Contacts of the helix formed by residues 177 - 187 (chain A) in PDB entry 1U8R
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 ASP 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A HIS 3.8 4.5 + - - +
174A VAL 3.2 11.6 + - - +
175A GLN 4.2 0.2 - - - -
176A GLY* 1.3 68.2 - - - +
178A ILE* 1.3 59.8 + - - +
179A ASP* 3.3 25.5 + - - +
180A LEU* 3.1 31.1 + - + +
181A ILE* 2.9 23.7 + - - +
221A MET* 5.1 8.9 - - - +
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Residues in contact with ILE 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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95A GLU* 4.1 22.9 - - + +
96A GLU* 5.6 5.6 - - + -
99A ALA* 5.9 7.9 - - + -
175A GLN 4.5 2.0 - - - +
176A GLY 2.7 12.3 + - - +
177A ASP* 1.3 72.3 + - - +
179A ASP* 1.3 78.2 + - - +
181A ILE* 3.2 8.0 - - + +
182A THR* 2.9 37.5 + - - +
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Residues in contact with ASP 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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177A ASP* 3.2 13.4 - - - +
178A ILE* 1.3 88.7 - - - +
180A LEU* 1.3 61.3 + - - +
182A THR* 3.6 5.2 - - - -
183A ARG* 3.3 36.3 + - - +
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Residues in contact with LEU 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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174A VAL* 3.7 8.1 - - + -
177A ASP* 3.1 26.1 + - + +
179A ASP* 1.3 76.0 - - - +
181A ILE* 1.3 63.4 + - - +
182A THR 2.9 5.5 + - - -
183A ARG* 3.1 29.7 + - + +
184A LEU* 2.9 44.5 + - + +
215A VAL* 4.5 4.0 - - + -
216A THR 5.6 0.2 - - - +
217A LEU* 3.6 30.3 - - + -
218A PRO* 5.8 0.7 - - + -
221A MET* 3.5 39.9 - - + -
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Residues in contact with ILE 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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94A TRP* 4.2 10.6 - - + -
95A GLU* 3.9 25.9 - - + +
98A HIS* 6.5 0.2 - - + -
128A PHE* 3.9 31.4 - - + -
170A LEU* 4.0 22.4 - - + -
174A VAL* 4.1 11.9 - - + +
175A GLN* 4.2 22.4 - - - +
177A ASP 2.9 10.6 + - - +
178A ILE* 3.2 23.8 - - + +
180A LEU* 1.3 76.4 - - - +
182A THR* 1.3 64.9 + - - +
184A LEU* 3.8 11.0 - - + +
185A LYS* 3.3 19.8 + - - +
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Residues in contact with THR 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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95A GLU* 3.7 27.4 - - + +
178A ILE* 2.9 25.5 + - - +
179A ASP* 3.6 7.2 - - - -
180A LEU 2.9 0.2 - - - -
181A ILE* 1.3 75.8 - - - +
183A ARG* 1.3 68.9 + - + +
185A LYS* 2.8 18.7 + - - +
186A ASP* 3.0 28.1 + - - +
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Residues in contact with ARG 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 ASP* 3.3 24.0 + - - +
180A LEU* 3.1 31.1 + - + +
182A THR* 1.3 78.7 - - + +
184A LEU* 1.3 57.8 + - - +
186A ASP* 3.2 11.2 + - - +
187A ALA* 2.9 32.2 + - - +
215A VAL* 4.5 17.6 - - + +
216A THR 4.9 7.9 + - - +
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Residues in contact with LEU 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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94A TRP* 5.5 0.9 - - + -
170A LEU* 4.3 15.7 - - + -
174A VAL* 3.8 29.2 - - + -
180A LEU* 2.9 36.1 + - + +
181A ILE* 3.8 16.6 - - + +
183A ARG* 1.3 77.0 - - - +
185A LYS* 1.3 61.0 + - - +
187A ALA* 3.5 1.0 + - - +
188A GLY 3.2 2.3 + - - -
189A VAL* 2.9 65.3 + - + +
207A ILE* 4.6 6.3 - - + -
215A VAL* 4.1 19.3 - - + -
217A LEU* 4.6 7.2 - - + -
225A VAL* 5.9 0.9 - - + -
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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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93A PRO* 5.3 2.6 - - - +
94A TRP* 4.0 29.7 - - + +
95A GLU* 3.0 40.9 + - + +
181A ILE 3.3 10.9 + - - +
182A THR* 2.8 11.6 + - - +
184A LEU* 1.3 77.2 - - - +
186A ASP* 1.3 75.8 + - - +
188A GLY* 2.8 20.6 + - - -
190A VAL* 4.4 12.3 - - + +
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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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182A THR* 3.0 26.1 + - - +
183A ARG* 3.5 10.0 - - - +
185A LYS* 1.3 92.1 - - - +
187A ALA* 1.3 56.9 + - - +
188A GLY* 3.2 2.8 + - - -
212A HIS* 3.1 22.3 + - - -
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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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183A ARG 2.9 16.8 + - - +
184A LEU* 4.7 0.2 - - - -
186A ASP* 1.3 75.3 - - - +
188A GLY* 1.3 55.3 + - - +
189A VAL* 3.0 23.3 + - + -
209A ILE* 3.0 36.1 - - + +
212A HIS* 3.8 25.8 - - + -
213A GLU* 4.5 5.4 - - + +
215A VAL* 5.2 6.3 - - + -
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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