Contacts of the helix formed by residues 158 - 168 (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 GLU 158 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86Y ASP* 3.3 5.8 - - - +
89Y PRO* 5.5 0.2 - - + -
90Y PRO* 3.2 32.6 - - + +
92Y LEU* 4.1 4.0 - - - +
155Y ALA* 4.2 1.1 - - - -
157Y SER* 1.3 77.9 - - - +
159Y ALA* 1.3 69.3 + - - +
160Y GLU* 3.4 5.6 - - + +
161Y ALA* 3.2 23.1 + - + +
162Y SER* 3.2 12.0 + - - -
181Y ASP* 5.4 0.2 - - - +
185Y PHE* 4.2 7.4 - - + -
234Y TYR* 2.5 47.9 + - - -
282Y LEU* 5.6 1.2 - - - +
287Y GLU* 4.1 8.8 + - - +
1003Y MG 3.2 23.4 - - - -
1004Y MG 4.2 5.5 - - - -
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Residues in contact with ALA 159 (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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34Y ASP* 3.7 13.5 - - - +
84Y VAL* 3.4 32.8 - - + +
85Y PHE 3.8 9.0 - - - +
86Y ASP* 2.4 26.6 + - - +
155Y ALA* 3.7 11.9 - - - -
157Y SER 3.5 2.2 + - - -
158Y GLU* 1.3 70.6 - - - +
160Y GLU* 1.3 52.4 + - - +
162Y SER* 2.3 29.5 + - - -
163Y CYS* 2.6 17.8 + - - -
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Residues in contact with GLU 160 (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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34Y ASP* 3.0 24.2 + - - +
37Y MET* 5.5 2.3 - - - +
86Y ASP* 5.7 0.2 - - - +
158Y GLU* 5.1 6.6 - - + +
159Y ALA* 1.3 77.1 - - - +
161Y ALA* 1.3 61.0 + - - +
163Y CYS* 3.5 8.9 - - - +
164Y ALA* 3.1 22.5 + - - +
177Y THR* 4.1 19.8 - - + +
179Y ASP* 3.6 16.4 - - - +
181Y ASP* 2.9 33.1 - - - +
182Y CYS* 3.6 17.5 + - - -
185Y PHE* 4.3 13.7 - - + -
1004Y MG 3.1 18.9 - - - -
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Residues in contact with ALA 161 (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* 3.2 15.5 + - + +
159Y ALA 2.7 1.8 + - - -
160Y GLU* 1.3 74.9 - - - +
162Y SER* 1.3 57.0 + - - +
164Y ALA* 3.4 4.7 + - - +
165Y ALA* 2.8 28.6 + - - +
185Y PHE* 3.6 31.3 - - + +
286Y PRO* 3.6 24.1 - - + +
287Y GLU* 4.4 1.1 - - - +
288Y VAL* 3.3 18.5 - - + +
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Residues in contact with SER 162 (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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84Y VAL* 4.6 6.5 - - - -
155Y ALA* 3.1 29.1 - - - +
156Y PRO* 3.8 2.4 - - - +
158Y GLU 3.2 5.0 + - - -
159Y ALA* 2.3 26.2 + - - -
161Y ALA* 1.3 68.1 - - - +
163Y CYS* 1.3 65.0 + - - -
165Y ALA* 2.8 22.1 + - - +
166Y LEU* 2.9 13.9 + - - +
287Y GLU 4.1 0.2 + - - -
288Y VAL* 3.1 25.3 - - - +
289Y LEU* 4.8 11.8 - - - +
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Residues in contact with CYS 163 (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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32Y ALA* 3.7 27.8 - - + -
33Y ILE 3.5 30.5 - - - -
34Y ASP* 4.5 3.1 - - - -
84Y VAL* 4.0 11.9 - - - +
159Y ALA 2.6 19.9 + - - -
160Y GLU* 3.5 12.8 - - - +
162Y SER* 1.3 71.5 - - - +
164Y ALA* 1.3 65.0 + - - +
166Y LEU* 2.8 18.7 + - - +
167Y VAL* 3.0 17.6 + - - +
175Y ALA* 3.9 13.9 - - + -
177Y THR* 5.3 2.9 - - - -
182Y CYS* 4.6 1.1 - - - -
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Residues in contact with ALA 164 (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 3.1 10.5 + - - +
161Y ALA 3.4 8.7 - - - +
163Y CYS* 1.3 78.0 - - - +
165Y ALA* 1.3 64.9 + - - +
166Y LEU 2.9 1.0 + - - -
167Y VAL* 3.1 2.1 + - - +
168Y LYS* 3.0 25.8 + - - +
175Y ALA* 4.6 1.2 - - - +
182Y CYS* 4.0 1.6 - - - +
185Y PHE* 3.8 24.7 - - + +
187Y SER* 3.5 38.9 - - - +
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Residues in contact with ALA 165 (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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161Y ALA 2.8 15.3 + - - +
162Y SER* 2.8 24.0 + - - +
164Y ALA* 1.3 72.0 - - - +
166Y LEU* 1.3 62.0 + - + +
168Y LYS* 3.7 8.9 + - - +
169Y ALA* 3.6 4.5 - - - +
288Y VAL* 3.7 23.3 - - + -
289Y LEU 4.6 9.0 - - - +
291Y PRO* 3.5 21.8 - - + +
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Residues in contact with LEU 166 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32Y ALA* 4.3 18.6 - - + -
82Y VAL* 5.3 7.2 - - + -
84Y VAL* 5.2 8.1 - - + -
153Y LEU* 4.6 18.4 - - + -
162Y SER* 2.9 16.7 + - - +
163Y CYS* 2.8 14.3 + - - +
165Y ALA* 1.3 65.9 - - - +
167Y VAL* 1.3 55.8 + - - +
168Y LYS 3.0 1.3 - - - -
169Y ALA* 2.5 40.2 + - - +
170Y GLY 3.6 2.8 + - - -
171Y LYS* 3.9 16.1 + - + -
172Y VAL* 3.9 17.3 - - + -
289Y LEU* 4.5 16.6 - - + +
291Y PRO* 3.9 28.3 - - + +
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Residues in contact with VAL 167 (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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32Y ALA* 4.7 0.7 - - + -
163Y CYS 3.0 11.2 + - - +
164Y ALA 3.6 5.4 - - - +
166Y LEU* 1.3 77.8 - - - +
168Y LYS* 1.3 55.3 + - - +
169Y ALA 3.1 5.0 + - - -
170Y GLY* 3.5 8.9 + - - -
172Y VAL* 3.3 33.0 - - + +
173Y TYR 3.4 19.2 - - - +
174Y ALA 3.5 19.5 - - - -
175Y ALA* 3.6 11.9 - - + +
187Y SER* 3.7 10.3 - - - +
188Y PRO* 3.2 33.1 - - + +
189Y VAL 4.0 4.9 - - - +
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Residues in contact with LYS 168 (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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164Y ALA 3.0 14.8 + - - +
165Y ALA* 3.8 5.8 - - - +
166Y LEU 2.7 3.0 + - - -
167Y VAL* 1.3 72.2 - - - +
169Y ALA* 1.3 59.3 + - - +
170Y GLY 3.8 0.4 - - - -
186Y GLY 4.5 9.4 - - - +
188Y PRO* 4.1 16.8 - - + -
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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