Contacts of the helix formed by residues 176 - 189 (chain B) in PDB entry 7UUT
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 GLY 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLY* 3.6 2.6 - - - -
175B ILE* 1.3 78.4 - - - +
177B PRO* 1.3 70.9 - - - +
178B VAL 3.2 3.1 - - - -
179B GLY 3.0 3.3 + - - +
180B LEU* 2.7 29.5 + - - +
200B ARG* 4.4 14.5 - - - +
203B CYS* 4.8 1.1 - - - -
242B ALA 5.1 4.4 + - - -
340B LYS* 5.9 0.4 - - - -
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Residues in contact with PRO 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 5.6 3.4 - - - +
151B MET* 3.5 32.3 - - + -
176B GLY* 1.3 81.9 - - - +
178B VAL* 1.3 63.2 + - + +
180B LEU* 3.4 1.9 + - - +
181B MET* 3.1 28.5 + - - +
200B ARG* 5.2 2.2 - - - +
319B LEU* 4.1 16.7 - - + +
337B MET* 5.8 1.3 - - + -
340B LYS* 4.8 13.7 - - - +
345B ILE* 3.9 38.8 - - + +
346B LYS* 4.2 11.4 - - + +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B MET* 3.9 34.8 - - + -
154B THR* 3.7 35.7 - - + +
155B GLY* 3.5 9.9 - - - +
176B GLY 3.2 0.6 - - - -
177B PRO* 1.3 76.9 - - + +
179B GLY* 1.3 59.6 + - - +
181B MET 3.1 2.3 + - - -
182B ALA* 2.9 23.7 + - - +
242B ALA* 4.1 13.9 - - + +
265B VAL* 3.9 21.3 - - + +
266B ASN* 6.2 0.2 - - - -
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.6 2.2 - - - +
174B GLY 3.3 25.6 - - - -
175B ILE* 4.3 2.5 - - - -
176B GLY 3.0 7.8 + - - +
178B VAL* 1.3 79.0 - - - +
180B LEU* 1.3 57.2 + - - +
182B ALA* 3.0 6.0 + - - +
183B VAL* 2.9 32.6 + - - +
242B ALA* 3.5 16.2 + - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 3.5 20.4 - - + +
176B GLY 2.7 21.5 + - - +
177B PRO 3.8 0.4 - - - +
179B GLY* 1.3 72.3 - - - +
181B MET* 1.3 59.6 + - - +
183B VAL* 3.3 7.2 + - + +
184B ALA* 3.1 24.8 + - - +
203B CYS* 3.6 9.6 - - - +
206B ALA* 3.7 19.5 - - + -
207B ALA* 3.5 39.5 - - + +
210B TYR* 3.9 11.4 - - + -
319B LEU* 3.6 31.4 - - + -
345B ILE* 3.9 20.6 - - + -
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Residues in contact with MET 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B MET 3.6 26.0 - - - +
152B MET* 3.7 33.0 - - - -
155B GLY* 3.9 5.6 - - - -
156B PHE* 3.1 26.2 - - + -
177B PRO 3.1 13.0 + - - +
178B VAL 3.1 7.8 + - - +
180B LEU* 1.3 74.9 - - - +
182B ALA* 1.3 55.2 + - - +
184B ALA* 4.3 3.6 - - + -
185B GLY 2.7 27.9 + - - -
210B TYR* 3.5 45.3 - - + +
314B VAL* 4.4 6.3 - - + -
316B PRO* 4.5 2.2 - - + -
319B LEU* 3.8 23.1 - - + -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLY* 3.4 21.0 - - - +
159B ALA* 4.2 0.3 - - - +
172B VAL* 3.9 11.7 - - + -
178B VAL 2.9 12.6 + - - +
179B GLY* 3.0 12.1 + - - +
181B MET* 1.3 74.8 - - - +
183B VAL* 1.3 58.8 + - - +
185B GLY* 3.6 0.3 - - - -
186B ALA* 2.8 30.1 + - - +
240B ILE* 3.7 33.0 - - + +
242B ALA* 4.9 1.8 - - + -
265B VAL* 5.6 0.4 - - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.8 26.7 - - + -
175B ILE* 4.6 4.7 - - + -
179B GLY 2.9 18.5 + - - +
180B LEU* 3.5 10.3 - - - +
182B ALA* 1.3 76.1 - - - +
