Contacts of the helix formed by residues 180 - 185 (chain Y) in PDB entry 1UL1
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 MET 180 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3Y ILE* 4.6 16.8 + - + +
6Y LEU* 3.3 32.7 - - + +
7Y ALA* 4.1 12.3 - - + +
10Y ILE* 3.6 20.4 - - + -
178Y GLU 3.8 0.2 + - - -
179Y ASP* 1.3 69.3 - - - +
181Y ASP* 1.3 66.1 + - - +
182Y CYS 3.2 0.7 - - - -
183Y LEU* 2.7 36.8 + - + +
184Y THR* 3.6 2.8 + - - +
190Y LEU* 3.9 13.0 - - - -
192Y ARG* 4.0 24.2 - - - +
207Y PHE* 3.5 45.5 - - + -
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Residues in contact with ASP 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y GLY* 2.7 32.1 + - - -
3Y ILE* 2.7 24.7 - - - +
160Y GLU* 2.9 24.6 - - - +
179Y ASP* 2.8 2.3 + - - +
180Y MET* 1.3 74.9 - - - +
182Y CYS* 1.3 54.8 + - - +
184Y THR* 2.2 45.6 + - - +
185Y PHE* 3.0 22.0 + - + -
233Y ASP* 3.3 6.6 - - - +
234Y TYR* 4.8 4.9 + - - -
283Y PHE* 4.6 0.9 - - - -
1004Y MG 3.0 21.0 - - - -
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Residues in contact with CYS 182 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Y GLU* 3.6 30.5 - - - -
163Y CYS* 4.6 1.3 - - - -
164Y ALA 4.9 0.2 - - - -
175Y ALA* 3.8 22.7 - - + -
177Y THR* 3.6 26.0 - - - -
179Y ASP 3.7 0.8 + - - -
180Y MET 3.2 0.4 - - - -
181Y ASP* 1.3 77.5 - - - +
183Y LEU* 1.3 62.1 + - - +
185Y PHE* 3.2 16.7 + - - +
186Y GLY 3.4 0.2 + - - -
187Y SER* 3.0 35.5 + - - +
190Y LEU* 4.4 17.3 - - + -
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Residues in contact with LEU 183 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y LEU* 4.8 2.7 - - + -
10Y ILE* 4.5 0.9 - - + -
180Y MET* 2.7 42.9 + - + +
181Y ASP 2.7 3.8 + - - -
182Y CYS* 1.3 74.7 - - - +
184Y THR* 1.3 61.6 + - + +
186Y GLY 3.1 7.8 + - - -
187Y SER 3.6 17.5 - - - +
190Y LEU* 4.0 24.2 - - + +
207Y PHE* 4.0 16.6 - - + +
209Y LEU* 3.0 47.5 - - + +
212Y ILE* 3.6 24.7 - - + -
220Y GLN* 3.1 2.6 + - - -
223Y PHE* 4.1 9.6 - - + -
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Residues in contact with THR 184 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y ILE* 3.5 23.8 - - + -
6Y LEU* 5.0 1.3 - - + -
180Y MET 4.2 4.9 - - - +
181Y ASP* 2.2 40.7 + - - +
183Y LEU* 1.3 70.3 - - - +
185Y PHE* 1.3 60.5 + - - -
186Y GLY 2.8 6.6 + - - -
220Y GLN* 2.9 18.4 + - - +
223Y PHE* 4.2 5.4 - - + -
224Y VAL* 4.5 5.6 - - - +
227Y CYS* 3.0 36.1 - - + -
283Y PHE* 3.3 40.9 - - - +
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Residues in contact with PHE 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158Y GLU* 4.2 7.6 - - - -
160Y GLU* 4.3 5.8 - - + -
161Y ALA* 3.6 31.6 - - + +
164Y ALA* 3.8 18.5 - - + +
181Y ASP* 3.0 32.1 + - + -
182Y CYS* 3.6 11.2 - - - +
183Y LEU 3.2 0.4 - - - -
184Y THR* 1.3 79.2 + - - +
186Y GLY* 1.3 58.6 + - - +
187Y SER 3.5 0.6 + - - -
220Y GLN* 5.6 0.2 - - - -
234Y TYR* 3.1 31.2 - + - -
282Y LEU* 3.6 11.7 - - + -
283Y PHE* 3.4 28.8 - + - +
284Y LEU 4.8 5.2 - - - +
286Y PRO* 3.3 36.5 - - + +
287Y GLU* 5.6 0.4 - - - -
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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