Contacts of the strand formed by residues 130 - 135 (chain C) in PDB entry 2OTM
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 130 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLU* 3.5 7.6 - - - +
29B TYR* 4.0 1.6 - - - -
30B SER* 2.6 39.4 + - - -
37B MSE 3.6 3.4 - - - +
39B SER* 3.4 15.5 - - - -
93C TYR 3.1 5.5 + - - -
94C ARG* 2.8 35.0 + - - -
95C LEU 3.0 22.2 + - - -
129C HIS* 1.3 75.9 - - - +
131C ARG* 1.3 62.7 + - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 4.2 2.2 - - - -
26B TYR* 3.2 30.2 - - + -
39B SER* 3.0 20.0 + - - -
40B GLY 4.0 0.9 + - - -
148B TYR* 3.4 16.1 + - - -
94C ARG* 4.4 3.4 - - - +
95C LEU* 3.0 22.7 - - + +
109C PRO* 3.1 27.2 + - - +
112C LEU* 3.6 23.6 - - - +
113C ASP* 2.8 35.0 + - - +
116C SER* 3.0 22.8 + - - -
129C HIS* 4.1 3.1 - - + -
130C SER* 1.3 77.1 - - - +
132C MSE 1.3 65.8 - - - +
155C ACT 2.7 42.4 + - - +
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Residues in contact with MSE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU* 3.5 25.4 - - + +
134B TRP* 3.8 11.4 - - + -
148B TYR* 3.4 41.7 - - + -
150B PHE* 4.7 0.2 - - - -
94C ARG* 3.1 32.3 - - - +
95C LEU 3.0 6.0 + - - +
96C GLU* 3.2 33.2 - - + +
97C GLY 3.1 23.4 + - - -
112C LEU* 3.8 5.7 - - - +
131C ARG* 1.3 73.4 - - - +
133C ILE* 1.3 62.3 + - - +
134C TRP* 3.5 30.1 - - + -
155C ACT 4.8 0.4 - - - -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 5.0 1.9 - - - +
136B ASN* 4.4 1.2 - - - +
140B PRO* 4.0 16.3 - - + +
146B LEU* 4.5 8.6 - - + +
148B TYR* 3.4 11.0 + - - +
97C GLY 3.3 6.3 - - - +
99C LEU* 4.3 6.1 - - + -
108C HIS* 3.5 48.5 - - + +
109C PRO* 3.8 12.8 - - + -
112C LEU* 3.6 24.9 - - + -
132C MSE 1.3 76.2 - - - +
134C TRP* 1.3 76.0 + - - +
155C ACT 3.6 31.9 - - + +
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Residues in contact with TRP 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A MSE 3.7 13.0 - - + -
134A TRP* 3.4 26.0 - + - -
98B VAL* 4.0 13.8 - - + +
134B TRP* 3.4 43.9 - + - -
136B ASN* 3.2 24.0 - - - +
148B TYR* 5.8 0.2 - - - -
96C GLU* 3.6 43.3 - - + -
97C GLY 2.9 27.0 + - - +
98C VAL* 3.4 12.8 - - + -
99C LEU* 3.0 23.1 + - - +
108C HIS* 5.0 0.7 - - - -
132C MSE 3.5 31.8 - - + +
133C ILE* 1.3 84.8 + - - +
135C THR* 1.3 65.7 + - - +
136C ASN* 4.1 12.6 - - - +
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Residues in contact with THR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASN* 3.0 24.1 + - - +
137B PRO* 3.3 10.4 - - - +
138B VAL* 2.6 45.3 + - + +
99C LEU 3.1 7.4 - - - -
101C VAL* 3.5 26.7 - - + -
108C HIS* 3.4 33.7 - - + +
134C TRP* 1.3 73.9 - - - +
136C ASN* 1.3 71.9 + - - +
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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