Contacts of the helix formed by residues 110 - 124 (chain B) in PDB entry 4KEU
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 SER 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ASN 4.4 0.2 + - - -
109B ARG* 1.3 76.2 - - - +
111B ILE* 1.3 63.5 + - - +
112B ASP* 3.3 15.4 + - - +
113B GLU* 2.9 48.5 + - - +
114B ILE* 3.4 15.1 + - - +
151B LYS* 5.4 0.2 - - - -
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Residues in contact with ILE 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 ARG 4.0 0.2 + - - -
110B SER* 1.3 73.6 - - - +
112B ASP* 1.4 58.2 + - - +
114B ILE* 3.4 10.4 + - - +
115B ALA* 3.0 23.0 + - - +
151B LYS* 3.8 38.4 - - + +
154B ARG* 4.0 31.6 - - + -
155B ALA* 3.6 29.2 - - - +
158B ILE* 3.9 14.4 - - + -
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Residues in contact with ASP 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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110B SER* 3.1 12.1 + - - +
111B ILE* 1.4 75.6 - - - +
113B GLU* 1.3 60.3 + - + +
115B ALA* 3.2 7.4 + - - +
116B ASP* 2.9 39.3 + - - +
158B ILE* 3.3 23.6 - - - +
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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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105B TYR* 5.4 0.2 + - - -
106B PHE* 5.8 1.6 - - + -
108B ASN 4.4 0.5 - - - +
109B ARG* 3.1 44.8 + - + -
110B SER* 2.9 38.8 + - - +
112B ASP* 1.3 75.1 - - + +
114B ILE* 1.3 63.8 + - - +
116B ASP* 3.3 25.1 + - - +
117B LEU* 3.4 13.4 + - - +
267D LYS* 3.6 14.6 + - - -
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Residues in contact with ILE 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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96B ILE* 4.1 14.1 - - + -
102B LEU* 4.1 26.2 - - + -
106B PHE* 3.8 19.7 - - + -
109B ARG* 5.2 2.2 - - + +
110B SER 3.4 15.2 + - - +
111B ILE* 3.5 10.5 - - - +
112B ASP 3.2 0.2 - - - -
113B GLU* 1.3 77.2 - - + +
115B ALA* 1.3 62.1 + - - +
117B LEU* 3.0 27.5 + - + +
118B PHE* 3.5 24.5 + - + -
151B LYS* 4.3 28.5 - - + +
152B VAL* 4.9 5.2 - - + +
155B ALA* 3.5 17.0 - - + -
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Residues in contact with ALA 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 ILE 3.0 13.8 + - - +
112B ASP* 3.2 9.4 + - - +
114B ILE* 1.3 76.8 - - - +
116B ASP* 1.3 57.8 + - - +
118B PHE* 3.1 7.9 + - - +
119B ILE* 2.9 35.3 + - + +
155B ALA* 3.6 27.3 - - + +
158B ILE* 3.6 28.5 - - + -
159B ALA* 4.7 1.3 - - - +
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Residues in contact with ASP 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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112B ASP* 2.9 23.6 + - - +
113B GLU* 3.4 17.6 - - - +
114B ILE 3.1 0.4 - - - -
115B ALA* 1.3 79.3 - - - +
117B LEU* 1.3 57.9 + - + +
119B ILE* 3.9 15.0 - - - +
120B HIS* 2.9 30.3 + - - +
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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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96B ILE* 5.2 1.6 - - + -
105B TYR* 4.8 3.8 - - + +
106B PHE* 3.6 37.0 - - + -
113B GLU 3.6 13.2 - - - +
114B ILE* 3.0 11.4 + - - +
116B ASP* 1.3 76.1 - - + +
118B PHE* 1.3 66.7 + - + +
120B HIS* 3.3 5.3 + - - +
121B ASP* 3.1 17.0 + - - -
32D VAL* 5.4 0.2 - - + -
