Contacts of the strand formed by residues 114 - 119 (chain Q) in PDB entry 5IJO
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 ARG 114 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108Q VAL* 3.6 3.3 - - - +
109Q PHE* 2.8 30.0 + - + +
112Q ILE* 3.9 17.0 - - + +
113Q SER* 1.3 79.5 - - - +
115Q ALA* 1.3 64.7 + - - +
125Q MET* 4.9 7.9 - - + -
126Q TRP 3.3 20.0 - - - +
127Q ASN* 4.7 2.5 - - - -
128Q TYR* 4.3 2.2 - - - +
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Residues in contact with ALA 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q GLY 3.4 11.7 - - - +
108Q VAL* 4.2 4.9 - - + +
109Q PHE 5.3 0.2 - - - -
114Q ARG* 1.3 74.8 - - - +
116Q TRP* 1.3 62.5 + - - +
125Q MET* 3.3 4.9 - - - +
126Q TRP* 2.8 38.3 + - + +
128Q TYR* 5.1 2.6 - - - +
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Residues in contact with TRP 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q MET* 3.2 6.7 - - - +
107Q GLY* 2.8 35.8 + - - +
108Q VAL* 4.8 0.6 - - - +
109Q PHE* 5.4 1.8 - - + +
115Q ALA* 1.3 77.6 - - - +
117Q LEU* 1.4 61.5 + - - +
123Q ILE* 6.1 1.6 - - + -
124Q PHE 3.1 13.7 - - - +
125Q MET* 4.8 3.1 - - + -
147Q VAL* 6.1 5.8 - - + -
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Residues in contact with LEU 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q PHE* 5.9 7.9 - - + -
105Q MET 3.6 6.1 - - - +
106Q MET* 4.1 6.5 - - + -
116Q TRP* 1.4 76.1 - - - +
118Q THR* 1.4 59.5 + - - +
119Q ILE* 4.2 1.0 + - + -
122Q ASP 4.1 0.3 - - - +
123Q ILE* 3.4 4.7 - - - +
124Q PHE* 2.9 43.2 + - + +
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Residues in contact with THR 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q ASN 4.3 0.4 - - - -
104Q CYS* 3.2 6.1 - - - +
105Q MET* 2.7 48.4 + - - +
106Q MET* 4.7 0.2 - - - +
117Q LEU* 1.4 74.6 - - - +
119Q ILE* 1.3 59.9 + - - +
120Q ASP 4.1 2.0 - - - -
122Q ASP 3.6 9.2 - - - -
123Q ILE* 5.1 4.5 - - - -
144Q ILE* 4.8 21.1 - - - -
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Residues in contact with ILE 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Q GLN 5.2 2.9 - - - +
97Q PHE* 4.6 24.7 - - + +
99Q HIS 4.9 3.6 - - - +
100Q MET* 4.2 20.4 - - + -
103Q ASN 3.3 4.7 - - - -
104Q CYS* 5.2 2.9 - - + -
117Q LEU* 4.2 1.2 + - + -
118Q THR* 1.3 72.6 - - - +
120Q ASP* 1.3 72.8 + - - +
121Q SER 3.1 2.3 + - - -
122Q ASP* 3.1 21.0 + - + +
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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