Contacts of the helix formed by residues 176 - 194 (chain A) in PDB entry 5GPY
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 LEU 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ILE* 4.2 27.6 - - + -
117A ASP* 5.7 6.5 - - + +
175A THR* 1.3 71.9 - - - +
177A LEU* 1.3 58.4 + - - +
179A ARG* 3.3 6.4 + - + +
180A PHE* 2.9 30.7 + - - +
215B GLU* 3.3 42.0 - - + +
216B PHE* 3.5 23.6 - - + -
219B LEU* 5.6 3.4 - - + -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 4.2 24.7 - - + -
114A ILE* 3.7 26.0 - - + +
115A GLU* 4.1 21.8 - - + +
118A GLU* 3.7 19.7 - - - +
175A THR* 3.2 10.8 - - + +
176A LEU* 1.3 76.2 - - - +
178A ALA* 1.3 60.4 + - - +
180A PHE* 3.3 11.4 + - + +
181A ASN* 2.9 50.8 + - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A THR* 3.3 21.8 - - + +
177A LEU* 1.3 80.1 - - - +
179A ARG* 1.3 62.4 + - - +
181A ASN* 3.4 7.6 + - - +
182A GLU* 3.1 32.1 + - + +
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A THR 3.3 13.4 + - - +
176A LEU* 3.5 12.1 - - - +
178A ALA* 1.3 77.6 - - - +
180A PHE* 1.3 58.2 + - - +
182A GLU* 3.1 17.7 + - - +
183A GLN* 2.9 54.6 + - - +
213B ASP* 2.7 30.8 + - - -
215B GLU* 4.5 8.7 + - - -
216B PHE* 4.0 9.6 - - + -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.0 22.9 - - + -
110A MET* 3.9 26.5 - - + -
111A ARG* 3.9 19.7 - - + -
114A ILE* 3.7 20.6 - - + -
176A LEU 2.9 17.6 + - - +
177A LEU* 3.5 11.9 - - + +
179A ARG* 1.3 75.8 - - - +
181A ASN* 1.3 68.4 + - - +
183A GLN 3.2 0.9 + - - -
184A ILE* 2.9 63.0 + - + +
188A TYR* 3.6 21.8 - - - -
216B PHE* 3.4 28.5 - + + -
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Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 5.3 4.3 - - - +
177A LEU* 2.9 40.7 + - - +
178A ALA* 3.8 6.7 - - - +
180A PHE* 1.3 90.8 - - - +
182A GLU* 1.3 62.5 + - - +
184A ILE* 4.8 3.3 - - - +
185A GLU* 3.5 23.9 + - - +
188A TYR* 4.4 14.6 + - - -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ALA* 3.1 25.1 + - + +
179A ARG* 3.1 21.4 + - - +
181A ASN* 1.3 79.6 - - + +
183A GLN* 1.3 65.9 + - + +
184A ILE 3.4 0.2 + - - -
185A GLU* 3.7 11.3 + - - +
186A PRO* 4.0 4.3 - - - +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 2.9 41.7 + - - +
180A PHE 4.0 2.7 - - - +
182A GLU* 1.3 79.8 - - + +
184A ILE* 1.3 60.0 + - + +
185A GLU 3.5 0.2 - - - -
186A PRO* 3.6 2.6 - - - +
210B PHE* 3.3 29.0 - - - -
211B SER 4.9 4.4 - - - +
212B VAL* 3.3 16.4 - - + -
213B ASP* 2.8 52.3 + - - -
216B PHE* 3.2 18.1 - - + -
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.9 18.4 - - + -
107A LEU* 3.8 23.3 - - + -
110A MET* 5.6 0.2 - - + -
180A PHE* 2.9 45.5 + - + +
181A ASN 4.8 0.4 - - - +
183A GLN* 1.3 79.5 - - + +
185A GLU* 1.3 58.4 + - - +
186A PRO* 3.3 3.8 - - - -
187A ILE* 2.8 43.3 + - + +
188A TYR* 3.1 47.6 + - + +
210B PHE* 4.4 2.7 - - + -
212B VAL* 4.8 4.5 - - + -
216B PHE* 6.2 1.6 - - + -
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASN 3.5 18.4 + - - +
