Contacts of the helix formed by residues 182 - 190 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B ARG* 4.3 1.3 - - - -
167C GLU* 3.0 21.9 + - - -
169C TYR* 4.4 0.4 + - - -
181C LYS* 1.3 72.7 - - - +
183C SER* 1.3 62.3 + - - +
184C MET 3.5 0.4 - - - -
185C GLU* 3.7 13.3 + - - +
186C GLU* 3.4 23.0 + - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ARG* 4.2 8.1 - - - +
165C GLY 4.7 1.9 + - - -
167C GLU* 3.0 8.3 + - - +
179C HIS 4.6 0.7 - - - -
180C PHE* 2.7 46.8 + - - +
181C LYS 3.2 1.0 - - - -
182C GLY* 1.3 76.2 - - - +
184C MET* 1.3 66.1 + - - +
186C GLU* 3.1 8.9 + - - +
187C TRP* 3.0 46.0 + - - -
195C TYR* 4.3 4.7 + - - -
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Residues in contact with MET 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ILE* 4.0 19.5 - - + +
166C GLN 4.1 1.3 - - - +
167C GLU* 3.0 21.3 + - + +
183C SER* 1.3 79.5 + - - +
185C GLU* 1.3 58.8 + - - +
187C TRP* 3.4 3.5 + - - +
188C GLN* 2.9 52.1 + - - +
195C TYR* 3.4 27.8 - - + +
223C ARG* 3.7 55.0 - - + +
224C THR* 5.6 0.9 - - + -
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Residues in contact with GLU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLU* 4.4 1.0 + - - +
182C GLY* 3.7 15.7 + - - +
183C SER 3.3 0.4 - - - -
184C MET* 1.3 76.0 - - - +
186C GLU* 1.3 64.3 + - - +
188C GLN* 3.4 16.6 + - + +
189C ALA* 3.1 24.7 + - + +
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Residues in contact with GLU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PRO* 4.8 4.3 - - - +
175B ARG* 4.5 7.3 + - - -
176B VAL 4.6 2.3 - - - +
177B VAL* 4.0 7.6 - - - +
178B ARG* 3.5 45.1 + - + +
182C GLY 3.4 14.7 + - - +
183C SER* 3.1 14.6 + - - +
185C GLU* 1.3 77.7 - - - +
187C TRP* 1.3 74.2 + - + +
189C ALA* 3.4 5.8 + - - +
190C MET* 3.1 53.8 + - + +
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Residues in contact with TRP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PRO* 3.8 27.8 - - + -
127A GLU* 4.0 7.6 - - - -
128A PHE* 4.4 4.5 - + - -
98C ILE* 4.0 7.4 - - + -
114C VAL* 3.8 21.5 - - + -
116C LEU* 3.6 35.2 - - + +
157C ALA* 4.5 4.7 - - + -
165C GLY 5.2 0.4 + - - -
180C PHE* 5.4 2.2 - + - -
183C SER* 3.0 33.8 + - - +
184C MET 3.8 2.7 - - - +
186C GLU* 1.3 79.6 - - + +
188C GLN* 1.3 61.5 + - - +
190C MET* 3.1 32.0 + - + -
191C GLY 3.2 0.2 + - - -
192C VAL* 3.0 54.2 + - + +
195C TYR* 3.2 31.3 + + - -
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Residues in contact with GLN 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ILE* 2.8 41.9 + - + +
99C GLN* 3.1 28.8 + - - +
100C PRO* 5.2 3.8 - - + +
184C MET* 2.9 34.3 + - - +
185C GLU* 3.4 27.8 + - + +
187C TRP* 1.3 77.2 - - - +
189C ALA* 1.3 60.7 + - - +
191C GLY* 3.2 4.9 + - - -
224C THR* 3.5 19.0 - - - +
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER 3.7 7.1 - - - +
209A GLN* 5.0 4.2 - - - -
175B ARG* 4.2 24.8 + - + -
185C GLU* 3.1 14.2 + - + +
186C GLU* 3.9 6.3 - - - +
188C GLN* 1.3 79.1 - - - +
190C MET* 1.3 59.3 + - - +
191C GLY 3.2 1.2 + - - -
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Residues in contact with MET 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE 3.6 19.1 - - - +
124A ALA* 4.1 13.7 - - - -
125A PRO* 3.9 8.1 - - + -
128A PHE* 4.0 19.6 - - + -
207A ALA 3.0 23.9 - - - +
208A SER* 3.3 15.7 - - - +
209A GLN* 5.7 0.2 - - - -
210A GLY 5.3 1.3 + - - -
175B ARG* 3.8 22.9 - - - +
177B VAL* 3.9 7.9 - - + -
186C GLU* 3.1 48.8 + - - +
187C TRP* 3.1 31.9 + - + +
189C ALA* 1.3 75.5 - - - +
191C GLY* 1.3 59.9 + - - +
192C VAL 3.3 1.0 + - - -
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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