Contacts of the helix formed by residues 117 - 130 (chain B) in PDB entry 3KKL
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 ALA 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLU* 3.6 26.0 - - + +
113B ASP 2.8 14.0 + - - +
114B TYR* 3.0 19.6 + - + +
115B PRO 3.4 1.0 - - - -
116B LYS* 1.3 73.6 - - - +
118B LYS* 1.3 63.3 + - - +
119B ASN 3.2 3.3 + - - -
120B LEU* 3.3 11.2 + - + -
121B GLN* 3.0 25.8 + - - +
143B LEU* 3.6 12.6 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 3.4 2.9 + - - +
115B PRO 4.7 4.6 + - - +
116B LYS* 2.8 43.6 + - + +
117B ALA* 1.3 72.1 - - - +
119B ASN* 1.3 64.4 + - - +
121B GLN* 3.4 16.8 + - - +
122B ASP* 3.1 31.1 + - - +
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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
----------------------------------------------------------
50B GLU* 3.0 27.6 + - - +
91B ALA* 3.5 20.6 - - + +
92B ASN* 3.6 30.1 + - - +
118B LYS* 1.3 77.1 - - - +
120B LEU* 1.3 65.9 + - - +
121B GLN 3.3 0.3 + - - -
122B ASP* 3.4 13.9 + - - +
123B ILE* 3.2 24.3 + - - +
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Residues in contact with LEU 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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9B SER* 3.7 26.2 - - - +
10B LEU 4.5 1.8 - - - +
48B VAL* 3.7 29.6 - - + -
49B SER 4.3 2.0 - - - -
50B GLU* 3.0 31.0 + - + +
91B ALA* 3.8 6.2 - - + +
102B PHE* 4.0 13.1 - - + -
113B ASP* 5.6 0.2 - - - +
114B TYR* 3.7 30.7 - - + -
117B ALA* 3.3 15.9 + - + +
119B ASN* 1.3 74.9 - - - +
121B GLN* 1.3 58.1 + - - +
123B ILE* 3.1 10.7 + - + +
124B ALA* 3.0 28.1 + - - +
143B LEU* 3.8 13.0 - - + -
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR 4.2 1.7 + - - -
115B PRO 3.9 8.2 + - - +
117B ALA 3.0 18.0 + - - +
118B LYS* 3.6 31.2 - - - +
119B ASN 3.2 0.2 - - - -
120B LEU* 1.3 74.6 - - - +
122B ASP* 1.3 60.3 + - - +
124B ALA* 4.6 1.8 - - - +
125B SER* 2.9 25.9 + - - -
143B LEU* 2.7 42.2 + - + +
145B ASP 2.8 28.8 + - - +
146B GLY 4.6 3.5 - - - +
147B LEU* 2.9 34.9 - - + +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS* 3.1 19.5 + - - +
119B ASN* 3.4 15.9 + - - +
121B GLN* 1.3 72.6 - - - +
123B ILE* 1.3 68.3 + - + +
125B SER* 3.5 6.7 - - - -
126B LYS* 3.0 49.6 + - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 12.3 - - + -
48B VAL* 5.9 0.4 - - + -
91B ALA* 3.7 25.4 - - + +
94B VAL* 3.9 37.9 - - + +
96B ALA* 3.9 16.8 - - + -
102B PHE* 4.1 4.7 - - + -
119B ASN 3.2 15.0 + - - +
120B LEU* 3.1 14.7 + - + +
122B ASP* 1.3 78.5 - - + +
124B ALA* 1.3 64.5 + - - +
126B LYS* 2.8 20.1 + - - +
127B ILE* 2.9 31.2 + - + +
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Residues in contact with ALA 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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102B PHE* 3.7 38.8 - - + -
120B LEU 3.0 17.1 + - - +
121B GLN* 4.0 4.0 - - - +
123B ILE* 1.3 73.5 - - - +
125B SER* 1.3 62.8 + - - +
127B ILE* 3.3 1.2 + - - +
128B TYR* 3.0 27.2 + - - +
134B ILE* 3.5 15.6 - - + +
143B LEU* 4.8 3.6 - - + -
144B PHE* 6.3 1.1 - - + -
147B LEU* 4.3 14.8 - - + -
156B LEU* 5.1 0.4 - - - -
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Residues in contact with SER 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 GLN 2.9 20.1 + - - -
122B ASP* 3.5 9.2 - - - -
124B ALA* 1.3 79.3 - - - +
126B LYS* 1.3 57.8 + - - +
128B TYR* 3.6 2.4 - - - +
129B ALA* 2.9 29.6 + - - +
147B LEU* 3.9 6.2 - - - +
148B ILE 2.7 28.2 + - - -
149B ASP* 4.2 0.9 - - - +
150B ILE* 3.3 27.2 + - - +
156B LEU* 4.3 7.1 - - - +
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Residues in contact with LYS 126 (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 ALA* 3.5 20.4 - - + -
97B SER* 5.5 0.4 - - - +
122B ASP* 3.0 42.8 + - - +
123B ILE* 2.8 10.7 + - - +
125B SER* 1.3 75.0 - - - +
127B ILE* 1.3 64.9 + - - +
129B ALA* 3.5 1.4 + - - +
130B ASN* 2.8 32.6 + - - +
150B ILE* 4.1 23.8 - - + -
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Residues in contact with ILE 127 (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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7B LEU* 4.6 1.6 - - + -
96B ALA* 3.5 24.5 - - + +
99B TYR* 3.7 35.9 - - + +
100B LYS 4.1 9.4 - - - +
102B PHE* 3.6 45.3 - - + +
123B ILE* 2.9 25.3 + - + +
124B ALA* 3.3 4.9 + - - +
126B LYS* 1.3 75.8 - - - +
128B TYR* 1.3 53.0 + - - +
130B ASN* 3.1 18.5 - - - +
132B GLY* 2.7 46.1 + - - -
133B VAL 4.2 2.0 - - - +
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Residues in contact with TYR 128 (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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124B ALA 3.0 18.5 + - - +
125B SER 3.6 3.1 - - - +
127B ILE* 1.3 75.4 - - - +
129B ALA* 1.3 60.6 + - - +
130B ASN 3.1 1.8 - - - -
131B GLY* 2.9 21.0 + - - -
132B GLY 3.6 15.5 - - - -
134B ILE* 3.3 36.8 - - + -
149B ASP* 3.9 23.3 - - - -
156B LEU* 3.5 40.1 + - + +
160B LYS* 3.7 26.7 + - - -
214B LYS* 3.6 22.7 + - + +
215B LEU* 4.8 0.3 - - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B SER 2.9 18.4 + - - +
126B LYS 4.0 3.6 - - - +
127B ILE 3.4 0.2 - - - -
128B TYR* 1.3 78.2 - - - +
130B ASN* 1.3 56.7 + - - +
131B GLY 3.2 3.3 + - - -
149B ASP* 4.9 2.9 - - - +
150B ILE* 3.6 29.2 - - + -
151B LYS* 3.9 40.1 - - + +
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Residues in contact with ASN 130 (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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97B SER* 4.2 33.3 + - - +
99B TYR 5.4 3.1 + - - +
100B LYS* 4.3 19.7 + - - +
126B LYS* 2.8 25.4 + - - +
127B ILE* 3.1 16.4 - - - +
128B TYR 3.1 0.8 - - - -
129B ALA* 1.3 76.7 - - - +
131B GLY* 1.3 59.9 + - - +
132B GLY 4.3 0.4 - - - +
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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