Contacts of the helix formed by residues 177 - 191 (chain A) in PDB entry 5F0X
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 ASN 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLY 5.3 1.8 + - - -
101A ARG* 5.7 4.2 - - - +
105A ASP* 5.9 0.6 + - - -
175A TYR 3.3 3.7 + - - +
176A PHE* 1.3 74.0 - - - +
178A ASP* 1.3 67.2 + - - +
179A ALA* 3.1 12.3 + - - +
180A GLN* 2.9 44.2 + - - +
181A ARG* 3.0 26.9 + - - +
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Residues in contact with ASP 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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177A ASN* 1.3 75.9 - - - +
179A ALA* 1.3 58.1 + - - +
181A ARG* 3.4 13.0 + - - +
182A GLN* 2.9 30.4 + - - +
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Residues in contact with ALA 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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100A GLY* 3.6 18.8 - - - +
177A ASN* 3.1 10.8 + - - +
178A ASP* 1.3 79.7 - - - +
180A GLN* 1.3 58.9 + - - +
182A GLN* 3.5 5.2 + - - +
183A ALA* 2.9 30.0 + - - +
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Residues in contact with GLN 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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96A LYS 5.2 1.0 + - - -
99A ILE* 3.5 19.0 + - - +
100A GLY* 4.1 14.1 - - - +
101A ARG* 3.2 40.6 + - + +
175A TYR* 4.2 3.5 - - - +
176A PHE* 3.3 47.7 - - + -
177A ASN* 2.9 48.3 + - - +
179A ALA* 1.3 75.2 - - - +
181A ARG* 1.3 62.9 + - - +
183A ALA* 3.5 2.1 + - - +
184A THR* 2.9 29.0 + - - -
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Residues in contact with ARG 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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172A VAL* 3.5 16.2 - - + +
173A PRO 3.5 6.3 + - - -
174A ALA 3.1 16.6 + - - -
176A PHE* 2.9 33.2 + - + -
177A ASN 3.0 19.3 + - - +
178A ASP* 3.7 11.9 + - - +
180A GLN* 1.3 74.0 - - - +
182A GLN* 1.3 64.5 + - - +
184A THR* 3.2 8.5 + - - -
185A LYS* 3.1 25.9 + - - +
198A ILE* 3.9 33.8 + - + +
199A ILE* 5.2 0.2 - - - +
200A ASN* 3.0 33.9 + - - +
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Residues in contact with GLN 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 ASP 2.9 17.5 + - - +
179A ALA* 3.9 6.1 - - - +
181A ARG* 1.3 76.4 - - - +
183A ALA* 1.3 57.7 + - - +
185A LYS* 3.2 24.3 + - - +
186A ASP* 2.8 64.1 + - - +
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Residues in contact with ALA 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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99A ILE* 3.7 12.0 - - + +
100A GLY* 3.6 28.3 - - - +
143A GLU* 3.8 14.5 - - - +
179A ALA 2.9 18.6 + - - +
180A GLN 3.8 2.5 - - - +
181A ARG 3.3 0.2 - - - -
182A GLN* 1.3 77.1 - - - +
184A THR* 1.3 57.8 + - - +
186A ASP* 3.4 11.9 + - - +
187A ALA* 2.9 26.3 + - - +
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Residues in contact with THR 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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35A LEU* 4.1 16.6 - - + +
99A ILE* 4.2 14.5 - - - +
150A LEU* 4.5 3.2 - - + +
170A VAL* 3.8 22.4 - - + -
171A THR 5.0 0.2 - - - +
172A VAL* 4.0 16.0 - - + +
176A PHE* 4.1 8.7 - - - -
180A GLN 2.9 14.9 + - - -
181A ARG 3.5 9.0 - - - -
182A GLN 3.2 0.2 - - - -
183A ALA* 1.3 75.1 - - - +
185A LYS* 1.3 64.8 + - - +
187A ALA* 3.3 5.3 + - - +
188A GLY* 3.1 17.2 + - - -
195A VAL* 4.5 2.3 - - - +
198A ILE* 3.7 19.7 - - + -
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Residues in contact with LYS 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 ARG 3.1 16.2 + - - +
182A GLN* 3.5 29.6 - - - +
184A THR* 1.3 75.4 - - - +
186A ASP* 1.3 58.1 + - - +
188A GLY* 3.1 4.5 + - - -
189A THR* 3.0 28.3 + - - -
193A LEU 4.7 0.5 - - - +
195A VAL* 3.5 40.0 + - + +
196A MET 4.4 8.5 + - - -
197A ARG* 4.9 0.8 - - - +
198A ILE* 3.7 31.9 - - + +
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Residues in contact with ASP 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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143A GLU* 4.7 11.3 - - + +
182A GLN* 2.8 46.0 + - - +
183A ALA* 3.5 12.8 - - - +
184A THR 3.2 0.2 - - - -
185A LYS* 1.3 72.6 - - - +
187A ALA* 1.3 65.4 + - - +
189A THR* 3.2 11.8 + - - -
190A ILE* 3.1 30.0 + - + +
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Residues in contact with ALA 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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35A LEU* 5.3 0.7 - - + -
99A ILE* 4.5 0.7 - - + -
143A GLU* 3.4 30.6 - - + +
146A SER* 3.9 19.5 - - - -
147A ALA* 3.2 14.6 - - - +
150A LEU* 3.8 11.7 - - + -
183A ALA 2.9 13.2 + - - +
184A THR* 3.4 12.3 - - - +
186A ASP* 1.3 74.7 - - - +
188A GLY* 1.3 63.1 + - - +
190A ILE* 3.3 2.3 + - - -
191A ALA* 3.2 16.5 + - - +
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Residues in contact with GLY 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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150A LEU* 3.6 15.3 - - - +
184A THR 3.1 7.3 + - - -
185A LYS 3.1 9.5 + - - -
187A ALA* 1.3 76.8 - - - +
189A THR* 1.3 62.2 + - - +
191A ALA* 2.9 11.3 + - - +
192A GLY 3.1 0.2 + - - -
193A LEU* 2.9 35.6 + - - -
195A VAL* 3.9 11.2 - - - -
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Residues in contact with THR 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 LYS 3.0 14.0 + - - -
186A ASP* 3.2 14.6 + - - -
188A GLY* 1.3 73.3 - - - +
190A ILE* 1.3 65.1 + - + +
192A GLY* 3.0 13.7 + - - -
193A LEU 3.3 10.0 + - - +
194A ASN* 5.8 0.5 - - - -
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Residues in contact with ILE 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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143A GLU* 4.0 33.9 - - + +
144A GLU* 4.2 20.2 - - + +
147A ALA* 3.5 19.7 - - + -
186A ASP* 3.1 17.6 + - + +
187A ALA 3.6 0.4 - - - +
188A GLY 3.2 0.2 - - - -
189A THR* 1.3 79.2 - - + +
191A ALA* 1.3 56.2 + - - +
192A GLY 3.2 3.5 + - - -
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Residues in contact with ALA 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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147A ALA* 3.4 24.5 - - - +
150A LEU* 3.9 16.6 - - + -
151A THR* 3.4 18.5 + - - +
154A LYS* 3.8 21.0 - - - +
187A ALA 3.2 10.2 + - - +
188A GLY* 2.9 10.1 + - - +
190A ILE* 1.3 75.7 - - - +
192A GLY* 1.3 60.9 + - - +
193A LEU* 3.4 4.6 + - + +
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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