Contacts of the helix formed by residues 106 - 119 (chain B) in PDB entry 3KHU
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 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B THR* 4.4 3.1 - - + -
104B ALA 3.8 5.4 + - - +
105B ASP* 1.3 71.9 + - - +
107B LYS* 1.3 64.2 + - - +
108B TYR 3.1 3.3 + - - -
109B ILE* 3.1 29.2 + - + +
110B GLU* 2.9 24.1 + - + +
133B PRO* 3.9 37.7 - - + -
135B ARG 5.7 0.4 - - - -
136B ALA* 4.3 15.7 - - + +
139B SER* 4.2 17.3 - - - +
323D PHE* 3.8 30.0 + - + +
325D THR* 4.2 18.5 - - + -
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Residues in contact with LYS 107 (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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92B PRO* 4.8 7.0 - - - -
96B TYR* 5.5 2.0 + - - -
105B ASP* 3.1 33.3 + - - +
106B LEU* 1.3 75.8 - - - +
108B TYR* 1.3 104.1 + - + +
110B GLU* 3.4 5.6 + - - +
111B ALA* 3.0 27.5 + - - +
325D THR* 4.0 15.3 - - + +
327D THR* 4.7 25.4 - - + +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 3.7 20.0 - - + -
90B ASN* 3.4 43.3 - - - +
91B THR* 6.0 0.2 - - + -
92B PRO* 4.0 13.2 - - + +
105B ASP 4.6 1.0 + - - -
106B LEU 3.2 0.4 - - - -
107B LYS* 1.3 112.4 + - + +
109B ILE* 1.3 66.1 + - - +
111B ALA* 3.4 7.1 + - + +
112B CYS* 3.0 27.9 + - - -
502B UPG 3.3 32.7 - + - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.6 26.9 - - + +
89B VAL* 3.9 14.8 - - + +
91B THR* 3.4 30.9 - - + +
106B LEU* 3.1 23.4 + - + +
108B TYR* 1.3 77.2 - - - +
110B GLU* 1.3 59.6 + - - +
112B CYS* 3.3 6.1 + - - +
113B ALA* 2.9 26.2 + - - +
128B GLU* 5.8 2.0 - - + -
130B SER* 6.2 0.9 - - - -
132B VAL* 4.1 17.0 - - + -
136B ALA* 5.2 5.2 - - + +
139B SER* 6.1 2.0 - - - -
140B ILE* 3.8 33.4 - - + -
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Residues in contact with GLU 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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106B LEU* 2.9 17.9 + - + +
107B LYS* 3.7 5.0 - - - +
109B ILE* 1.3 76.7 - - - +
111B ALA* 1.3 65.3 + - - +
113B ALA* 3.3 2.0 + - - +
114B ARG* 2.8 64.1 + - - +
143B ILE* 3.7 17.0 - - + -
323D PHE* 3.6 17.7 - - + -
325D THR* 3.8 8.8 - - - +
329D LYS* 2.8 41.6 + - - -
409D HIS* 3.9 1.4 - - - -
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Residues in contact with ALA 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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107B LYS 3.0 17.6 + - - +
108B TYR* 3.7 9.6 - - + +
110B GLU* 1.3 75.6 - - - +
112B CYS* 1.3 62.9 + - - +
114B ARG* 3.3 7.9 + - - +
115B ARG* 3.0 25.1 + - - +
502B UPG 5.1 6.5 - - - +
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Residues in contact with CYS 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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10B ILE* 3.6 38.1 - - + -
87B ILE* 4.2 24.2 - - + -
89B VAL* 3.8 18.6 - - - -
108B TYR 3.0 18.6 + - - -
109B ILE 3.5 7.9 - - - +
111B ALA* 1.3 76.4 - - - +
113B ALA* 1.3 57.0 + - - +
115B ARG* 3.3 6.5 + - - +
116B ILE* 2.8 35.9 + - - +
502B UPG 5.2 4.9 - - - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.7 2.6 - - + +
