Contacts of the helix formed by residues 152 - 159 (chain E) in PDB entry 1KYZ
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 ILE 152 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E GLY* 1.3 83.5 - - - +
153E PRO* 1.3 76.3 - - + +
154E PHE 3.8 7.2 - - - +
155E ASN* 3.0 39.8 + - + +
156E LYS* 2.9 27.1 + - - +
321E LEU 4.6 1.1 - - - +
322E ALA 3.9 7.0 - - - +
323E HIS 4.0 15.3 - - - +
324E ASN 4.4 6.3 - - - +
325E PRO* 3.8 31.6 - - + +
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Residues in contact with PRO 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 5.1 2.5 - - + -
139E SER* 3.3 26.5 - - - +
142E HIS* 3.7 17.6 - - + +
143E LEU* 3.9 23.6 - - + -
146E ALA* 3.6 22.6 - - + -
151E GLY 4.0 0.7 - - - +
152E ILE* 1.3 91.2 - - + +
154E PHE* 1.3 62.5 + - - +
156E LYS* 3.2 4.3 + - + +
157E ALA* 3.0 22.5 + - - +
321E LEU 3.6 13.2 - - - +
322E ALA* 3.2 16.6 - - + +
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Residues in contact with PHE 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E VAL* 4.2 15.5 - - + -
136E LEU* 4.7 7.6 - - + -
139E SER* 3.2 26.6 + - - +
152E ILE* 3.3 0.8 - - + -
153E PRO* 1.3 78.1 - - - +
155E ASN* 1.3 65.6 + - - +
157E ALA* 3.1 3.6 + - - -
158E TYR* 2.9 55.9 + + + +
160E MET 3.6 12.3 - - - -
161E THR 3.6 8.5 - - - -
162E ALA* 3.4 35.7 - - + -
165E TYR* 3.7 27.8 - + + -
172E PHE* 6.0 0.4 - + - -
322E ALA 3.1 12.2 + - - +
323E HIS* 3.8 25.4 - + + +
1698E FER 5.1 2.9 - - - -
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Residues in contact with ASN 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ILE* 3.0 42.5 + - + +
154E PHE* 1.3 81.1 - - - +
156E LYS* 1.3 56.9 + - + +
159E GLY* 2.7 33.6 + - - -
160E MET 3.4 22.8 + - - +
161E THR* 3.8 24.3 - - - +
162E ALA 4.4 1.8 - - - +
323E HIS 4.5 3.4 + - - -
325E PRO* 5.4 7.0 - - - +
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Residues in contact with LYS 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E HIS* 4.1 21.4 + - + +
145E ASP* 3.9 31.6 - - - -
146E ALA* 4.1 16.2 - - + +
149E ASP* 4.3 12.9 + - - +
150E GLY 3.4 19.7 + - - +
151E GLY* 4.8 1.9 - - - -
152E ILE 2.9 29.9 + - - +
153E PRO 3.6 5.6 - - - +
155E ASN* 1.3 77.8 - - + +
157E ALA* 1.3 62.0 + - - +
159E GLY* 4.4 2.3 + - - -
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Residues in contact with ALA 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E GLU* 4.0 14.9 - - + +
142E HIS* 3.5 34.5 - - + +
153E PRO 3.0 10.7 + - - +
154E PHE* 3.1 9.4 + - - +
156E LYS* 1.3 79.6 - - - +
158E TYR* 1.3 79.5 + - + +
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Residues in contact with TYR 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LYS 3.9 0.5 + - - -
135E VAL* 2.7 40.2 + - + +
138E GLU* 3.3 20.4 - - + +
139E SER* 4.9 1.1 - - - -
154E PHE* 2.9 58.8 + + + +
157E ALA* 1.3 90.4 - - + +
159E GLY* 1.3 64.3 + - - +
160E MET* 3.3 26.7 + - + +
165E TYR* 3.4 34.3 - + + -
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Residues in contact with GLY 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ASN* 2.7 21.3 + - - -
156E LYS 4.4 2.7 + - - -
157E ALA 3.7 1.4 - - - -
158E TYR* 1.3 73.3 - - - +
160E MET* 1.3 60.0 + - - +
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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