36D TRP* 3.4 46.5 + - + +
38D HIS* 4.1 14.4 - - + +
39D LEU* 3.8 37.9 - - + -
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Residues in contact with PHE 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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94B THR* 3.6 22.6 - - + +
95B GLY* 3.3 37.5 - - - -
96B ILE* 3.9 19.7 - - + -
114B ILE* 3.7 25.4 - - + -
115B ALA* 3.1 5.9 + - - +
117B LEU* 1.3 76.7 - - + +
119B ILE* 1.3 63.3 + - - +
121B ASP* 3.0 4.9 + - - +
122B ILE* 3.0 28.5 + - - +
136B VAL* 3.8 19.5 - - + -
152B VAL* 4.3 10.8 - - + -
155B ALA* 3.8 35.4 - - + -
156B ALA* 3.9 7.0 - - - -
159B ALA* 3.9 12.8 - - + -
36D TRP* 4.2 6.7 - + - -
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Residues in contact with ILE 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 ALA* 2.9 24.9 + - + +
116B ASP* 3.9 14.1 - - - +
118B PHE* 1.3 75.2 - - - +
120B HIS* 1.3 57.9 + - - +
122B ILE* 3.8 7.1 - - - +
123B LYS* 2.8 61.9 + - + +
158B ILE* 4.6 8.5 - - + -
159B ALA* 4.2 18.8 - - + -
162B GLU* 3.9 30.7 - - + +
163B THR* 4.5 7.6 - - + -
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Residues in contact with HIS 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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116B ASP 2.9 18.9 + - - +
117B LEU 3.5 4.9 - - - +
119B ILE* 1.3 76.6 - - - +
121B ASP* 1.3 64.2 + - - +
124B GLU* 2.7 58.5 + - + +
125B GLY 3.0 25.5 + - - -
127B GLN 5.7 1.1 + - - -
128B GLY* 5.7 4.6 + - - -
36D TRP* 4.8 0.7 - + - -
38D HIS* 3.7 53.0 + + + +
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Residues in contact with ASP 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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74B ARG* 2.8 31.5 + - - -
94B THR* 2.7 37.8 + - - +
117B LEU 3.1 4.8 + - - -
118B PHE 3.0 4.0 + - - +
120B HIS* 1.3 80.1 - - - +
122B ILE* 1.3 61.6 + - - +
125B GLY* 3.4 28.3 + - - +
126B ILE* 4.0 14.7 - - + +
127B GLN 4.5 2.1 + - - -
132B LYS* 3.6 3.8 - - - -
133B ALA* 3.2 16.7 + - + -
36D TRP* 2.9 24.9 + - - -
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Residues in contact with ILE 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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4B PRO* 5.8 0.2 - - - +
94B THR* 4.0 9.6 - - + -
118B PHE 3.0 24.9 + - - +
119B ILE* 3.8 3.8 - - - +
121B ASP* 1.3 77.0 - - - +
123B LYS* 1.3 61.2 + - + +
132B LYS* 3.4 24.1 - - - +
133B ALA* 3.7 21.1 - - + +
135B PHE 5.1 0.9 - - - +
136B VAL* 4.1 15.0 - - + -
159B ALA* 4.2 6.5 - - + -
163B THR* 3.5 37.9 - - + +
165B VAL* 3.6 35.4 - - + -
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Residues in contact with LYS 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 ILE* 2.8 42.8 + - + +
120B HIS* 5.3 0.2 - - - -
122B ILE* 1.3 76.8 - - + +
124B GLU* 1.3 73.2 + - + +
132B LYS* 3.1 24.9 + - - +
162B GLU* 4.8 9.5 + - - +
163B THR* 4.2 17.9 - - + -
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Residues in contact with GLU 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 HIS* 2.7 54.2 + - + +
123B LYS* 1.3 87.7 - - + +
125B GLY* 1.3 57.2 + - - +
129B THR 4.1 4.9 - - - +
130B LEU* 4.4 13.0 - - - +
132B LYS* 3.9 12.6 - - - -
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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