Contacts of the helix formed by residues 188 - 200 (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 VAL 188 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136L PHE* 3.8 11.2 - - + -
137L GLU* 6.2 0.2 - - - +
140L LYS* 5.1 3.8 - - - +
186L ASN 4.0 9.0 - - - +
187L LEU* 1.3 79.6 - - - +
189L VAL* 1.3 69.7 + - + +
190L ALA* 3.9 17.9 - - + +
191L ASP* 2.8 32.0 + - - +
192L LEU* 3.5 3.3 + - - +
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Residues in contact with VAL 189 (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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131L LEU* 3.7 45.8 - - + +
133L SER* 5.7 3.1 - - - +
136L PHE* 3.6 34.2 - - + -
188L VAL* 1.3 72.6 - - + +
190L ALA* 1.3 63.3 + - - +
192L LEU* 2.9 6.2 + - - +
193L GLU* 2.9 37.4 + - + +
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Residues in contact with ALA 190 (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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188L VAL* 2.8 17.9 + - + +
189L VAL* 1.3 75.0 - - - +
191L ASP* 1.3 53.8 + - - +
193L GLU* 3.2 15.9 + - - +
194L SER* 2.8 41.5 + - - +
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Residues in contact with ASP 191 (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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65L ASN* 4.9 11.3 - - + +
68L VAL* 4.1 6.2 - - + +
186L ASN* 4.1 3.3 - - - +
187L LEU* 3.6 29.9 - - + +
188L VAL* 2.8 40.1 + - - +
190L ALA* 1.3 73.4 - - - +
192L LEU* 1.3 61.8 + - + +
194L SER* 3.4 7.2 + - - -
195L PHE* 3.0 25.1 + - - +
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Residues in contact with LEU 192 (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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68L VAL* 4.0 15.5 - - + +
71L LEU* 3.8 21.5 - - + +
72L TRP* 3.1 69.9 + - + +
75L ILE* 5.2 2.2 - - + -
131L LEU* 4.1 13.5 - - + -
136L PHE* 3.5 34.3 - - + -
187L LEU* 5.0 2.5 - - + -
188L VAL 4.0 5.8 - - - +
189L VAL 2.9 9.2 + - - +
191L ASP* 1.3 80.4 - - + +
193L GLU* 1.3 59.1 + - - +
195L PHE* 3.3 0.7 + - - +
196L ALA 3.0 23.7 + - - -
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Residues in contact with GLU 193 (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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72L TRP* 4.6 2.0 - - - -
127L LYS 4.6 6.1 - - - +
128L ALA* 5.8 1.2 - - - -
131L LEU* 3.7 24.7 - - + +
189L VAL* 2.9 27.5 + - + +
190L ALA* 3.5 16.2 - - - +
192L LEU* 1.3 73.4 - - - +
194L SER* 1.3 64.6 + - - +
196L ALA* 3.1 7.2 + - - +
197L ASN* 2.8 38.4 + - - +
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Residues in contact with SER 194 (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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190L ALA* 2.8 26.2 + - - +
191L ASP* 3.7 7.7 - - - -
193L GLU* 1.3 72.4 - - - +
195L PHE* 1.3 57.5 + - - +
197L ASN* 3.5 4.6 + - - +
198L ASN* 2.7 41.8 + - - +
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Residues in contact with PHE 195 (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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56L SER* 5.0 2.0 - - - -
57L GLY 4.3 13.0 - - - -
60L ASN* 4.1 10.1 - - + -
61L GLU* 4.1 11.0 - - + -
65L ASN* 4.1 10.1 - - - +
68L VAL* 3.7 29.4 - - + -
69L SER* 3.4 25.6 - - - -
72L TRP* 4.4 12.6 - + - +
101L GLN* 3.8 13.2 - - - -
191L ASP 3.0 16.4 + - - +
192L LEU 3.6 4.0 - - - +
194L SER* 1.3 74.0 - - - +
196L ALA* 1.3 56.8 + - - +
198L ASN* 3.0 3.0 + - - +
199L HIS* 2.6 79.7 + + + +
200L PHE* 4.4 6.5 - + - -
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Residues in contact with ALA 196 (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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72L TRP* 3.4 31.2 - - + -
127L LYS* 4.8 7.0 - - + -
192L LEU 3.0 6.3 + - - -
193L GLU* 3.5 7.6 - - - +
195L PHE* 1.3 75.1 - - - +
197L ASN* 1.3 64.0 + - - +
200L PHE* 2.8 58.4 + - + +
230L GLN* 4.7 0.6 - - - +
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Residues in contact with ASN 197 (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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193L GLU* 2.8 30.2 + - - +
194L SER* 3.8 6.1 - - - +
196L ALA* 1.3 78.8 - - - +
198L ASN* 1.3 63.2 + - - +
201L LEU* 3.3 12.5 - - - +
230L GLN* 3.2 37.8 + - - +
233L THR* 5.2 1.9 - - - +
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Residues in contact with ASN 198 (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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194L SER* 2.7 34.5 + - - +
195L PHE* 3.0 3.1 + - - +
197L ASN* 1.3 87.4 - - - +
199L HIS* 1.3 70.7 + - + +
201L LEU* 3.3 16.7 - - - +
234L LYS 5.0 0.2 - - - +
235L PRO* 3.5 18.7 - - - +
236L VAL* 3.7 24.9 - - + +
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Residues in contact with HIS 199 (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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54L PHE* 4.3 0.9 - - - -
56L SER* 3.2 28.7 + - - -
60L ASN* 4.0 24.7 + - + -
195L PHE* 2.6 63.1 + + + +
198L ASN* 1.3 88.5 + - + +
200L PHE* 1.3 59.5 + - + +
201L LEU* 2.7 20.5 + - - +
204L ASN* 3.2 21.9 + - - +
235L PRO* 3.9 17.1 - - + +
236L VAL* 4.5 17.4 + - + +
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Residues in contact with PHE 200 (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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54L PHE* 3.5 46.2 - + + -
72L TRP* 3.7 42.6 - + - -
101L GLN* 3.2 35.2 - - - -
103L TYR* 4.0 9.4 - + - -
123L PHE* 4.3 19.3 - + + -
127L LYS* 4.5 6.7 - - - -
195L PHE* 4.4 10.5 - + - -
196L ALA* 2.8 36.0 + - + +
199L HIS* 1.3 68.9 - - + +
201L LEU* 1.3 68.4 + - - +
229L LEU* 5.3 6.8 - - - +
230L GLN* 4.2 4.7 - - - +
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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