Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 2OM5
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 SER 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 1.3 74.3 - - - +
136A TYR* 1.3 65.9 + - - +
137A ARG* 3.9 24.9 + - - -
157A GLN* 3.8 4.3 - - - -
178A LEU 4.5 0.2 - - - -
179A ALA* 3.5 3.6 - - - -
180A THR* 2.8 41.3 + - - -
182A HIS* 3.5 26.0 + - - -
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Residues in contact with TYR 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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125A CYS* 4.1 22.0 - - - -
127A PRO* 4.0 15.6 - - + +
130A HIS* 4.3 8.5 + - - -
134A LEU* 3.4 40.6 + - + +
135A SER* 1.3 79.0 - - - +
137A ARG* 1.3 82.4 + - - +
155A VAL* 3.5 22.7 - - + +
156A SER 3.8 4.0 - - - +
157A GLN* 2.8 39.0 + - - +
158A THR 3.9 23.2 + - - -
159A THR 4.5 1.3 - - - -
160A GLY* 3.5 21.8 - - - +
177A CYS* 4.2 4.7 - - - -
178A LEU 3.5 2.5 - - - +
179A ALA* 4.0 20.2 - - + -
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Residues in contact with ARG 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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135A SER* 3.9 19.7 + - - -
136A TYR* 1.3 113.6 + - - +
138A TRP* 1.3 63.6 + - - +
146A PHE* 3.6 33.4 - - + -
147A ILE 6.2 0.2 - - - +
155A VAL* 4.6 4.3 - - - -
157A GLN* 3.9 12.1 + - - +
177A CYS* 3.8 1.4 - - - -
178A LEU* 2.7 47.9 + - + +
180A THR* 5.7 1.8 - - - +
182A HIS* 6.0 0.6 - - - -
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Residues in contact with TRP 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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110A ARG* 6.2 0.2 - - - -
123A LEU* 3.4 33.4 - - + -
124A PRO 3.5 20.0 - - - -
125A CYS 3.7 5.4 - - - -
137A ARG* 1.3 77.4 - - - +
139A LEU* 1.3 62.5 + - - +
146A PHE* 3.6 9.5 - - - -
147A ILE* 3.1 42.0 + - + +
155A VAL* 3.7 33.6 - - + +
160A GLY 2.8 20.6 + - - -
162A LEU* 3.4 25.4 - - + +
175A TYR* 3.8 21.8 - - + -
176A SER* 3.2 42.2 - - - -
177A CYS* 3.6 22.7 - - + -
192A SER* 5.5 0.9 - - - -
195A ALA* 5.7 3.1 - - + -
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Residues in contact with LEU 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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138A TRP* 1.3 78.1 - - - +
140A LEU* 1.3 59.8 + - - +
142A GLU 3.7 12.8 - - - +
143A PHE* 3.7 21.8 - - + -
144A PRO* 3.7 13.5 - - + -
145A ASN 3.4 33.0 - - - +
146A PHE* 3.8 18.8 - - + -
147A ILE* 4.2 4.3 - - - -
174A ASN 3.6 0.2 - - - +
175A TYR* 3.5 7.8 - - - +
176A SER* 2.8 38.7 + - - +
178A LEU* 3.8 28.3 - - + -
191A PHE* 4.2 14.6 - - + -
194A PHE* 3.7 5.8 - - + -
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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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139A LEU* 1.3 68.6 - - - +
141A ASN* 1.3 78.3 + - - +
142A GLU* 2.6 19.3 + - - +
145A ASN* 2.8 46.3 + - - +
146A PHE 5.5 0.9 - - - +
147A ILE* 3.7 17.7 - - + +
170A SER 5.3 9.0 - - - +
171A ASP 5.0 0.7 - - - +
172A LEU 5.0 3.8 - - - +
173A GLY* 4.6 7.0 - - - -
174A ASN 3.7 2.9 - - - +
175A TYR* 3.7 36.1 - - + +
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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