Contacts of the helix formed by residues 110 - 120 (chain B) in PDB entry 3K1L
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 ASN 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B GLY* 1.3 73.7 - - - -
111B ILE* 1.3 68.4 + - - +
112B TYR* 3.4 25.0 + - - +
113B TYR* 3.2 35.0 + - + +
114B ASP* 3.0 32.6 + - - +
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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 GLY 4.1 1.8 + - - -
110B ASN* 1.3 76.0 + - - +
112B TYR* 1.3 85.2 + - + +
114B ASP* 2.7 30.2 + - + +
115B ILE* 2.8 24.4 + - + +
152B ILE* 3.4 29.8 - - + -
153B PRO* 4.1 30.3 - - + +
155B LEU* 4.0 20.9 - - + -
179B LEU* 4.9 9.0 - - + +
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Residues in contact with TYR 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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295A TRP* 6.1 1.8 - + - -
299A PRO* 4.0 24.0 - - + +
300A LYS* 3.7 23.8 + - - +
301A LEU* 5.3 6.1 - - + -
110B ASN* 3.4 19.0 + - - +
111B ILE* 1.3 88.4 - - + +
113B TYR* 1.3 63.1 + - - +
115B ILE* 3.3 8.8 + - + +
116B LEU* 3.2 29.8 + - + +
132B CYS* 3.8 36.8 + - + -
152B ILE* 4.1 15.2 - - + +
153B PRO* 4.8 6.8 - - + +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.2 29.5 - - + +
111B ILE 3.1 0.2 - - - -
112B TYR* 1.3 79.1 - - - +
114B ASP* 1.3 68.7 + - - +
116B LEU* 3.3 17.0 + - + +
117B ALA* 3.0 37.2 + - + +
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Residues in contact with ASP 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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109B GLY* 5.3 2.8 - - - -
110B ASN 3.0 22.5 + - - +
111B ILE* 2.7 22.1 + - - +
113B TYR* 1.3 81.4 - - - +
115B ILE* 1.3 63.0 + - - +
117B ALA* 3.3 10.2 + - - +
118B LEU* 3.2 26.1 + - + +
178B ASN* 4.4 18.4 - - - +
179B LEU* 4.5 19.3 + - + +
180B GLU* 5.7 2.5 - - - +
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Residues in contact with ILE 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* 2.8 26.1 + - + +
112B TYR* 3.6 14.4 - - + +
114B ASP* 1.3 69.7 - - - +
116B LEU* 1.3 60.2 + - + +
118B LEU* 2.8 23.6 + - - +
119B TYR* 2.8 17.2 + - + -
126B LEU* 3.9 15.0 - - + +
128B VAL* 4.1 23.3 - - + -
132B CYS* 3.8 28.7 - - - -
135B ILE* 4.0 15.7 - - + -
152B ILE* 4.2 11.9 - - + -
179B LEU* 3.8 21.1 - - + -
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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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112B TYR* 3.2 15.5 + - + +
113B TYR* 3.4 16.8 - - + +
115B ILE* 1.3 78.4 - - + +
117B ALA* 1.3 61.7 + - - +
118B LEU 3.3 0.3 + - - -
119B TYR* 3.5 16.4 + - + +
120B LYS* 4.7 2.1 + - - +
389B AU 4.2 18.6 - - - -
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Residues in contact with ALA 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 TYR* 3.0 27.7 + - + +
114B ASP* 3.3 16.8 - - - +
115B ILE 3.0 0.2 - - - -
116B LEU* 1.3 77.7 - - - +
118B LEU* 1.3 69.3 + - + +
119B TYR 3.5 0.2 - - - -
120B LYS 5.0 4.0 + - - +
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Residues in contact with LEU 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 ASP* 3.5 11.9 - - + +
115B ILE* 2.8 6.9 + - - +
117B ALA* 1.3 85.5 - - + +
119B TYR* 1.3 68.0 + - - +
120B LYS 3.3 7.9 + - - +
124B TYR* 3.0 34.1 + - + +
126B LEU* 3.9 10.3 - - + -
137B PHE* 4.2 11.9 - - + -
179B LEU* 4.1 22.4 - - + -
180B GLU* 4.0 45.8 - - + +
183B LEU* 4.3 10.3 - - + -
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Residues in contact with TYR 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 ILE* 2.8 15.4 + - + +
116B LEU* 3.5 16.6 + - + +
118B LEU* 1.3 80.5 - - - +
120B LYS* 1.3 81.0 + - + +
121B SER* 3.7 2.4 + - - -
124B TYR* 4.9 2.1 - - - +
125B CYS* 5.8 0.2 - - - -
126B LEU* 3.6 47.6 + - + +
127B GLN* 5.4 0.2 - - - -
128B VAL* 4.4 18.6 - - + -
389B AU 3.2 26.7 - - - -
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Residues in contact with LYS 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 LEU 4.7 2.0 + - - -
117B ALA 5.0 3.9 + - - +
118B LEU* 3.8 5.0 - - - +
119B TYR* 1.3 93.9 - - + +
121B SER* 1.3 64.5 + - - +
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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