Contacts of the helix formed by residues 152 - 158 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ALA* 4.4 0.2 - - - -
151C GLY* 1.3 79.0 - - - +
153C PRO* 1.3 77.7 - - + +
154C PHE 4.0 0.7 - - - +
155C ASN* 2.8 51.3 + - - +
156C LYS* 2.9 17.4 + - - +
161C THR* 6.2 0.9 - - + -
321C LEU 4.5 1.1 - - - +
322C ALA 3.8 12.3 - - - +
323C HIS 4.1 5.4 - - - +
324C ASN 3.2 17.7 - - - +
325C PRO* 3.4 38.1 - - + +
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Residues in contact with PRO 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C SER* 3.5 23.8 - - - +
142C HIS* 3.7 16.3 - - + +
143C LEU* 3.9 23.3 - - + +
146C ALA* 3.6 22.6 - - + -
151C GLY 4.1 1.1 - - - +
152C ILE* 1.3 86.0 - - + +
154C PHE* 1.3 61.5 + - - +
156C LYS* 3.3 2.0 + - + -
157C ALA* 3.2 24.1 + - - +
321C LEU* 3.4 24.5 - - + +
322C ALA* 3.3 14.6 - - + +
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Residues in contact with PHE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 4.1 13.9 - - + -
136C LEU* 4.6 9.0 - - + -
139C SER* 3.2 27.6 - - - +
152C ILE* 3.3 0.8 - - - +
153C PRO* 1.3 75.5 - - - +
155C ASN* 1.3 74.8 + - - +
157C ALA* 4.0 1.3 - - - -
158C TYR* 3.4 53.4 + + - +
160C MET 3.7 4.0 - - - -
161C THR 3.2 27.1 - - - -
162C ALA* 3.6 17.7 - - + -
165C TYR* 3.8 27.4 - + + -
172C PHE* 5.6 2.7 - + - -
322C ALA 3.0 16.4 + - - +
323C HIS* 3.8 17.7 - - + +
366C FER 6.1 0.9 - - - -
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 2.8 48.3 + - + +
154C PHE* 1.3 84.3 - - - +
156C LYS* 1.3 63.0 + - + +
157C ALA 3.1 4.9 - - - -
158C TYR 3.7 0.2 - - - -
159C GLY* 3.0 28.3 + - - +
160C MET 3.6 24.3 + - - +
161C THR* 3.8 21.3 - - - +
162C ALA 4.7 0.6 - - - +
323C HIS 4.9 2.4 + - - -
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C HIS* 3.7 20.2 + - + +
145C ASP* 2.7 47.9 + - + +
146C ALA* 3.9 13.5 - - + +
149C ASP* 3.7 17.9 + - - +
150C GLY 3.4 18.3 + - - +
151C GLY* 4.4 3.1 - - - -
152C ILE 2.9 22.9 + - - +
153C PRO 3.9 4.5 - - - +
155C ASN* 1.3 77.4 - - + +
157C ALA* 1.3 57.1 + - - +
158C TYR 5.1 0.6 - - - -
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLU* 3.9 13.5 - - + +
139C SER* 4.7 0.7 - - - -
142C HIS* 3.2 35.7 + - + +
153C PRO 3.2 11.6 + - - +
154C PHE 4.2 0.9 - - - +
155C ASN 3.1 0.8 - - - -
156C LYS* 1.3 80.9 - - - +
158C TYR* 1.3 82.2 + - + +
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Residues in contact with TYR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LYS 4.2 0.2 + - - -
135C VAL* 2.6 40.9 + - + +
138C GLU* 3.4 30.2 - - + +
139C SER 5.0 0.2 - - - -
154C PHE* 3.4 34.0 + + + +
155C ASN 3.5 2.3 + - - -
156C LYS 5.1 0.7 - - - -
157C ALA* 1.3 88.5 - - + +
159C GLY* 1.3 60.9 + - - +
160C MET* 4.5 14.8 - - + +
165C TYR* 3.2 46.2 - + + -
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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