24.6 + - - +
180R LEU* 1.3 76.8 - - - +
182R ALA* 1.3 60.3 + - - +
183R LYS* 3.8 3.6 + - - +
184R ASN* 3.2 28.8 + - - +
185R TYR* 2.9 27.5 + - - +
211R PHE 3.7 10.1 - - - -
212R MET* 3.8 1.1 - - - -
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Residues in contact with ALA 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K GLN* 5.1 2.0 - - - +
157K VAL* 5.7 4.9 - - + -
181R SER* 1.3 73.6 - - - +
183R LYS* 1.3 62.4 + - - +
185R TYR* 3.2 4.3 + - - +
186R GLY 3.1 18.0 + - - -
211R PHE 4.6 0.6 + - - -
212R MET* 3.7 23.5 - - + +
216R ASP* 3.5 34.5 - - + -
217R ARG* 3.6 16.2 - - - +
220R PHE* 3.6 15.6 - - + +
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Residues in contact with LYS 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K ASP* 3.5 44.5 + - + +
163K ASN* 2.9 26.5 - - - +
165K TYR* 2.7 32.5 + - - +
71P ARG* 5.0 7.6 + - - +
72P TYR* 2.6 49.9 + - + +
106P ARG* 5.9 0.4 - - - +
117P GLN* 5.0 0.4 + - - -
181R SER* 3.3 2.5 + - - +
182R ALA* 1.3 78.7 - - - +
184R ASN* 1.3 58.3 + - - +
186R GLY 3.3 0.2 + - - -
187R ARG* 2.9 39.5 + - - +
220R PHE* 3.5 14.1 - - + -
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Residues in contact with ASN 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H LEU* 3.8 33.4 + - + +
110P PHE* 4.9 4.8 - - - -
115P GLN* 3.0 42.9 + - - +
116P VAL* 6.0 0.6 - - - +
180R LEU* 4.2 13.7 - - + +
181R SER* 3.2 14.0 + - - +
183R LYS* 1.3 74.5 - - - +
185R TYR* 1.3 60.7 + - - +
187R ARG* 2.9 30.3 + - - +
188R ALA* 2.9 30.8 + - - +
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Residues in contact with TYR 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174R ILE* 3.6 40.4 + - + +
176R PRO 5.0 1.8 - - - -
177R LYS 4.9 4.9 - - - -
180R LEU* 3.9 20.6 - - + +
181R SER 2.9 10.1 + - - +
182R ALA 3.3 10.1 - - - +
183R LYS 3.2 0.2 - - - -
184R ASN* 1.3 76.1 - - - +
186R GLY* 1.3 57.2 + - - +
188R ALA* 3.2 5.3 + - - +
189R VAL* 2.8 33.5 + - + +
202R ASP* 3.3 23.1 - - - -
203R ASP 3.3 26.2 + - - -
206R VAL* 3.6 15.0 - - + +
212R MET* 3.6 32.3 - - + -
217R ARG* 3.7 17.5 - - + -
221R VAL* 4.2 8.3 - - + -
238R HIS* 3.9 10.3 - - - -
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Residues in contact with GLY 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P TYR* 3.2 18.4 - - - -
182R ALA 3.1 9.5 + - - -
185R TYR* 1.3 75.7 - - - +
187R ARG* 1.3 58.9 + - - +
189R VAL* 4.2 6.7 - - - -
190R TYR* 2.9 27.0 + - - +
220R PHE 4.0 17.5 - - - -
221R VAL* 4.4 4.1 - - - +
224R ALA* 3.2 10.0 - - - +
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Residues in contact with ARG 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H TRP* 5.2 2.7 - - + -
74H LEU* 4.7 10.3 - - + -
43P GLU* 3.0 29.7 + - - -
72P TYR* 3.3 19.7 + - + -
75P MET* 3.8 29.1 - - + +
106P ARG* 5.9 0.4 - - - +
110P PHE* 3.8 30.8 - - - -
117P GLN* 4.4 7.1 + - - -
183R LYS* 2.9 44.9 + - - +
184R ASN* 2.9 34.9 + - - +
186R GLY* 1.3 78.4 - - - +
188R ALA* 1.3 63.6 + - - +
190R TYR* 3.4 4.4 + - - +
191R GLU* 3.2 30.6 + - + +
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Residues in contact with ALA 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H TRP* 5.2 3.6 - - + -
71H THR* 4.6 11.2 - - + -
174R ILE* 4.2 23.8 - - + -
180R LEU* 5.0 1.3 - - + -
184R ASN 2.9 15.8 + - - +
185R TYR 3.7 3.6 - - - +
187R ARG* 1.3 78.1 - - - +
189R VAL* 1.3 57.5 + - - +
191R GLU* 3.4 1.4 + - - -
192R CYS* 3.0 28.9 + - - -
407R LEU* 4.3 6.3 - - + -
413R ASN* 3.1 26.6 + - - +
