Contacts of the helix formed by residues 183 - 191 (chain A) in PDB entry 1UES
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 ASP 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLN 2.9 18.9 + - - +
82A ARG* 3.3 23.3 + - + +
85A LYS* 3.3 35.6 + - - +
181A ILE 3.4 1.0 + - - -
182A VAL* 1.3 71.4 - - - +
184A TRP* 1.3 62.6 + - - +
185A ASP* 2.9 23.8 + - - +
186A ILE* 3.0 41.1 + - + +
187A VAL* 3.3 12.8 + - - +
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Residues in contact with TRP 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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85A LYS* 5.3 1.4 - - - +
86A GLY 3.2 26.7 + - - +
87A GLY 3.2 18.8 + - - -
88A ALA 3.9 3.6 - - - +
89A PRO* 3.5 32.8 - - + -
90A LYS* 5.8 1.1 - - + +
93A LEU* 3.9 13.9 - - + -
97A ILE* 4.2 5.8 - - + -
104A PHE* 3.5 29.8 - + - -
107A PHE* 4.3 7.9 - + - -
126A LEU* 4.9 2.2 - - + -
154A LEU* 3.8 20.9 - - + -
179A TRP* 3.8 16.3 + + - -
182A VAL* 3.5 24.5 + - + +
183A ASP* 1.3 73.4 + - - +
185A ASP* 1.3 56.9 + - - +
186A ILE 3.2 0.2 - - - -
187A VAL* 3.8 30.7 - - + +
188A GLU* 2.8 50.1 + - - +
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Residues in contact with ASP 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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85A LYS* 3.6 17.4 - - - +
90A LYS* 3.4 31.5 + - - -
183A ASP* 2.9 16.1 + - - +
184A TRP* 1.3 78.0 - - - +
186A ILE* 1.3 62.2 + - + +
188A GLU* 3.7 8.6 - - - +
189A SER* 3.2 21.5 + - - -
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Residues in contact with ILE 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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79A THR* 3.4 17.5 - - - +
80A GLN* 4.1 5.8 - - - +
82A ARG* 3.3 38.8 - - - +
183A ASP* 3.0 37.5 + - + +
185A ASP* 1.3 77.4 - - + +
187A VAL* 1.3 66.8 + - - +
189A SER* 2.7 28.0 + - - +
190A ARG* 3.3 26.5 - - - +
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Residues in contact with VAL 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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80A GLN* 4.5 11.4 - - + -
93A LEU* 3.6 20.2 - - + -
126A LEU* 5.0 1.1 - - + -
153A LEU* 3.5 34.1 - - + +
154A LEU* 4.1 13.9 - - + -
182A VAL* 4.0 20.6 - - + -
183A ASP 3.3 13.5 + - - +
184A TRP* 3.4 19.3 + - + +
186A ILE* 1.3 74.6 - - - +
188A GLU* 1.3 64.9 + - - +
190A ARG* 2.9 25.1 + - - +
191A TYR* 3.5 5.5 + - - +
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Residues in contact with GLU 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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89A PRO* 3.7 0.2 - - - +
90A LYS* 3.0 59.8 + - - +
91A GLY* 5.6 0.4 - - - -
92A LYS* 5.2 5.9 + - + +
93A LEU* 3.8 35.0 - - + +
184A TRP* 2.8 38.9 + - + +
185A ASP* 3.7 10.8 - - - +
187A VAL* 1.3 75.5 - - - +
189A SER* 1.3 62.5 + - - +
191A TYR* 3.0 22.2 + - - +
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Residues in contact with SER 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 ASP 3.2 11.8 + - - -
186A ILE* 2.7 24.9 + - - +
188A GLU* 1.3 80.4 - - - +
190A ARG* 1.3 62.9 + - - +
191A TYR 3.2 5.5 + - - +
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Residues in contact with ARG 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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76A LEU* 3.0 47.8 + - - +
79A THR* 3.1 18.2 + - - -
80A GLN* 3.2 33.1 + - - +
125A TRP* 5.0 0.8 - - - -
151A ASN* 2.5 32.2 + - - +
152A PRO 3.8 13.2 + - - +
153A LEU* 2.9 39.4 + - + -
154A LEU* 4.5 0.2 - - - +
186A ILE* 3.3 28.2 - - + +
187A VAL* 2.9 6.8 + - - +
189A SER* 1.3 79.8 - - - +
191A TYR* 1.3 55.3 + - - +
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Residues in contact with TYR 191 (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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92A LYS* 3.1 56.6 + - + -
93A LEU* 3.7 37.2 - - + -
96A ALA* 3.1 19.0 - - + +
100A GLN* 4.2 0.3 + - - -
128A SER* 3.6 33.4 + - - -
132A GLY* 2.6 34.9 + - - -
134A LEU* 3.6 8.3 - - + -
151A ASN* 4.1 3.3 + - - +
153A LEU* 3.7 19.3 - - + -
187A VAL 3.5 5.5 + - - +
188A GLU* 3.0 19.7 + - - +
189A SER 4.0 4.2 - - - +
190A ARG* 1.3 82.6 - - - +
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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