Contacts of the helix formed by residues 137 - 142 (chain B) in PDB entry 2O05
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 LEU 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 5.7 1.8 - - + -
61B ASN* 4.2 15.0 - - + +
62B VAL 5.3 0.2 - - - -
63B LEU* 4.0 18.4 - - + +
71B CYS* 3.6 30.1 - - - -
73B GLU* 3.9 24.9 - - + +
104B ASP* 3.9 10.1 - - + -
132B VAL* 6.4 0.4 - - + -
133B SER* 2.8 37.4 + - - +
136B PHE* 1.3 89.1 - - + +
138B PRO* 1.3 59.1 - - - +
139B GLY 3.2 3.1 - - - -
140B MET* 3.0 20.7 + - + -
141B ALA 2.8 24.6 + - - -
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Residues in contact with PRO 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN* 5.2 0.7 - - - +
73B GLU* 3.7 12.1 - - - +
133B SER 4.4 2.7 - - - +
134B LYS 4.5 12.1 - - - +
135B LYS 4.1 8.3 - - - +
136B PHE 3.3 9.6 - - - +
137B LEU* 1.3 89.8 - - - +
139B GLY* 1.3 62.0 + - - +
141B ALA* 3.9 3.7 - - + +
142B ILE* 3.4 21.8 + - - +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 4.9 3.2 + - - -
76B GLU* 5.1 0.9 - - - -
109B ARG* 2.7 36.3 + - - -
137B LEU 3.2 1.4 - - - -
138B PRO* 1.3 80.6 - - - +
140B MET* 1.3 56.0 + - - +
142B ILE* 3.4 9.4 - - - +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B CYS* 3.6 25.4 - - - -
72B THR 5.3 0.9 - - - +
73B GLU* 5.5 3.6 - - + -
76B GLU* 3.6 49.4 - - + +
80B GLN* 3.6 20.0 - - + +
104B ASP* 3.2 42.0 - - - +
105B GLY 3.2 19.2 - - - +
106B GLY* 4.0 4.1 - - - +
109B ARG* 3.4 8.8 - - - +
137B LEU* 3.0 26.2 + - + +
139B GLY* 1.3 78.7 - - - +
141B ALA* 1.3 57.9 + - - +
142B ILE 3.0 10.0 + - - -
143B GLY 3.3 6.2 + - - -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ASP 3.2 12.3 + - - +
133B SER 3.6 2.2 - - - +
134B LYS* 3.5 41.5 - - + +
137B LEU 2.8 17.7 + - - +
138B PRO* 3.8 4.7 + - + -
140B MET* 1.3 68.1 - - - +
142B ILE* 1.3 60.8 + - - +
143B GLY 3.0 5.4 - - - -
144B TYR* 3.0 29.2 + - + +
145B SER* 4.3 1.4 + - - -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG* 3.6 21.1 - - + -
138B PRO 3.4 15.1 + - - +
139B GLY* 3.4 21.8 - - - +
140B MET 3.0 1.0 + - - -
141B ALA* 1.3 76.5 - - - +
143B GLY* 1.3 62.4 + - - +
144B TYR 3.2 0.4 - - - -
145B SER* 3.2 34.2 - - - +
146B SER 4.4 0.3 + - - -
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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