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Residues in contact with VAL 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174R ILE* 3.8 16.8 - - + -
185R TYR* 2.8 24.1 + - + +
186R GLY* 3.7 5.6 - - - +
187R ARG 3.2 0.2 - - - -
188R ALA* 1.3 73.6 - - - +
190R TYR* 1.3 67.1 + - - +
192R CYS* 3.1 3.5 + - - +
193R LEU* 2.9 38.8 + - + +
200R THR* 3.3 17.5 - - - +
221R VAL* 4.2 11.9 - - + +
224R ALA* 3.8 12.8 - - + -
225R ILE* 4.9 0.2 - - + -
238R HIS* 3.3 36.8 - - + +
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Residues in contact with TYR 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P TYR* 4.9 9.4 - + + -
73P TRP 3.6 20.0 - - - -
74P THR* 2.8 20.5 + - - -
186R GLY 2.9 17.9 + - - +
187R ARG* 3.8 4.3 - - - +
189R VAL* 1.3 75.4 - - - +
191R GLU* 1.3 88.0 + - + +
193R LEU* 3.4 0.9 + - - +
194R ARG* 3.0 45.4 + - + +
224R ALA* 3.6 19.5 - - + +
227R LYS* 3.5 36.6 - - + -
228R ALA* 4.0 15.3 - - + -
231R GLU* 2.6 30.2 + - - -
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Residues in contact with GLU 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H TRP* 5.8 2.5 - - + -
73P TRP 4.1 1.6 - - - +
74P THR* 3.8 0.3 - - - -
75P MET* 2.9 53.0 + - + +
187R ARG* 3.2 20.3 + - + +
188R ALA* 3.9 1.6 - - - +
190R TYR* 1.3 93.6 - - + +
192R CYS* 1.3 61.9 + - - +
194R ARG* 2.9 36.6 + - - +
413R ASN* 3.6 22.4 - - + +
414R ALA* 3.1 33.3 + - - +
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Residues in contact with CYS 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172R CYS* 3.8 23.6 - - - -
174R ILE* 4.0 11.0 - - - -
188R ALA 3.0 24.6 + - - +
189R VAL 3.5 0.2 - - - +
191R GLU* 1.3 74.1 - - - +
193R LEU* 1.3 67.4 + - - +
195R GLY 3.3 1.9 + - - -
197R LEU* 3.8 12.3 + - + +
200R THR* 3.4 20.0 - - + -
406R THR* 3.9 6.1 - - - -
407R LEU* 4.1 2.5 - - - -
413R ASN* 3.5 29.2 - - - -
417R ALA* 3.1 24.9 - - - +
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Residues in contact with LEU 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R VAL* 2.9 38.3 + - + +
192R CYS* 1.3 74.2 - - - +
194R ARG* 1.3 61.7 + - - +
195R GLY 3.2 1.0 + - - -
196R GLY 3.2 4.2 + - - -
197R LEU* 3.3 15.5 - - - +
198R ASP 3.8 4.3 - - - +
199R PHE* 3.6 33.4 - - - +
200R THR* 3.6 7.9 - - + +
224R ALA 4.3 1.1 - - - +
225R ILE* 3.9 27.1 - - + -
228R ALA* 3.5 16.2 - - + -
236R LYS* 2.8 43.1 + - + -
237R GLY 3.6 13.9 - - - +
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Residues in contact with ARG 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M VAL* 4.7 1.8 - - - +
4M TRP* 2.6 64.4 + - - +
6M PRO* 3.6 11.7 - - - +
17M TYR* 4.2 1.9 + - - -
74P THR* 3.4 19.6 - - - +
75P MET 4.6 4.8 + - - -
190R TYR* 3.0 52.8 + - + +
191R GLU* 2.9 30.4 + - - +
193R LEU* 1.3 76.0 - - - +
195R GLY* 1.3 60.2 + - - +
196R GLY 3.3 0.2 - - - -
228R ALA* 3.8 5.6 - - + +
231R GLU* 2.9 30.9 + - - +
232R THR* 3.5 23.2 - - + +
414R ALA* 3.6 10.0 - - + +
415R PRO* 5.8 0.2 - - - +
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Residues in contact with GLY 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M TRP* 4.2 9.8 - - - -
17M TYR* 3.4 12.5 - - - -
191R GLU 3.7 0.6 + - - -
192R CYS 3.3 4.2 + - - -
193R LEU 3.2 1.4 - - - -
194R ARG* 1.3 80.2 - - - +
196R GLY* 1.3 56.3 + - - +
414R ALA* 3.5 24.7 - - - -
417R ALA* 3.6 10.5 - - - -
418R ALA* 3.1 27.4 + - - +
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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