Contacts of the strand formed by residues 135 - 141 (chain A) in PDB entry 1OBZ
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 GLY 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A SER* 3.3 9.0 + - - -
132A ILE 2.9 32.1 + - - -
133A ASP 3.1 2.6 + - - -
134A ASN* 1.3 80.0 - - - +
136A ILE* 1.3 65.2 + - - +
137A PHE* 4.1 2.2 - - - -
157A GLN* 4.6 5.6 - - - -
166A CYS* 4.9 4.7 - - - -
167A ALA* 5.0 2.2 - - - -
169A TRP 4.6 0.7 - - - +
233B LEU* 3.8 15.7 - - - +
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Residues in contact with ILE 136 (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 LEU* 3.9 34.8 - - + -
130A LYS 3.5 2.0 - - - +
131A SER* 3.9 14.6 - - - +
135A GLY* 1.3 77.7 - - - +
137A PHE* 1.3 63.2 + - - +
157A GLN* 3.4 8.6 - - - +
158A VAL* 2.8 46.2 + - + +
161A ILE* 5.5 0.2 - - + -
166A CYS* 3.8 36.3 - - + +
169A TRP* 3.4 27.4 - - + +
170A SER 4.0 13.0 - - - +
171A SER* 4.7 0.4 - - - +
174A ALA* 4.1 11.4 - - + -
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Residues in contact with PHE 137 (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 LEU* 3.3 8.6 - - - -
130A LYS* 2.8 39.9 + - + +
132A ILE* 3.4 44.0 - - + -
135A GLY 4.1 8.3 - - - -
136A ILE* 1.3 79.8 - - - +
138A VAL* 1.3 64.1 + - - +
155A GLY 3.5 18.4 - - - -
156A ASP 3.2 7.2 - - - -
157A GLN* 3.6 32.1 - - + -
158A VAL* 4.9 0.2 - - - -
194A PRO* 4.0 7.4 - - + -
195A PHE* 3.5 33.7 - + - -
1274A ACT 3.6 23.1 - - + +
233B LEU* 3.8 12.3 - - + -
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Residues in contact with VAL 138 (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 LEU* 3.6 18.8 - - + -
128A ARG 3.9 4.0 - - - -
129A LEU* 4.0 2.5 - - + -
137A PHE* 1.3 71.9 - - - +
139A GLN* 1.3 60.3 + - - +
140A LEU 4.4 1.3 - - - +
141A VAL* 3.3 31.6 - - + -
152A LEU* 4.5 14.6 - - + -
153A ARG 3.3 24.5 - - - +
154A PHE* 3.6 3.0 - - - +
155A GLY* 2.9 25.3 + - - -
156A ASP* 2.9 27.9 + - + +
158A VAL* 4.1 17.7 - - + -
1274A ACT 3.9 5.4 - - - +
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Residues in contact with GLN 139 (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 ARG* 2.8 39.0 + - - +
129A LEU 4.3 0.7 - - - -
130A LYS* 3.4 48.8 + - + +
137A PHE 3.4 0.2 + - - -
138A VAL* 1.3 74.1 - - - +
140A LEU* 1.3 60.6 + - + +
154A PHE* 3.1 42.8 - - - -
247A ILE* 4.2 4.9 - - - +
1274A ACT 4.2 9.2 - - - +
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Residues in contact with LEU 140 (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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126A GLY 3.8 0.9 - - - +
127A LEU* 3.4 5.9 - - - +
128A ARG* 2.9 49.2 + - + +
138A VAL* 3.9 0.8 - - - +
139A GLN* 1.3 81.6 - - + +
141A VAL* 1.3 71.8 + - - +
142A GLN* 3.4 29.2 + - - +
154A PHE* 5.2 1.3 - - - -
247A ILE* 4.1 29.4 - - + +
248A GLY* 4.8 7.9 - - - -
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Residues in contact with VAL 141 (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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126A GLY 3.5 2.5 - - - -
127A LEU* 4.2 6.3 - - + -
138A VAL* 3.3 31.6 - - + -
140A LEU* 1.3 83.0 - - - +
142A GLN* 1.3 67.9 + - - +
143A ALA 3.7 0.7 + - - -
147A ALA* 3.9 7.2 - - + -
148A SER* 3.6 33.7 - - - +
152A LEU* 3.6 27.4 - - + +
153A ARG* 4.1 5.8 - - - -
154A PHE* 4.3 3.2 - - - +
245A ASN* 5.1 9.0 + - - +
247A ILE* 5.9 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