Contacts of the helix formed by residues 109 - 118 (chain B) in PDB entry 4KMR
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B THR 3.3 12.5 + - - +
107B GLY* 3.2 13.4 - - - +
108B GLY* 1.3 81.8 - - - +
110B ARG* 1.3 68.1 + - - +
111B GLU* 4.5 11.2 - - + +
112B ARG* 3.1 19.7 + - + +
113B GLU* 2.9 23.9 + - - +
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Residues in contact with ARG 110 (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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108B GLY 3.9 1.8 + - - -
109B LEU* 1.3 70.9 - - - +
111B GLU* 1.3 69.6 + - - +
113B GLU* 3.1 14.0 + - - +
114B LEU* 2.9 48.2 + - + +
134B GLY* 3.8 21.3 - - - +
135B LEU* 3.6 19.7 - - + +
136B THR 5.9 0.4 - - - +
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Residues in contact with GLU 111 (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 LEU* 3.3 12.0 - - + +
110B ARG* 1.3 85.5 - - - +
112B ARG* 1.3 108.5 + - + +
114B LEU* 3.6 8.4 + - - +
115B GLU* 3.0 28.4 + - - +
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Residues in contact with ARG 112 (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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105B GLN 5.1 3.8 - - - -
106B THR* 3.1 42.2 - - - +
109B LEU* 3.1 15.7 + - + +
111B GLU* 1.3 113.6 + - - +
113B GLU* 1.3 63.3 + - - +
115B GLU* 3.2 31.7 + - - +
116B ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 113 (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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106B THR* 3.9 22.9 + - + +
108B GLY* 3.3 15.1 - - - -
109B LEU 2.9 18.9 + - - +
110B ARG* 3.5 5.7 - - - +
112B ARG* 1.3 76.3 - - - +
114B LEU* 1.3 63.0 + - - +
116B ALA* 3.3 16.5 + - - +
117B LEU* 3.6 12.7 - - - +
130B LEU* 4.3 15.0 - - + +
131B ALA 4.4 0.7 - - - +
132B PRO* 3.3 12.6 - - + +
133B LEU 2.7 28.1 + - - -
134B GLY* 3.1 23.7 + - - -
135B LEU* 3.4 26.1 - - + +
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Residues in contact with LEU 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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110B ARG* 2.9 52.9 + - + +
111B GLU* 4.0 5.8 - - - +
113B GLU* 1.3 72.1 - - - +
115B GLU* 1.3 65.7 + - - +
117B LEU* 3.0 36.2 + - + +
118B ARG* 3.4 6.8 + - - +
135B LEU* 3.8 21.8 - - + -
157B PHE* 5.5 2.5 - - + -
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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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111B GLU 3.0 19.1 + - - +
112B ARG* 3.2 35.6 + - - +
114B LEU* 1.3 79.0 - - - +
116B ALA* 1.3 60.9 + - - +
117B LEU 3.0 0.2 - - - -
118B ARG* 2.9 61.9 + - - +
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Residues in contact with ALA 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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74B ALA* 4.4 13.7 - - + -
104B GLU* 3.6 35.2 - - - +
106B THR* 4.9 2.2 - - + -
112B ARG 3.1 13.1 + - - +
113B GLU* 3.4 14.1 - - - +
114B LEU 3.2 0.4 - - - -
115B GLU* 1.3 76.7 - - - +
117B LEU* 1.3 59.0 + - - +
118B ARG 3.8 1.7 + - - +
128B LEU* 3.7 9.5 - - + +
130B LEU* 4.7 2.0 - - + -
147B ARG* 3.1 19.9 + - - -
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Residues in contact with LEU 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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113B GLU 3.6 15.3 - - - +
114B LEU* 3.0 26.3 + - + +
116B ALA* 1.3 79.5 - - - +
118B ARG* 1.3 59.2 + - - +
128B LEU* 3.7 23.8 - - + -
130B LEU* 4.1 9.2 - - + -
135B LEU* 5.4 0.2 - - + -
145B ALA* 4.1 20.3 - - + +
147B ARG* 3.8 12.3 + - - +
149B LEU* 3.9 24.9 - - + -
157B PHE* 3.6 31.4 - - + -
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Residues in contact with ARG 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 LEU 3.4 5.6 + - - +
115B GLU* 2.9 56.6 + - - +
116B ALA 4.8 1.7 - - - +
117B LEU* 1.3 80.3 - - - +
147B ARG* 5.4 2.8 + - - -
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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