Contacts of the helix formed by residues 180 - 187 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A PRO 4.8 0.4 - - - +
66A ASN* 3.3 28.0 - - + +
147A VAL* 4.7 0.7 - - - -
176A PRO* 4.5 8.1 - - + -
179A GLY* 1.3 77.0 - - - +
181A LEU* 1.3 59.2 + - - +
182A GLU* 3.3 2.2 + - - +
183A SER* 2.6 37.7 + - - -
184A LEU* 3.3 24.4 + - - +
32E SER* 4.3 15.9 - - - +
34E TYR* 4.7 17.0 - - + -
35E ARG* 4.0 21.5 + - + +
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Residues in contact with LEU 181 (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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144A LEU* 4.0 35.9 - - + +
147A VAL* 3.6 27.7 - - + +
148A GLN* 4.1 26.2 - - + +
151A GLU* 6.3 3.6 - - + -
180A THR* 1.3 74.3 - - - +
182A GLU* 1.3 71.4 + - + +
184A LEU* 4.2 2.3 - - - +
185A GLU* 4.0 20.6 + - - +
32E SER* 4.9 2.9 + - - +
34E TYR* 6.2 0.2 - - - -
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Residues in contact with GLU 182 (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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180A THR* 3.3 2.6 + - - +
181A LEU* 1.3 86.1 - - + +
183A SER* 1.3 66.0 + - - +
184A LEU 3.0 2.1 + - - -
185A GLU* 3.1 33.4 + - - +
186A ASN* 3.4 8.7 + - - +
31E LYS* 4.5 6.9 + - - -
32E SER* 3.1 46.1 + - - -
35E ARG* 4.3 19.5 + - - +
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Residues in contact with SER 183 (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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63A PRO 4.1 0.2 - - - -
64A TYR 3.5 24.9 - - - -
66A ASN* 2.6 41.3 + - - +
180A THR* 2.6 24.2 + - - -
182A GLU* 1.3 77.8 - - - +
184A LEU* 1.3 62.1 + - - +
186A ASN* 3.3 11.7 + - - +
187A LEU* 3.0 24.4 + - - +
35E ARG* 4.1 11.1 - - - +
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Residues in contact with LEU 184 (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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66A ASN 3.4 20.4 - - - +
67A GLY* 3.6 24.9 - - - +
70A ASN* 5.0 0.4 - - + +
71A LEU* 4.0 15.7 - - + +
140A LYS* 3.3 14.7 + - - +
143A VAL* 3.5 31.9 - - + +
144A LEU* 3.6 21.2 - - + +
147A VAL* 3.8 21.5 - - + -
178A ARG 3.8 6.3 - - - +
180A THR 3.3 17.4 + - - +
181A LEU* 4.3 3.8 - - + +
182A GLU 3.0 0.8 - - - -
183A SER* 1.3 83.7 + - - +
185A GLU* 1.3 61.4 + - - +
186A ASN 3.3 1.0 + - - -
187A LEU* 3.4 11.8 + - + +
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Residues in contact with GLU 185 (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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140A LYS* 3.2 23.8 + - - +
144A LEU* 4.1 22.7 - - + +
181A LEU* 4.0 14.9 + - - +
182A GLU* 3.1 27.8 + - - +
184A LEU* 1.3 77.5 - - - +
186A ASN* 1.3 58.8 + - + +
187A LEU 4.5 0.2 - - - +
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Residues in contact with ASN 186 (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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64A TYR* 4.8 7.9 - - - +
182A GLU 3.4 8.8 + - - +
183A SER* 3.3 10.7 + - - +
184A LEU 3.2 0.8 - - - -
185A GLU* 1.3 78.2 - - + +
187A LEU* 1.3 68.5 + - - +
188A VAL* 3.7 10.1 + - - +
191A ASP* 4.2 3.1 - - - +
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Residues in contact with LEU 187 (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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64A TYR 3.8 4.9 - - - +
65A ASN* 3.4 31.9 - - + +
66A ASN 4.6 2.0 - - - +
67A GLY 4.1 6.1 - - - +
68A VAL* 3.5 40.6 - - + +
71A LEU* 4.3 13.7 - - + -
136A PHE* 4.2 5.8 - - + -
140A LYS* 2.8 26.0 + - - +
183A SER 3.0 25.7 + - - +
184A LEU* 3.4 12.2 + - - +
186A ASN* 1.3 80.6 - - + +
188A VAL* 1.3 63.1 + - - +
191A ASP* 3.6 20.4 - - + -
192A LEU* 4.5 7.0 - - + -
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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