Contacts of the helix formed by residues 113 - 125 (chain B) in PDB entry 1R6T
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 ASP 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B LYS* 3.2 17.0 + - + +
112B ILE* 1.3 76.2 - - - +
114B LYS* 1.3 65.8 + - - +
115B GLU* 2.9 39.3 - - - +
116B LEU* 3.0 20.3 + - - +
117B ILE* 3.1 15.8 + - - +
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Residues in contact with LYS 114 (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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113B ASP* 1.3 75.8 - - - +
115B GLU* 1.3 63.3 + - - +
117B ILE* 3.1 23.4 + - + +
118B ASN* 2.8 60.0 + - - +
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Residues in contact with GLU 115 (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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113B ASP* 2.9 40.3 - - - +
114B LYS* 1.3 81.4 + - - +
116B LEU* 1.3 55.3 + - - +
118B ASN* 3.4 10.6 + - - +
119B ARG* 2.9 27.9 + - - +
122B ARG* 5.0 2.6 + - - -
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Residues in contact with LEU 116 (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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111B LYS 5.0 0.7 - - - +
112B ILE* 4.1 21.3 - - + -
113B ASP* 3.0 21.9 + - - +
115B GLU* 1.3 73.8 - - - +
117B ILE* 1.3 61.9 + - - +
119B ARG* 3.1 6.9 + - - +
120B ILE* 2.9 39.8 + - + +
140B HIS* 3.6 35.2 - - + +
143B MSE 4.2 16.4 - - + -
144B ASN* 3.5 28.5 - - - +
147B LEU* 3.7 22.2 - - + -
335B LEU* 5.9 0.2 - - + -
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Residues in contact with ILE 117 (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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112B ILE* 3.7 23.1 - - + +
113B ASP 3.5 16.6 - - - +
114B LYS* 3.1 25.5 + - + +
116B LEU* 1.3 77.8 - - - +
118B ASN* 1.3 65.2 + - - +
120B ILE* 3.2 12.0 + - - +
121B GLU* 3.0 20.0 + - - +
128B PRO* 3.8 32.9 - - + +
132B LEU* 3.5 36.1 - - + +
133B ARG* 5.1 2.9 - - - +
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Residues in contact with ASN 118 (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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114B LYS* 2.8 59.8 + - - +
115B GLU* 3.7 8.8 - - - +
117B ILE* 1.3 70.6 - - - +
119B ARG* 1.3 61.5 + - - +
121B GLU* 3.1 17.2 + - - +
122B ARG* 2.9 47.9 + - + +
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Residues in contact with ARG 119 (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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115B GLU 2.9 15.4 + - - +
116B LEU* 3.4 11.0 - - - +
118B ASN* 1.3 77.6 - - - +
120B ILE* 1.3 56.7 + - - +
122B ARG* 3.3 27.0 + - + +
123B ALA* 2.9 29.2 + - - +
144B ASN* 3.0 39.4 + - - +
147B LEU* 3.6 20.7 - - + +
148B ASP* 2.7 35.6 + - - +
151B GLU* 2.9 38.7 + - - +
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Residues in contact with ILE 120 (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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112B ILE* 5.7 1.3 - - + -
116B LEU* 2.9 30.6 + - + +
117B ILE* 3.4 12.8 - - + +
118B ASN 3.2 0.2 - - - -
119B ARG* 1.3 76.2 - - - +
121B GLU* 1.3 61.6 + - - +
123B ALA* 3.5 5.2 + - - +
124B THR* 2.9 33.6 + - + +
128B PRO* 5.5 2.7 - - + -
132B LEU* 4.2 26.7 - - + -
143B MSE 4.4 21.5 - - + -
147B LEU* 4.0 19.1 - - + -
182B TRP* 4.3 23.6 - - + -
183B LEU* 6.2 2.0 - - + -
187B PHE* 4.2 15.9 - - + -
335B LEU* 5.8 4.3 - - + -
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Residues in contact with GLU 121 (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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117B ILE* 3.0 13.1 + - - +
118B ASN* 3.1 20.2 + - - +
120B ILE* 1.3 78.7 - - - +
122B ARG* 1.3 58.2 + - + +
125B GLY* 2.6 38.4 + - - -
126B GLN 3.4 26.7 + - - +
127B ARG* 4.0 10.7 - - - +
128B PRO* 3.9 18.5 - - + +
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Residues in contact with ARG 122 (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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115B GLU 5.0 2.0 + - - -
118B ASN* 2.9 35.3 + - + +
119B ARG* 3.8 29.3 - - + +
121B GLU* 1.3 81.6 - - + +
123B ALA* 1.3 63.3 + - - +
124B THR 3.4 0.3 + - - -
125B GLY* 3.7 6.5 + - - -
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Residues in contact with ALA 123 (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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119B ARG 2.9 18.4 + - - +
120B ILE 3.8 4.0 - - - +
122B ARG* 1.3 79.9 - - - +
124B THR* 1.3 61.7 + - + +
147B LEU* 4.1 22.4 - - + -
150B TYR* 3.9 26.8 - - + -
151B GLU* 4.2 18.4 + - + +
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Residues in contact with THR 124 (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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120B ILE* 2.9 24.3 + - + +
121B GLU 3.6 0.5 + - - -
123B ALA* 1.3 77.3 - - - +
125B GLY* 1.3 62.9 + - - +
126B GLN* 3.1 35.0 + - - +
150B TYR* 5.0 1.8 - - + -
182B TRP* 5.5 1.2 - - - -
186B VAL* 3.5 35.6 - - + +
187B PHE* 3.5 37.2 - - + -
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Residues in contact with GLY 125 (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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121B GLU* 2.6 24.0 + - - -
122B ARG* 3.7 5.5 + - - -
123B ALA 3.6 1.4 - - - -
124B THR* 1.3 74.4 - - - +
126B GLN* 1.3 63.3 + - - +
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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