Contacts of the helix formed by residues 188 - 200 (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 VAL 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.7 13.7 - - + -
186A ASN 3.9 8.7 - - - +
187A LEU* 1.3 80.1 - - - +
189A VAL* 1.3 56.3 + - + +
190A ALA* 3.5 23.8 - - + +
191A ASP* 2.7 47.0 + - - +
192A LEU* 3.3 6.8 + - - +
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Residues in contact with VAL 189 (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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131A LEU* 3.4 48.9 - - + +
133A SER* 4.9 9.6 - - - +
136A PHE* 3.6 36.4 - - + -
137A GLU* 5.6 0.9 - - - +
188A VAL* 1.3 73.8 - - + +
190A ALA* 1.3 60.8 + - - +
192A LEU* 3.4 3.6 + - - +
193A GLU* 3.1 33.9 + - - +
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Residues in contact with ALA 190 (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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188A VAL* 2.9 16.4 + - + +
189A VAL* 1.3 80.2 - - - +
191A ASP* 1.3 57.3 + - - +
193A GLU* 3.8 11.0 - - - +
194A SER* 2.9 30.5 + - - -
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Residues in contact with ASP 191 (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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65A ASN* 4.9 10.2 - - + +
68A VAL* 4.0 4.8 - - + +
186A ASN 4.2 2.8 - - - +
187A LEU* 3.6 25.6 - - + +
188A VAL* 2.7 48.3 + - - +
190A ALA* 1.3 70.7 - - - +
192A LEU* 1.3 58.8 + - - +
194A SER* 3.6 6.3 - - - -
195A PHE* 2.8 33.6 + - - +
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Residues in contact with LEU 192 (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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68A VAL* 3.8 22.4 - - + +
71A LEU* 4.0 19.7 - - + -
72A TRP* 3.0 59.4 + - + +
75A ILE* 4.2 7.9 - - + -
131A LEU* 4.2 11.0 - - + -
136A PHE* 3.7 26.9 - - + -
187A LEU* 4.5 9.0 - - + -
188A VAL 3.3 12.2 + - - +
189A VAL 3.6 9.0 - - - +
191A ASP* 1.3 79.3 - - - +
193A GLU* 1.3 56.4 + - - +
196A ALA* 2.9 25.5 + - - +
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Residues in contact with GLU 193 (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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72A TRP* 4.6 1.8 - - - -
127A LYS 5.0 1.6 - - - +
128A ALA* 5.9 1.0 - - - -
131A LEU* 4.0 29.9 - - + +
189A VAL* 3.1 26.4 + - + +
190A ALA* 3.8 9.8 - - - +
192A LEU* 1.3 76.3 - - - +
194A SER* 1.3 66.8 + - - +
196A ALA* 3.1 7.3 + - - +
197A ASN* 2.8 38.7 + - - +
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Residues in contact with SER 194 (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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190A ALA 2.9 20.0 + - - -
191A ASP* 3.6 8.3 - - - -
193A GLU* 1.3 77.5 - - - +
195A PHE* 1.3 61.7 + - - +
197A ASN* 3.1 8.4 + - - +
198A ASN* 2.7 32.3 + - - +
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Residues in contact with PHE 195 (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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56A SER* 4.9 3.4 - - - -
57A GLY 4.8 5.6 - - - -
60A ASN 4.3 12.3 - - - -
61A GLU* 4.5 5.6 - - + -
65A ASN* 4.6 9.6 - - - +
68A VAL* 3.7 29.8 - - + -
69A SER* 3.8 21.3 - - - -
72A TRP* 4.1 12.3 - + - -
101A GLN* 4.0 9.9 - - - -
191A ASP 2.8 20.8 + - - +
192A LEU 3.9 1.6 - - - +
194A SER* 1.3 71.9 - - - +
196A ALA* 1.3 70.6 + - - +
197A ASN 3.0 0.9 + - - -
198A ASN* 3.0 4.6 + - - +
199A HIS* 3.0 62.6 + + + +
200A PHE* 4.0 24.0 - + - -
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Residues in contact with ALA 196 (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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72A TRP* 3.5 22.0 - - + +
127A LYS* 5.5 2.7 - - + -
192A LEU 2.9 20.0 + - - +
193A GLU* 3.4 5.4 - - - +
195A PHE* 1.3 82.0 - - - +
197A ASN* 1.3 58.0 + - - +
200A PHE* 2.7 57.1 + - + +
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Residues in contact with ASN 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLU* 2.8 38.6 + - - +
194A SER* 3.5 9.4 - - - +
195A PHE 3.0 0.2 + - - -
196A ALA* 1.3 74.8 - - - +
198A ASN* 1.3 62.9 + - - +
201A LEU* 3.1 27.7 - - - +
230A GLN* 3.1 34.2 + - - +
233A THR* 5.9 0.2 - - - +
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Residues in contact with ASN 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A SER* 2.7 34.1 + - - +
195A PHE* 3.0 5.4 + - - +
197A ASN* 1.3 80.3 - - - +
199A HIS* 1.3 68.8 + - + +
201A LEU* 3.7 8.0 - - - +
233A THR* 6.2 2.2 - - - -
234A LYS 4.8 0.2 - - - +
235A PRO* 3.5 27.5 - - - +
236A VAL* 4.3 21.2 + - + +
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Residues in contact with HIS 199 (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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54A PHE* 4.4 1.1 - - + -
56A SER* 3.5 22.8 + - - -
60A ASN* 3.8 32.6 + - + -
195A PHE* 3.0 64.8 + + + +
197A ASN 3.2 0.4 - - - -
198A ASN* 1.3 92.6 + - + +
200A PHE* 1.3 56.5 + - + +
201A LEU* 2.6 19.9 + - - +
204A ASN* 2.9 26.4 + - - +
235A PRO* 4.2 11.4 - - + +
236A VAL* 4.8 18.3 - - + +
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Residues in contact with PHE 200 (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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54A PHE* 3.7 41.6 - + + -
72A TRP* 3.8 39.3 - + - -
101A GLN* 3.7 18.6 - - - -
103A TYR* 3.7 20.9 - + - -
123A PHE* 4.3 22.4 - + + -
127A LYS* 4.8 5.2 - - - -
195A PHE* 4.0 15.0 - + - -
196A ALA* 2.7 38.4 + - + +
199A HIS* 1.3 71.2 - - + +
201A LEU* 1.3 68.7 + - - +
229A LEU* 5.7 3.1 - - - +
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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