Contacts of the helix formed by residues 182 - 190 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ARG* 4.2 2.2 - - - -
167F GLU* 2.9 21.3 + - - -
169F TYR* 4.5 0.4 + - - -
181F LYS* 1.3 71.0 - - - +
183F SER* 1.3 61.7 + - - +
184F MET 3.4 0.4 - - - -
185F GLU* 3.5 13.0 + - - +
186F GLU* 3.3 22.9 + - - +
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG* 3.9 10.3 - - - +
165F GLY 4.8 0.9 + - - -
167F GLU* 3.0 6.4 + - - +
179F HIS 4.6 0.7 - - - -
180F PHE* 2.7 47.5 + - - +
181F LYS 3.2 1.4 - - - -
182F GLY* 1.3 75.8 - - - +
184F MET* 1.3 67.6 + - - +
186F GLU* 3.2 8.2 + - - +
187F TRP* 3.0 47.3 + - - -
195F TYR* 4.3 5.0 + - - -
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Residues in contact with MET 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ILE* 3.9 21.7 - - + +
166F GLN 4.2 0.9 - - - +
167F GLU* 2.9 21.2 + - + +
183F SER* 1.3 77.7 + - - +
185F GLU* 1.3 57.6 + - - +
187F TRP* 3.3 4.3 + - - +
188F GLN* 2.9 52.8 + - - +
195F TYR* 3.5 25.8 - - + +
223F ARG* 3.7 50.3 - - + +
224F THR* 5.6 1.6 - - + -
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Residues in contact with GLU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLU* 4.4 0.4 + - - -
182F GLY* 3.5 14.2 + - - +
183F SER 3.3 0.2 - - - -
184F MET* 1.3 76.7 - - - +
186F GLU* 1.3 63.4 + - + +
188F GLN* 3.4 17.6 + - + +
189F ALA* 3.0 24.8 + - - +
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Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 5.6 4.4 + - - -
176A VAL 4.6 6.6 - - - +
177A VAL* 3.9 3.2 - - - +
178A ARG* 3.2 46.4 + - + +
125B PRO* 5.4 0.5 - - - +
182F GLY 3.3 12.7 + - - +
183F SER* 3.2 13.7 + - - +
185F GLU* 1.3 78.6 - - + +
187F TRP* 1.3 70.4 + - + +
189F ALA* 3.3 9.1 + - - +
190F MET* 3.0 51.1 + - + +
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Residues in contact with TRP 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO* 3.7 32.5 - - + -
127B GLU* 3.8 7.9 - - - -
128B PHE* 4.5 4.7 - + - -
98F ILE* 3.9 7.4 - - + -
114F VAL* 3.8 24.0 - - + -
116F LEU* 3.6 36.6 - - + +
157F ALA* 4.5 4.3 - - + -
165F GLY 5.2 0.2 + - - -
180F PHE* 5.3 2.7 - + - -
183F SER* 3.0 32.7 + - - -
184F MET* 3.7 3.6 - - - +
186F GLU* 1.3 78.0 - - + +
188F GLN* 1.3 63.2 + - - +
190F MET* 3.1 27.6 + - + -
191F GLY 3.2 0.2 + - - -
192F VAL* 3.0 50.5 + - + +
195F TYR* 3.3 32.2 + + - -
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Residues in contact with GLN 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ILE* 2.8 40.5 + - + +
99F GLN* 2.9 29.2 + - - +
100F PRO* 5.2 4.2 - - - +
184F MET* 2.9 33.9 + - - +
185F GLU* 3.4 29.5 + - + +
187F TRP* 1.3 76.1 - - - +
189F ALA* 1.3 61.9 + - - +
191F GLY* 3.2 4.3 + - - -
224F THR* 3.5 18.6 - - - +
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Residues in contact with ALA 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 4.2 25.1 + - + -
208B SER 3.7 8.0 - - - +
209B GLN* 5.2 2.1 - - - -
185F GLU 3.0 16.7 + - - +
186F GLU* 3.7 8.7 - - - +
188F GLN* 1.3 76.9 - - - +
190F MET* 1.3 59.8 + - - +
191F GLY 3.2 1.1 + - - -
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Residues in contact with MET 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 3.9 15.0 - - - +
177A VAL* 3.9 3.8 - - + -
123B PHE 3.7 16.4 - - - +
124B ALA* 4.0 16.8 - - - -
125B PRO* 3.9 16.8 - - + -
128B PHE* 4.1 20.2 - - + -
207B ALA 3.2 23.0 - - - +
208B SER* 3.4 23.7 - - - +
210B GLY 5.5 1.1 + - - -
186F GLU* 3.0 48.0 + - + +
187F TRP* 3.1 27.5 + - + +
189F ALA* 1.3 77.0 - - - +
191F GLY* 1.3 60.6 + - - +
192F VAL 3.4 1.6 + - - -
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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