184B ALA* 1.3 63.2 + - - +
186B ALA* 3.2 5.9 + - - +
187B LYS* 3.0 20.1 + - - +
194B ILE* 3.7 15.9 - - + +
196B ALA* 4.4 14.4 - - + -
207B ALA* 3.9 9.6 - - + +
210B TYR* 3.7 14.8 - - + +
211B GLY 4.1 0.9 - - - -
212B ALA* 3.7 28.5 - - + +
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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
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156B PHE* 4.0 13.0 - - + -
180B LEU 3.1 15.6 + - - +
181B MET* 3.8 8.7 - - + +
182B ALA 3.3 0.2 - - - -
183B VAL* 1.3 76.2 - - - +
185B GLY* 1.3 62.5 + - - +
187B LYS* 3.3 5.3 + - - +
188B LEU* 3.0 26.3 + - - +
210B TYR* 3.7 34.3 + - + +
314B VAL* 4.0 14.3 - - + +
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 3.6 18.3 - - - -
159B ALA* 3.4 20.7 - - - +
181B MET 2.7 22.0 + - - -
182B ALA 3.6 1.8 - - - -
184B ALA* 1.3 73.2 - - - +
186B ALA* 1.3 61.2 + - - +
188B LEU* 3.1 17.6 + - - +
189B ARG* 3.1 13.5 + - - +
166C LEU* 5.2 1.7 - - - +
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 3.6 1.0 - - - +
164B ILE* 3.8 25.5 - - + +
170B VAL* 4.0 17.5 - - + -
172B VAL* 5.1 0.4 - - + -
182B ALA 2.8 19.8 + - - +
183B VAL* 3.2 7.4 + - - +
185B GLY* 1.3 72.7 - - - +
187B LYS* 1.3 63.2 + - - +
189B ARG* 3.2 8.7 + - - +
190B GLY 3.5 0.2 + - - -
191B ALA* 3.1 27.1 + - + +
194B ILE* 3.8 15.0 - - + -
240B ILE* 4.6 1.8 - - + -
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Residues in contact with LYS 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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183B VAL 3.0 12.9 + - - +
184B ALA* 3.5 9.4 - - - +
186B ALA* 1.3 75.8 - - - +
188B LEU* 1.3 65.1 + - + +
190B GLY* 3.3 12.1 + - - -
191B ALA* 4.6 5.2 - - - +
194B ILE* 3.6 11.8 - - + +
209B TYR 5.2 6.3 + - - -
210B TYR 3.7 18.9 + - - +
211B GLY* 4.3 4.1 - - - -
313B ARG 5.9 2.6 + - - +
187C LYS* 5.1 11.4 - - - +
188C LEU* 4.5 9.4 - - + +
313C ARG* 4.2 33.5 - - - +
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Residues in contact with LEU 188 (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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156B PHE* 3.6 40.6 - - + -
184B ALA 3.0 15.9 + - - +
185B GLY* 3.1 9.1 + - - +
187B LYS* 1.3 80.9 - - + +
189B ARG* 1.3 51.3 + - - +
190B GLY 3.2 0.2 - - - -
308B LEU* 4.0 15.0 - - + -
313B ARG* 4.1 32.8 - - + +
314B VAL* 3.7 9.2 - - + -
166C LEU* 4.0 8.7 - - + -
187C LYS* 4.7 7.4 - - + +
188C LEU 2.7 15.4 - - - +
190C GLY* 2.7 44.6 + - - -
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 4.2 23.6 - - + +
160B GLU* 4.4 17.4 + - - +
163B ASP* 5.1 3.4 - - - +
164B ILE* 3.2 46.8 + - + +
165B GLU 4.5 0.5 - - - +
185B GLY 3.1 15.8 + - - +
186B ALA 3.2 4.8 + - - +
188B LEU* 1.3 75.8 - - - +
190B GLY* 1.3 59.1 + - - +
191B ALA 3.5 2.8 + - - -
164C ILE 3.9 18.3 + - - +
166C LEU* 4.5 14.0 - - + +
188C LEU 2.9 7.0 - - - -
189C ARG* 2.5 78.8 + - - +
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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