Contacts of the helix formed by residues 180 - 187 (chain L) in PDB entry 1KYO
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 THR 180 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L PRO* 4.7 1.1 - - + +
66L ASN* 3.3 22.5 - - + +
175L LEU* 5.8 1.3 - - + -
176L PRO* 4.3 8.7 - - + -
179L GLY* 1.3 76.2 - - - +
181L LEU* 1.3 60.5 + - - +
182L GLU* 3.3 2.9 + - - +
183L SER* 2.8 34.8 + - - +
184L LEU* 3.2 25.9 + - - +
32P SER* 4.0 23.6 - - - +
34P TYR* 4.5 13.7 - - + -
35P ARG* 4.0 18.5 + - + +
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Residues in contact with LEU 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L LEU* 4.3 25.4 - - + +
147L VAL* 4.5 19.6 - - + +
148L GLN* 4.3 33.2 - - + +
151L GLU* 5.4 9.2 - - + -
179L GLY 3.8 0.4 + - - -
180L THR* 1.3 74.1 - - - +
182L GLU* 1.3 70.0 + - + +
184L LEU* 4.0 6.2 - - - +
185L GLU* 3.6 25.7 + - - +
32P SER* 5.1 0.8 + - - -
34P TYR* 6.0 0.4 - - - -
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Residues in contact with GLU 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L THR* 3.2 3.4 + - - +
181L LEU* 1.3 86.8 + - + +
183L SER* 1.3 64.2 + - - +
184L LEU 2.8 5.9 + - - -
185L GLU* 3.0 23.8 + - - +
186L ASN* 3.5 10.8 + - - +
31P LYS* 3.8 9.6 - - - +
32P SER* 3.1 46.6 + - - -
35P ARG* 4.4 14.9 + - - +
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Residues in contact with SER 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L PRO 3.5 21.1 - - - -
64L TYR* 3.5 17.8 - - - +
66L ASN* 2.5 32.5 + - - +
180L THR* 2.8 23.4 + - - -
182L GLU* 1.3 77.1 - - - +
184L LEU* 1.3 59.3 + - - +
186L ASN* 3.6 6.0 + - - +
187L LEU* 3.0 32.2 + - - +
35P ARG* 3.7 8.1 - - - +
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Residues in contact with LEU 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L ASN 3.2 8.1 - - - +
67L GLY* 3.2 43.3 - - - +
70L ASN* 5.0 0.9 - - - +
71L LEU* 4.9 3.9 - - + +
140L LYS* 3.6 11.1 - - + +
143L VAL* 3.8 29.4 - - + +
144L LEU* 3.5 19.9 - - + +
147L VAL* 4.0 18.6 - - + -
178L ARG 3.7 13.9 - - - +
179L GLY 4.1 0.4 - - - -
180L THR 3.2 20.3 + - - +
181L LEU* 4.0 3.6 - - + +
182L GLU 2.8 1.8 - - - -
183L SER* 1.3 78.8 + - - +
185L GLU* 1.3 56.3 + - - +
186L ASN 3.1 9.2 + - - -
187L LEU* 3.3 21.2 + - + +
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Residues in contact with GLU 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L LYS* 3.0 24.4 + - - +
144L LEU* 3.6 30.5 - - + +
181L LEU* 3.6 19.5 - - - +
182L GLU* 3.0 16.6 + - - +
184L LEU* 1.3 76.7 - - - +
186L ASN* 1.3 57.0 + - - +
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Residues in contact with ASN 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L TYR* 4.9 6.9 - - - +
140L LYS* 4.5 0.7 - - - -
182L GLU 3.5 8.6 + - - +
183L SER* 4.0 11.4 - - - +
184L LEU 3.1 1.0 - - - -
185L GLU* 1.3 78.6 - - + +
187L LEU* 1.3 67.0 + - + +
188L VAL* 3.6 11.2 + - - +
191L ASP* 4.1 3.8 - - - +
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Residues in contact with LEU 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L TYR 3.8 4.3 - - - +
65L ASN* 3.7 38.6 - - + +
66L ASN 4.2 2.0 - - - +
67L GLY 3.9 4.7 - - - +
68L VAL* 3.7 26.7 - - + +
71L LEU* 3.8 21.3 - - + -
136L PHE* 3.9 7.9 - - - -
140L LYS* 3.0 24.9 + - - +
183L SER 3.0 22.7 - - - +
184L LEU* 3.3 13.4 + - - +
186L ASN* 1.3 80.3 - - - +
188L VAL* 1.3 60.2 + - - +
191L ASP* 3.6 25.4 - - + +
192L LEU* 5.0 0.9 - - + -
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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