Contacts of the helix formed by residues 182 - 190 (chain A) in PDB entry 1U1C
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.0 21.9 + - - -
169A TYR* 4.4 0.2 + - - -
181A LYS* 1.3 73.9 - - - +
183A SER* 1.3 62.1 + - - +
184A MET 3.5 0.4 - - - -
185A GLU* 3.8 11.7 + - - +
186A GLU* 3.5 22.2 + - - +
178D ARG* 3.9 3.0 + - - -
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Residues in contact with SER 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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165A GLY 4.6 1.9 + - - -
167A GLU* 3.1 6.2 + - - +
179A HIS 4.5 1.1 - - - -
180A PHE* 2.7 46.8 + - - +
181A LYS 3.3 1.0 - - - -
182A GLY* 1.3 77.0 - - - +
184A MET* 1.3 67.8 + - - +
186A GLU* 3.1 7.6 + - - +
187A TRP* 3.0 47.5 + - - -
195A TYR* 4.3 4.0 + - - -
178D ARG* 3.9 9.6 - - - +
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Residues in contact with MET 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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98A ILE* 4.1 14.1 - - + -
166A GLN 4.2 1.1 - - - +
167A GLU* 3.0 19.7 + - + +
183A SER* 1.3 78.0 + - - +
185A GLU* 1.3 58.7 + - - +
187A TRP* 3.2 5.0 + - - +
188A GLN* 2.8 55.2 + - + +
195A TYR* 3.4 30.1 - - + +
223A ARG* 3.8 55.2 - - + +
224A THR* 5.5 0.7 - - + -
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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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167A GLU* 4.3 0.8 + - - +
182A GLY* 3.8 14.5 + - - +
184A MET* 1.3 77.9 - - - +
186A GLU* 1.3 57.4 + - - +
188A GLN* 3.4 18.9 + - + +
189A ALA* 3.1 28.4 + - - +
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Residues in contact with GLU 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 GLY 3.5 12.0 + - - +
183A SER* 3.1 13.1 + - - +
185A GLU* 1.3 75.5 - - + +
187A TRP* 1.3 71.9 + - + +
189A ALA* 3.4 7.4 + - - +
190A MET* 3.1 52.3 + - + +
125C PRO* 5.3 1.0 - - - +
175D ARG* 4.8 10.2 - - - -
176D VAL 4.5 6.9 - - - +
177D VAL* 3.7 4.3 - - - +
178D ARG* 3.3 45.6 + - + +
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Residues in contact with TRP 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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98A ILE* 4.0 7.6 - - + -
114A VAL* 3.8 23.8 - - + -
116A LEU* 3.6 35.6 - - + +
157A ALA* 4.5 4.3 - - + -
165A GLY 5.2 0.6 + - - -
180A PHE* 5.5 2.4 - + - -
183A SER* 3.0 37.8 + - - -
184A MET 3.6 4.3 - - - +
186A GLU* 1.3 78.2 - - + +
188A GLN* 1.3 61.6 + - - +
190A MET* 3.2 28.3 + - + -
191A GLY 3.2 0.2 + - - -
192A VAL* 3.0 51.4 + - + +
195A TYR* 3.3 30.7 + + - -
125C PRO* 3.7 31.9 - - + -
127C GLU* 4.1 6.7 - - - -
128C PHE* 4.6 3.6 - + - -
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Residues in contact with GLN 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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98A ILE* 2.8 40.9 + - + +
99A GLN* 2.9 30.7 + - - +
100A PRO* 5.3 2.6 - - + +
184A MET* 2.8 33.9 + - - +
185A GLU* 3.4 30.5 + - + +
186A GLU 3.3 0.2 - - - -
187A TRP* 1.3 75.9 - - - +
189A ALA* 1.3 61.9 + - - +
191A GLY* 3.1 4.7 + - - -
224A THR* 3.5 19.8 - - - +
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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 3.1 16.8 + - - +
186A GLU* 3.8 8.5 - - - +
187A TRP 3.4 0.2 - - - -
188A GLN* 1.3 77.5 - - - +
190A MET* 1.3 59.7 + - - +
191A GLY* 3.2 1.6 + - - -
208C SER 3.7 7.1 - - - +
209C GLN* 5.1 3.3 - - - -
175D ARG* 4.4 24.1 + - + -
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Residues in contact with MET 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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186A GLU* 3.1 46.8 + - + +
187A TRP* 3.6 31.0 - - + +
188A GLN 3.2 0.6 - - - -
189A ALA* 1.3 76.2 - - - +
191A GLY* 1.3 59.8 + - - +
192A VAL* 3.3 1.2 + - + -
123C PHE 3.7 17.3 - - - +
124C ALA* 4.1 13.2 - - - -
125C PRO* 3.8 16.6 - - + -
128C PHE* 4.0 18.4 - - + -
207C ALA 3.1 23.7 - - - +
208C SER* 3.3 14.9 - - - +
210C GLY 5.3 1.0 + - - -
175D ARG* 3.8 23.8 - - - +
177D VAL* 3.9 3.8 - - + -
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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