Contacts of the helix formed by residues 212 - 222 (chain A) 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 GLY 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY* 2.5 21.1 + - - -
211A THR* 1.3 73.7 - - - +
213A ALA* 1.3 64.1 + - - +
214A VAL 3.2 2.7 - - - -
215A ILE* 3.2 10.3 - - - +
216A ASN* 3.2 24.9 + - - +
229A ASN* 2.9 22.1 + - - -
242A TYR* 3.6 9.9 - - - -
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Residues in contact with ALA 213 (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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209A GLY 4.2 1.4 + - - -
211A THR* 3.5 7.3 - - + -
212A GLY* 1.3 78.0 - - - +
214A VAL* 1.3 56.5 - - + +
216A ASN* 3.8 3.6 + - - +
217A THR* 2.7 33.1 + - - -
242A TYR* 3.6 13.9 + - + +
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Residues in contact with VAL 214 (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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184A SER* 3.6 24.2 - - - +
188A MET* 3.8 19.5 - - + +
206A ASP* 3.7 19.1 - - - +
209A GLY* 5.2 3.1 + - - +
212A GLY* 3.2 0.8 - - - -
213A ALA* 1.3 78.6 - - + +
215A ILE* 1.3 66.5 + - - +
217A THR* 3.2 14.4 + - - -
218A ILE* 3.3 15.3 + - + +
263A PHE* 3.8 30.7 - - + -
265A LYS* 4.0 5.8 - - + +
1698A SAH 4.0 19.1 - - - +
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Residues in contact with ILE 215 (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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204A LEU* 3.8 32.1 - - + +
206A ASP* 4.2 22.8 + - + -
212A GLY* 3.2 21.2 - - - +
214A VAL* 1.3 79.8 - - - +
216A ASN* 1.3 64.4 + - - +
218A ILE* 2.9 8.6 + - + +
219A VAL* 2.8 45.1 + - + +
225A ILE* 5.6 0.2 - - + -
227A GLY* 3.7 37.5 - - - -
228A ILE 3.9 3.6 - - - +
229A ASN* 4.1 8.7 - - + -
245A VAL* 3.6 24.0 - - + -
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Residues in contact with ASN 216 (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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212A GLY 3.2 9.5 + - - +
213A ALA 4.0 4.9 - - - +
215A ILE* 1.3 83.1 - - - +
217A THR* 1.3 58.5 + - - +
219A VAL* 4.1 2.5 - - - +
220A SER* 3.0 26.3 + - - -
242A TYR* 2.9 54.7 - - + +
243A PRO* 3.9 16.0 + - - +
245A VAL* 4.1 9.5 - - + +
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Residues in contact with THR 217 (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 MET* 4.8 16.5 - - + +
189A LYS* 5.7 1.6 - - - +
192A LEU* 3.4 30.4 - - + +
213A ALA 2.7 20.3 + - - -
214A VAL* 3.2 9.9 + - - -
215A ILE 3.1 1.0 - - - -
216A ASN* 1.3 78.5 + - - +
218A ILE* 1.3 64.5 + - - +
220A SER* 3.7 7.1 - - - -
221A LYS* 3.4 14.4 + - - +
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Residues in contact with ILE 218 (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 MET* 4.0 14.4 - - + -
192A LEU* 4.4 9.9 - - + -
198A PHE* 3.8 42.6 - - + -
204A LEU* 3.7 27.4 - - + -
206A ASP* 5.5 0.4 - - - +
214A VAL* 3.3 15.3 - - + +
215A ILE* 2.9 13.6 + - + +
217A THR* 1.3 76.0 - - - +
219A VAL* 1.3 60.6 + - + +
220A SER 3.1 1.6 - - - -
221A LYS 3.3 0.5 + - - -
222A TYR* 2.9 39.7 + - + +
225A ILE* 4.8 7.2 - - + -
263A PHE* 4.0 24.5 - - + -
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Residues in contact with VAL 219 (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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215A ILE* 2.8 34.4 + - + +
216A ASN 4.3 3.4 - - - +
218A ILE* 1.3 76.9 - - - +
220A SER* 1.3 58.3 + - - +
222A TYR 3.7 7.6 - - - +
223A PRO* 2.8 35.4 - - + +
225A ILE* 3.7 28.0 - - + +
227A GLY* 3.8 15.9 - - - +
243A PRO 3.7 21.5 - - - +
244A GLY* 4.0 8.3 - - - +
245A VAL* 4.1 9.9 - - + -
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Residues in contact with SER 220 (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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216A ASN* 3.0 24.2 + - - -
217A THR* 3.7 10.5 - - - -
218A ILE 3.1 0.4 - - - -
219A VAL* 1.3 78.8 - - - +
221A LYS* 1.3 60.9 + - - +
222A TYR 3.2 0.8 + - - -
223A PRO* 3.5 15.4 - - - +
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Residues in contact with LYS 221 (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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189A LYS* 5.1 2.4 + - - +
192A LEU* 3.7 50.9 + - + +
193A GLU* 4.6 12.7 - - - +
217A THR 3.4 7.9 + - - +
218A ILE 3.3 2.6 + - - -
220A SER* 1.3 79.5 - - - +
222A TYR* 1.3 85.9 + - + +
223A PRO* 3.6 4.6 - - - +
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Residues in contact with TYR 222 (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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192A LEU* 4.3 13.1 + - + -
195A TYR 4.2 12.8 + - - -
196A THR* 4.2 13.2 - - - +
198A PHE* 3.7 55.1 - + + +
199A GLU* 3.9 15.9 - - + +
218A ILE* 2.9 20.5 + - + +
219A VAL* 3.0 9.2 - - - +
221A LYS* 1.3 111.4 - - + +
223A PRO* 1.3 59.3 - - - +
224A THR* 2.9 13.8 + - - -
225A ILE* 2.9 31.6 + - + +
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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