Contacts of the helix formed by residues 144 - 152 (chain A) in PDB entry 3KYB
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 GLY 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LYS* 3.6 27.8 - - - -
125A GLY* 4.4 1.0 - - - -
139A ALA 3.0 9.3 + - - -
140A LEU* 3.9 10.9 + - - -
142A PHE 3.8 0.6 - - - -
143A ILE* 1.3 80.8 - - - +
145A LYS* 1.3 66.2 + - - -
146A GLU 3.3 2.2 - - - -
147A LEU 3.6 0.2 + - - -
148A TYR* 3.0 26.5 + - - +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 4.6 2.8 + - - +
140A LEU* 3.8 23.0 - - + +
144A GLY* 1.3 72.2 - - - -
146A GLU* 1.3 64.6 + - + +
148A TYR* 3.4 2.9 + - + +
149A GLU* 2.9 65.9 + - + +
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PHE* 3.7 22.7 - - + -
108A PHE* 3.8 18.7 - - + -
124A LYS* 3.2 33.1 + - - +
144A GLY 3.3 0.8 - - - -
145A LYS* 1.3 80.0 - - + +
147A LEU* 1.3 62.5 - - - +
149A GLU* 4.0 3.4 - - - +
150A ALA* 3.0 30.5 + - - +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 4.6 23.6 - - + -
103A THR* 5.5 1.3 - - + -
104A ILE* 4.8 3.8 - - + -
107A PHE* 3.8 21.1 - - + -
108A PHE* 4.0 13.2 - - + -
121A ILE* 3.6 26.5 - - + -
143A ILE* 3.3 45.1 + - + +
144A GLY 3.6 1.2 + - - -
146A GLU* 1.3 76.3 - - - +
148A TYR* 1.3 60.7 + - - +
150A ALA* 4.6 0.4 - - - -
151A PHE* 2.8 64.7 + - + +
152A PHE* 3.9 1.4 + - - -
177A VAL* 5.4 1.3 - - + -
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 4.0 16.4 - + - -
136A GLU* 2.8 42.7 + - + +
139A ALA* 3.3 31.0 - - + -
140A LEU* 4.2 17.3 - - + -
143A ILE* 3.9 8.3 - - + +
144A GLY 3.0 20.7 + - - +
145A LYS* 3.6 2.5 - - + +
147A LEU* 1.3 77.9 - - - +
149A GLU* 1.3 67.8 - - + +
152A PHE* 3.0 18.8 + - + -
153A LYS* 2.8 57.5 + - + +
164A PRO* 3.2 25.3 - - + +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LYS* 2.9 58.8 + - + +
146A GLU* 4.2 3.3 - - - +
148A TYR* 1.3 86.8 - - + +
150A ALA* 1.3 65.5 + - - +
153A LYS* 4.1 33.4 + - + +
154A GLY* 4.6 4.2 + - - -
272A CYS 5.6 0.2 - - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.4 16.9 - - + +
91A ASN* 4.1 13.9 - - - +
107A PHE* 3.6 26.5 - - + -
146A GLU 3.0 18.6 + - - +
147A LEU 3.9 2.7 - - - +
149A GLU* 1.3 81.9 - - - +
151A PHE* 1.3 68.4 + - + +
154A GLY 5.8 0.2 + - - -
272A CYS* 3.3 22.3 - - - +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 4.9 1.8 - - + -
90A VAL* 3.7 10.5 - - + -
95A PHE* 3.6 49.6 - + + -
97A LEU* 4.1 17.5 - - + +
99A ILE* 4.3 11.0 - - + -
103A THR* 3.8 17.0 - - + -
107A PHE* 3.8 21.1 - + - -
147A LEU* 2.8 47.9 + - + +
150A ALA* 1.3 76.9 - - + +
152A PHE* 1.3 79.5 + - + +
155A TYR* 3.7 18.3 - - - +
272A CYS* 3.7 27.6 - - - -
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 5.9 3.6 - - + -
99A ILE* 3.3 31.6 - - + -
135A PHE* 4.1 17.3 - + + -
143A ILE* 3.5 25.4 - - + -
147A LEU 4.3 0.9 - - - -
148A TYR* 3.0 22.6 + - + +
151A PHE* 1.3 93.3 - - + +
153A LYS* 1.3 64.0 + - - +
154A GLY 3.5 2.0 - - - -
155A TYR* 4.0 6.7 - + - -
156A THR* 2.7 33.1 + - - -
172A LEU* 3.6 29.2 - - + -
175A LEU* 4.6 21.5 - - + -
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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