182A GLU* 4.0 5.4 - - - +
183A GLN 3.5 0.2 - - - -
184A ILE* 1.3 77.3 - - - +
186A PRO* 1.4 65.7 - - + +
188A TYR* 3.2 21.4 + - - +
189A ALA* 2.8 39.4 + - + +
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Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 4.3 15.9 - - + -
182A GLU 4.0 6.3 - - - +
183A GLN 3.6 9.2 - - - +
184A ILE 3.5 4.0 - - - -
185A GLU* 1.4 94.3 - - + +
187A ILE* 1.3 57.6 + - - +
189A ALA* 3.4 7.2 + - + +
190A LEU* 3.0 32.8 + - - +
210B PHE* 4.0 25.1 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.8 18.4 - - + -
20A TYR* 3.9 27.4 - - + -
21A VAL* 4.0 18.8 - - + -
25A PHE* 5.0 2.0 - - + -
103A VAL* 4.1 4.7 - - + -
107A LEU* 3.8 22.2 - - + -
184A ILE* 2.8 27.4 + - + +
186A PRO* 1.3 69.4 - - - +
188A TYR* 1.3 56.7 + - - +
190A LEU* 3.2 6.2 + - + +
191A LEU* 2.8 35.4 + - + +
210B PHE* 3.6 38.8 - - + -
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.0 26.8 + - + -
111A ARG* 4.5 15.9 + - - -
180A PHE* 3.6 22.0 - - - -
181A ASN* 4.4 16.2 + - - -
184A ILE* 3.1 34.2 + - + -
185A GLU* 3.5 27.4 - - - +
187A ILE* 1.3 75.3 - - - +
189A ALA* 1.3 58.0 + - - +
191A LEU* 3.2 13.9 + - + +
192A ARG* 2.9 29.6 + - - +
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLU* 2.8 30.4 + - + +
186A PRO* 3.6 7.6 - - + +
188A TYR* 1.3 73.2 - - - +
190A LEU* 1.3 58.3 + - + +
192A ARG* 3.3 7.0 + - - +
193A GLU* 3.0 41.2 + - + +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.5 5.8 - - - +
16A ARG* 3.9 37.9 - - + +
17A LEU* 4.0 29.6 - - + +
20A TYR* 3.7 39.9 - - + -
186A PRO 3.0 22.2 + - - +
187A ILE* 3.8 6.3 - - + +
189A ALA* 1.3 74.1 - - + +
191A LEU* 1.3 65.7 + - - +
193A GLU* 3.4 19.7 + - - +
194A THR* 3.2 28.3 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.7 30.7 - - + -
100A VAL* 4.1 19.7 - - + -
103A VAL* 4.3 9.2 - - + -
104A LYS* 4.0 28.7 - - + -
107A LEU* 4.2 23.8 - - + -
187A ILE 2.8 23.2 + - - +
188A TYR* 3.4 15.3 - - + +
190A LEU* 1.3 72.7 - - - +
192A ARG* 1.3 61.8 + - - +
194A THR* 2.5 22.1 + - - +
195A GLU* 3.5 11.5 + - - +
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A TYR 2.9 13.3 + - - +
189A ALA* 3.6 10.1 - - - +
191A LEU* 1.3 74.2 - - - +
193A GLU* 1.3 64.8 + - + +
195A GLU* 3.1 43.6 + - - +
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.2 22.2 - - + +
16A ARG* 4.2 11.1 + - - -
189A ALA* 3.0 28.7 + - + +
190A LEU* 3.6 22.5 - - - +
191A LEU 3.3 0.2 - - - -
192A ARG* 1.3 77.2 - - + +
194A THR* 1.3 58.2 + - - +
196A ASP* 3.4 16.5 - - - +
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 6.3 0.2 - - + -
13A ALA* 3.8 36.3 - - + +
14A LEU* 3.9 26.5 - - + +
17A LEU* 4.8 6.0 - - + +
100A VAL* 5.1 6.0 - - - +
190A LEU 3.2 14.2 + - - +
191A LEU* 2.5 28.6 + - - +
193A GLU* 1.3 75.7 - - - +
195A GLU* 1.3 51.5 + - - +
196A ASP* 2.7 29.1 + - - +
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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