Contacts of the helix formed by residues 134 - 139 (chain B) in PDB entry 1O5K
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 VAL 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 4.1 9.4 - - + -
102B VAL* 4.0 9.9 - - + -
103B THR* 4.8 0.8 + - - -
132B TYR* 3.6 35.1 + - + +
133B ASN* 1.3 73.8 + - - +
135B PRO* 1.3 68.3 - - + +
136B GLY* 3.2 2.9 - - - +
137B ARG* 3.0 36.5 + - + +
138B THR* 3.1 28.4 + - + +
163B ALA* 3.9 15.7 - - + +
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Residues in contact with PRO 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 3.7 13.9 - - - +
134B VAL* 1.3 89.1 - - - +
136B GLY* 1.3 57.9 - - - +
138B THR* 3.5 1.3 - - - +
139B GLY* 3.0 26.7 + - - -
140B VAL 3.4 25.8 - - - +
141B ASN* 3.5 25.8 - - + +
163B ALA 4.5 1.1 - - - +
164B ASN* 4.0 25.1 - - + +
165B PRO* 5.6 2.0 - - + -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 3.9 11.6 - - - +
139A GLY* 3.7 20.1 - - - +
134B VAL* 3.1 5.0 + - - +
135B PRO* 1.3 78.5 - - - +
137B ARG* 1.3 59.9 + - - +
139B GLY 5.2 0.2 + - - -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 2.9 70.9 + - + +
107A ASN* 3.6 21.0 + - - +
108A LYS* 4.0 28.5 - - + +
137A ARG 4.6 0.5 - - - +
138A THR 3.6 12.1 - - - +
139A GLY* 4.9 1.6 - - - -
43B THR* 4.1 25.0 + - - +
105B TYR* 4.6 0.7 - - - +
132B TYR* 4.9 2.3 + - - -
134B VAL* 3.0 26.3 + - + +
136B GLY* 1.3 78.5 - - - +
138B THR* 1.3 61.9 + - - +
139B GLY 3.6 0.4 - - - -
247B PHE* 5.7 0.6 - - - -
250B THR* 4.0 6.7 - - - +
251B ASN* 3.1 44.5 + - - +
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.8 17.0 - - + -
137A ARG 3.6 6.1 - - - +
102B VAL* 3.8 6.5 - - + -
103B THR* 3.7 22.3 + - - +
104B PRO 4.5 1.2 - - - +
105B TYR* 3.5 16.6 - - + -
106B TYR* 3.0 25.5 + - - -
108B LYS* 4.8 2.1 - - - +
134B VAL* 3.2 32.5 + - + +
135B PRO* 3.5 0.3 - - - +
137B ARG* 1.3 79.5 - - - +
139B GLY* 1.3 61.0 + - - +
140B VAL* 3.0 29.8 + - - +
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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
----------------------------------------------------------
136A GLY 3.6 21.7 - - - +
137A ARG 4.5 3.3 + - - -
139A GLY* 5.8 1.2 - - - +
108B LYS* 3.6 22.7 - - - +
135B PRO* 3.0 14.8 + - - -
136B GLY 4.9 0.4 + - - -
137B ARG 3.6 0.8 - - - -
138B THR* 1.3 78.7 - - - +
140B VAL* 1.3 59.4 + - - +
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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