Contacts of the strand formed by residues 159 - 165 (chain A) in PDB entry 2GWU
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 TRP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.4 25.4 - - + +
139A SER* 4.8 3.8 - - - -
152A LEU* 4.9 7.4 - - + -
153A THR 3.3 6.5 - - - +
154A GLU* 2.8 44.9 + - + -
156A ASN 4.6 6.3 - - - -
157A GLY* 2.7 31.0 - - - -
158A PHE* 1.3 75.0 - - - +
160A TYR* 1.3 61.0 + - - +
191A SER* 3.0 5.5 - - - -
192A PHE* 2.8 77.7 + + + -
193A THR* 3.5 4.5 - - - -
194A LEU* 2.9 59.7 - - + -
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Residues in contact with TYR 160 (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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151A ARG 3.5 1.0 - - - +
152A LEU* 3.3 8.4 - - - -
153A THR* 2.7 54.9 + - - +
154A GLU* 4.8 0.9 - - - -
155A GLU* 4.1 26.7 + - + -
158A PHE* 3.4 32.5 - - + +
159A TRP* 1.3 74.1 - - - +
161A LEU* 1.3 60.0 + - - +
162A ASP* 3.9 3.1 + - - +
188A LYS* 3.0 48.5 - - + -
190A TYR 3.4 1.6 - - - -
191A SER* 3.1 30.7 - - - -
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Residues in contact with LEU 161 (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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120A ILE* 5.4 0.9 - - + -
131A MET* 3.4 33.7 - - + -
135A LEU* 5.4 2.7 - - + -
150A PHE* 4.1 18.4 - - + -
151A ARG 3.4 17.7 - - - +
152A LEU* 3.5 22.9 - - + -
159A TRP 4.3 0.2 - - - -
160A TYR* 1.3 71.3 - - - +
162A ASP* 1.3 73.9 + - - +
188A LYS* 3.5 0.7 - - - +
189A ILE* 2.9 42.5 + - + +
190A TYR* 2.9 48.4 + - + +
192A PHE* 4.6 2.1 - - + -
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Residues in contact with ASP 162 (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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150A PHE* 3.2 9.4 - - - +
151A ARG* 2.8 68.7 + - + +
153A THR* 4.0 11.8 + - - +
160A TYR 4.6 1.8 - - - -
161A LEU* 1.3 74.1 - - - +
163A GLN* 1.3 63.9 + - - +
186A TYR* 5.1 8.5 - - + -
187A ARG 3.0 13.0 - - - +
188A LYS* 2.7 43.2 - - - +
189A ILE 4.3 0.2 - - - +
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Residues in contact with GLN 163 (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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129A TYR* 4.2 32.4 + - + +
148A CYS* 5.4 1.6 - - + -
149A VAL 3.7 5.2 - - - +
150A PHE* 3.4 32.3 - - + -
162A ASP* 1.3 73.4 - - - +
164A ILE* 1.3 69.2 + - - +
165A ARG* 3.4 10.4 + - + +
186A TYR 3.6 0.2 - - - -
187A ARG* 2.8 63.4 + - - +
188A LYS 4.3 0.5 - - - -
189A ILE* 3.3 40.6 + - - +
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Residues in contact with ILE 164 (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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129A TYR* 5.8 0.2 - - - -
142A ASP* 5.8 1.3 - - - +
148A CYS* 3.1 27.8 - - + +
149A VAL* 2.9 43.1 + - + +
150A PHE 6.1 0.4 - - - -
151A ARG* 6.6 0.2 - - + -
163A GLN* 1.3 74.5 - - - +
165A ARG* 1.3 56.1 + - - +
183A ASP* 5.7 0.7 - - + -
184A SER* 3.0 41.2 - - - +
185A LYS 3.0 7.6 - - - +
186A TYR* 3.0 59.5 - - + +
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Residues in contact with ARG 165 (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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96A THR* 5.6 4.4 - - - +
129A TYR* 4.3 28.7 + - + +
148A CYS* 5.0 1.8 - - - -
163A GLN* 3.4 13.6 + - + +
164A ILE* 1.3 72.9 - - - +
166A ARG* 1.3 69.3 + - - +
168A GLN* 4.5 19.0 - - - +
184A SER* 2.7 23.5 - - - -
185A LYS* 2.6 22.3 + - + +
187A ARG* 3.0 57.2 - - + +
242A ARG* 4.2 22.0 - - - +
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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