109B ILE 2.9 16.7 + - - +
110B GLU* 3.3 5.1 + - - +
112B CYS* 1.3 75.8 - - - +
114B ARG* 1.3 63.5 + - - +
116B ILE* 3.3 5.2 + - - -
117B VAL* 3.1 25.1 + - - +
140B ILE* 4.2 18.8 - - + -
143B ILE* 3.9 22.9 - - + -
144B PHE* 3.4 24.1 - - + -
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Residues in contact with ARG 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 GLU* 2.8 53.8 + - + +
111B ALA* 3.8 6.7 - - - +
112B CYS 3.2 0.2 - - - -
113B ALA* 1.3 77.1 - - - +
115B ARG* 1.3 60.3 + - - +
117B VAL* 3.1 10.7 - - + +
118B GLN* 3.1 31.8 + - - +
143B ILE* 3.9 17.6 - - + +
147B ASN* 4.2 8.3 + - - +
323D PHE* 5.1 2.0 - - - -
329D LYS* 5.3 0.2 - - - +
409D HIS* 3.5 24.9 + - - -
433D LEU* 4.5 14.0 - - - +
434D LYS 3.0 33.7 + - - +
435D PRO* 4.4 9.3 - - - +
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Residues in contact with ARG 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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10B ILE* 5.7 0.9 - - + -
37B VAL* 4.3 11.7 - - - +
75B ILE* 3.6 37.3 - - + +
76B ASP* 3.0 34.1 + - - -
79B ILE* 3.8 19.5 - - + -
111B ALA 3.0 18.6 + - - +
112B CYS* 3.7 6.7 - - - +
114B ARG* 1.3 74.0 - - - +
116B ILE* 1.3 64.2 + - - +
118B GLN* 3.4 9.3 + - - -
119B ASN* 3.0 35.2 + - - +
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Residues in contact with ILE 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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10B ILE* 3.9 20.4 - - + -
79B ILE* 4.0 14.5 - - + +
85B VAL* 3.7 29.2 - - + -
87B ILE* 4.0 11.9 - - + -
112B CYS 2.8 25.7 + - - +
113B ALA* 3.7 5.8 - - - +
115B ARG* 1.3 73.2 - - - +
117B VAL* 1.3 60.4 + - - +
119B ASN 3.2 2.4 + - - -
120B SER* 2.5 39.8 + - - +
124B LYS* 5.3 0.4 - - + -
126B VAL* 3.9 38.4 - - + -
144B PHE* 4.3 8.7 - - + -
154B LEU* 4.4 7.0 - - + -
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Residues in contact with VAL 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 ALA 3.1 20.0 + - - +
114B ARG* 3.1 20.0 - - - +
116B ILE* 1.3 76.2 - - - +
118B GLN* 1.3 52.7 + - - +
119B ASN 3.3 0.3 + - - -
120B SER* 3.4 6.3 + - - +
143B ILE* 4.4 12.6 - - + -
144B PHE* 4.2 15.7 - - + +
147B ASN* 3.1 41.7 - - + +
149B LYS* 2.7 34.0 + - - -
152B LEU* 4.0 12.5 - - + +
154B LEU* 4.5 8.7 - - + -
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Residues in contact with GLN 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 ARG* 3.1 26.1 + - - +
115B ARG* 3.6 10.5 - - - +
117B VAL* 1.3 78.4 - - - +
119B ASN* 1.3 64.6 + - - +
149B LYS* 3.2 16.4 + - - +
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Residues in contact with ASN 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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76B ASP* 3.0 51.5 + - - +
79B ILE* 3.9 14.9 - - + +
80B LYS* 3.6 31.4 - - + +
115B ARG* 3.0 36.4 + - - +
116B ILE 3.2 0.2 + - - -
118B GLN* 1.3 84.0 - - - +
120B SER* 1.3 60.7 + - - +
121B ASN* 5.4 1.7 + - - -
149B LYS* 4.6 0.2 - - - -
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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