Contacts of the strand formed by residues 142 - 146 (chain A) in PDB entry 3OM0
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 ALA 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.8 2.5 - - + -
140A PRO 4.0 0.9 + - - +
141A SER* 1.3 76.2 - - - +
143A SER* 1.3 65.2 + - - +
162A PHE* 4.1 12.3 - - + -
168A THR* 2.9 8.3 + - - +
169A LEU* 3.2 21.8 - - + -
170A SER* 3.0 21.1 + - - -
192A VAL* 3.7 8.6 - - - +
194A THR* 3.3 26.9 - - + +
196A ILE* 4.2 7.9 - - + -
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Residues in contact with SER 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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142A ALA* 1.3 74.3 + - - +
144A LEU* 1.3 55.1 + - - +
169A LEU* 4.1 2.7 - - - -
170A SER* 2.8 24.4 + - - -
172A ARG* 4.5 0.6 + - - -
187A ILE* 3.7 41.7 + - - +
190A ASP* 5.0 2.4 + - - +
192A VAL* 4.5 11.1 + - - +
194A THR 2.9 10.5 + - - +
195A ILE* 3.4 5.0 - - - -
196A ILE* 2.8 35.5 + - - +
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Residues in contact with LEU 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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143A SER* 1.3 76.1 - - - +
145A ILE* 1.3 67.6 + - - +
146A CYS* 3.5 24.2 - - - -
151A CYS* 4.1 7.0 - - - +
152A LEU* 4.8 5.8 - - + -
155A LEU* 3.9 24.5 - - + -
158A LEU* 5.5 2.2 - - + -
159A VAL* 5.0 4.3 - - + -
169A LEU* 4.1 19.1 - - + -
170A SER 2.7 14.7 + - - +
171A VAL* 3.4 16.4 - - + -
172A ARG* 2.9 29.1 + - - +
187A ILE* 5.5 0.3 - - - +
196A ILE* 3.4 35.4 - - + +
198A ASP* 4.3 3.8 - - + -
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Residues in contact with ILE 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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144A LEU* 1.3 72.8 - - - +
146A CYS* 1.3 61.6 + - - +
172A ARG 3.4 4.9 - - - +
174A LEU* 4.1 31.4 - - + -
180A PRO* 5.8 0.4 - - + -
183A LEU* 3.7 18.4 - - + -
184A LEU* 4.0 7.9 - - + -
187A ILE* 3.5 34.3 - - + -
195A ILE* 3.7 20.0 - - + -
196A ILE 2.9 9.1 + - - +
197A ILE* 3.6 8.3 - - + +
198A ASP* 2.9 28.9 + - - +
199A ALA* 5.5 0.4 - - + +
207A VAL* 3.9 31.0 - - + -
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Residues in contact with CYS 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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144A LEU* 3.5 26.0 - - - -
145A ILE* 1.3 73.3 - - - +
147A ALA* 1.3 61.0 + - - +
148A LYS 3.4 10.1 - - - +
151A CYS* 2.0 49.1 - - + -
171A VAL* 4.0 10.5 - - - -
172A ARG 2.9 6.5 + - - -
173A MET* 3.4 12.4 - - - -
174A LEU* 2.9 31.6 + - - +
198A ASP* 3.6 5.2 - - - -
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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