Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 3OYG
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 TYR 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A TYR* 4.1 11.2 - - + -
130A ILE 3.3 17.7 - - - +
131A GLY* 3.4 9.2 - - - -
132A PRO* 3.4 36.9 - - + +
133A LEU* 5.2 0.7 - - - -
140A LEU* 1.3 101.2 - - + +
142A VAL* 1.3 65.6 + - - +
157A PRO* 3.4 5.2 - - - +
158A THR* 2.8 40.2 + - - +
159A LYS 3.8 13.0 - - - -
160A ALA* 3.8 1.3 - - + -
161A PRO* 3.5 44.5 - - + +
242A TRP* 3.7 4.7 - - - -
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Residues in contact with VAL 142 (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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128A ASP 3.7 0.5 - - - +
129A TYR* 3.2 8.3 - - - -
130A ILE* 2.9 44.4 + - + +
133A LEU* 4.1 13.0 - - + -
141A TYR* 1.3 79.5 - - - +
143A LEU* 1.3 72.2 + - - +
144A VAL* 3.7 15.1 + - + +
155A LEU* 4.3 13.7 - - + -
156A TYR 3.3 13.0 - - - +
227A ILE* 5.6 3.4 - - + -
231A LEU* 5.8 1.6 - - + -
242A TRP* 3.6 24.7 - - + -
246A LEU* 4.0 16.8 - - + -
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Residues in contact with LEU 143 (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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127A ILE* 4.6 5.6 - - + -
128A ASP 3.7 19.7 - - - +
129A TYR* 3.6 35.8 - - + +
142A VAL* 1.3 71.7 - - - +
144A VAL* 1.3 61.4 + - - +
145A VAL* 4.2 19.1 - - + -
154A TRP 3.5 1.7 - - - +
155A LEU* 3.5 5.7 - - - -
156A TYR* 2.6 43.9 + - + +
158A THR* 4.5 3.1 - - + -
166A THR* 4.2 22.2 - - + +
169A SER* 3.7 27.1 - - - -
170A LEU* 4.5 4.9 - - + -
190A PHE* 4.3 14.6 - - + -
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Residues in contact with VAL 144 (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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127A ILE* 3.2 5.9 - - - +
128A ASP 2.9 33.5 + - - +
130A ILE* 3.7 20.2 - - + -
142A VAL* 3.7 17.9 - - + +
143A LEU* 1.3 76.5 - - - +
145A VAL* 1.3 63.8 + - - +
146A VAL* 4.0 5.4 - - + -
153A THR* 3.9 14.6 - - + -
154A TRP 3.6 2.7 - - - -
155A LEU* 4.0 1.3 - - + -
220A VAL* 3.6 14.0 - - + +
223A LYS* 4.6 1.1 - - + -
224A ASN* 3.5 24.5 - - - +
227A ILE* 3.6 26.7 - - + -
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Residues in contact with VAL 145 (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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125A PHE* 3.6 26.9 - - + -
126A PHE 3.5 2.9 - - - -
127A ILE* 3.7 19.7 - - + -
143A LEU* 4.2 15.5 - - + -
144A VAL* 1.3 76.5 - - - +
146A VAL* 1.3 65.1 + - - +
147A ASP 4.2 0.2 - - - -
153A THR* 3.3 4.9 - - - +
154A TRP* 2.8 45.5 + - + +
156A TYR* 4.5 4.5 - - + -
170A LEU* 4.0 13.5 - - + -
173A LEU* 3.6 34.1 - - + -
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Residues in contact with VAL 146 (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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125A PHE* 3.5 4.3 - - - -
126A PHE* 2.8 42.9 + - + +
144A VAL* 4.0 8.5 - - + -
145A VAL* 1.3 76.7 - - - +
147A ASP* 1.3 76.2 + - - +
148A GLY 3.4 1.2 + - - -
151A GLY* 4.1 17.5 - - - +
152A PHE 3.6 2.2 - - - -
153A THR* 3.5 22.2 - - + +
219A LYS* 4.3 25.1 - - + +
220A VAL* 4.1 11.7 - - + -
223A LYS* 3.8 25.4 - - + -
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Residues in contact with ASP 147 (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 LYS 4.5 0.9 - - - +
121A PRO* 3.5 7.1 - - - +
122A PHE* 2.8 30.6 + - - -
124A LYS 3.6 5.8 + - - +
125A PHE* 3.6 20.4 - - + -
145A VAL 4.2 0.6 - - - -
146A VAL* 1.3 74.1 - - - +
148A GLY* 1.3 61.7 + - - +
149A MET 3.4 3.8 + - - -
150A THR* 2.6 46.7 + - - +
151A GLY* 2.8 31.9 + - - -
152A PHE* 2.9 15.0 + - + +
154A TRP* 4.2 10.9 - - + -
219A LYS* 4.8 0.2 - - - +
269A LEU* 5.5 1.3 - - + -
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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