Contacts of the helix formed by residues 174 - 185 (chain A) in PDB entry 1UN0
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 ALA 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A VAL* 3.9 23.3 - - + -
139A MET* 3.9 5.9 - - + +
155A LEU* 4.6 0.9 - - + -
169A VAL* 3.3 39.0 + - + +
170A VAL 4.2 0.8 + - - -
172A ALA 3.4 1.2 - - - -
173A ASP* 1.3 75.3 - - - +
175A VAL* 1.3 59.4 + - - +
176A PRO 3.5 0.4 - - - -
177A LEU* 3.3 6.5 + - - +
178A PHE* 3.0 40.3 + - + -
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Residues in contact with VAL 175 (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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169A VAL* 6.2 0.9 - - + -
170A VAL* 4.5 11.2 + - + -
173A ASP* 3.5 0.4 - - - +
174A ALA* 1.3 78.5 - - + +
176A PRO* 1.3 67.0 - - + +
178A PHE* 3.0 10.8 + - + +
179A ILE* 2.8 48.1 + - + +
197A LEU* 3.8 18.6 - - + -
200A VAL* 4.1 26.7 - - + -
210A TYR* 3.7 30.3 - - + -
211A VAL* 4.5 7.2 - - + -
214A CYS* 4.1 6.5 - - + -
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Residues in contact with PRO 176 (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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173A ASP* 3.4 31.2 - - - +
174A ALA 3.7 2.0 - - - -
175A VAL* 1.3 97.7 - - + +
177A LEU* 1.3 62.7 + - + +
179A ILE* 3.6 13.2 - - + +
180A GLN* 3.1 30.0 + - - +
210A TYR* 3.7 13.2 - - - +
214A CYS* 4.6 11.9 - - + +
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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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136A VAL* 3.5 41.1 - - + +
139A MET* 4.0 18.1 - - + +
140A ARG* 3.8 29.2 - - + +
173A ASP* 4.2 12.3 - - - +
174A ALA 3.3 5.1 + - - +
175A VAL 3.1 0.8 - - - -
176A PRO* 1.3 81.0 - - + +
178A PHE* 1.3 66.2 + - - +
179A ILE 3.2 1.1 - - - -
180A GLN* 3.6 29.8 - - + +
181A LEU* 3.1 31.3 + - - +
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Residues in contact with PHE 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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139A MET* 3.7 23.8 - - + -
152A ALA* 3.9 17.5 - - + -
155A LEU* 3.9 23.3 - - + -
156A THR* 4.1 2.9 - - - -
159A ALA* 5.6 0.2 - - + -
169A VAL* 4.0 12.6 - - + -
174A ALA* 3.0 40.6 + - + -
175A VAL* 3.0 13.0 + - + +
177A LEU* 1.3 75.8 - - - +
179A ILE* 1.3 64.1 + - - +
181A LEU* 3.3 10.6 + - + +
182A LEU* 3.5 6.2 + - - +
193A ALA* 3.4 36.8 - - + +
196A ALA* 3.8 28.0 - - + -
197A LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 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 VAL* 2.8 29.2 + - + +
176A PRO* 3.6 8.1 - - + +
177A LEU 3.2 0.2 - - - -
178A PHE* 1.3 78.0 - - - +
180A GLN* 1.3 61.1 + - + +
182A LEU* 3.0 31.9 + - + +
183A TYR* 4.0 9.6 - - + -
197A LEU* 3.9 12.1 - - + -
211A VAL 4.1 0.9 - - - +
214A CYS* 3.4 40.2 - - + +
215A ASN 3.9 17.0 - - - +
216A ALA* 3.6 25.1 - - + -
219A PRO* 4.0 12.7 - - + +
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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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139A MET 4.8 2.0 + - - -
140A ARG* 4.7 3.6 - - - +
141A GLU* 3.4 46.3 + - - +
176A PRO* 3.1 19.9 + - - +
177A LEU* 3.6 32.6 - - - +
179A ILE* 1.3 78.7 - - + +
181A LEU* 1.3 63.8 + - + +
182A LEU 3.2 1.0 + - - -
183A TYR* 3.3 24.0 + - + +
184A THR* 3.3 23.0 + - + +
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Residues in contact with LEU 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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139A MET* 4.1 35.0 - - + +
148A GLN* 3.8 36.8 - - + +
152A ALA* 4.2 9.4 - - + -
177A LEU 3.1 26.4 + - - +
178A PHE* 3.5 11.9 - - + +
179A ILE 3.2 0.4 - - - -
180A GLN* 1.3 79.1 - - + +
182A LEU* 1.3 56.5 + - - +
183A TYR 3.2 0.2 - - - -
184A THR* 4.0 13.2 - - - +
185A GLY* 3.0 26.5 + - - +
189A VAL* 3.9 30.7 - - + +
190A LYS* 4.0 6.2 - - - +
193A ALA* 4.6 6.1 - - + -
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Residues in contact with LEU 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 PHE 3.7 7.0 - - - +
179A ILE* 3.0 19.5 + - + +
181A LEU* 1.3 77.9 - - - +
183A TYR* 1.3 57.4 + - - +
190A LYS* 3.0 49.9 - - - +
193A ALA* 4.1 5.4 - - + -
194A ILE* 3.9 16.6 - - + +
197A LEU* 3.8 20.2 - - + -
216A ALA 4.7 0.2 - - - +
219A PRO* 3.9 25.4 - - + +
220A ILE* 3.9 25.1 - - + +
223A LEU* 3.8 28.9 - - + +
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Residues in contact with TYR 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 ILE* 4.0 8.3 - - + -
180A GLN* 3.5 25.1 - - + +
182A LEU* 1.3 79.4 - - - +
184A THR* 1.3 72.0 + - + +
190A LYS* 3.7 11.3 + - - -
215A ASN 5.1 2.1 + - - -
218A GLU* 3.2 27.6 + - - +
219A PRO* 3.7 39.3 - - + +
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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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141A GLU* 5.3 14.5 - - + +
145A GLU* 4.9 0.5 - - - +
148A GLN* 4.8 6.4 + - - -
180A GLN* 3.3 20.2 + - + +
181A LEU* 4.0 15.2 - - - +
183A TYR* 1.3 85.0 - - + +
185A GLY* 1.3 81.7 + - - +
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Residues in contact with GLY 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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145A GLU* 3.8 10.8 - - - -
148A GLN* 5.5 0.2 - - - -
181A LEU* 3.0 19.4 + - - -
184A THR* 1.3 93.6 + - - +
186A SER* 1.3 69.4 + - - +
189A VAL* 4.2 13.7 - - - -
190A LYS* 3.3 17.5 + - - -
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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