Contacts of the strand formed by residues 221 - 226 (chain B) in PDB entry 1KY9
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 LEU 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B VAL* 4.5 6.7 - - + -
93B ILE* 3.9 19.3 - - + -
101B VAL* 4.9 0.7 - - + -
150B ILE* 3.9 12.9 - - + +
151B LYS 2.9 16.6 + - - +
152B MSE 3.6 25.8 - - + -
153B ALA* 2.9 25.8 + - - +
213B ALA* 4.2 17.0 - - + -
214B LEU 3.6 15.7 - - - +
215B VAL* 4.0 5.7 - - + +
219B GLY 4.0 0.8 + - - -
220B GLU* 1.3 69.9 - - - +
222B ILE* 1.3 59.4 - - - +
223B GLY 3.6 15.0 - - - +
224B ILE* 3.6 26.2 - - + -
244B SER* 3.2 13.5 + - - -
247B VAL* 5.1 4.5 - - + -
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ALA* 4.2 6.3 - - + -
154B ASP 6.3 0.2 - - - -
155B SER* 3.6 4.7 + - - -
158B LEU* 4.1 34.8 - - + +
163B TYR 4.8 1.8 - - - +
164B THR* 3.5 24.9 - - - +
182B VAL* 5.0 2.5 - - + -
199B ILE* 3.7 6.8 - - - +
214B LEU* 2.8 33.9 + - + +
215B VAL 3.9 13.7 - - - +
216B ASN* 3.7 29.2 - - + +
220B GLU 3.6 10.1 - - - +
221B LEU* 1.3 77.1 - - - +
223B GLY* 1.3 55.1 + - - +
243B PRO* 3.5 5.2 - - - +
244B SER* 2.6 32.3 + - - -
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Residues in contact with GLY 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ILE* 4.8 0.4 - - - -
214B LEU* 2.8 36.3 + - - +
221B LEU* 3.6 2.4 - - - +
222B ILE* 1.3 81.5 - - - +
224B ILE* 1.3 71.5 + - - +
241B ALA* 4.3 5.4 - - - -
242B ILE 2.8 15.5 - - - -
243B PRO* 4.2 0.2 - - - -
244B SER* 3.7 5.9 - - - -
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL* 4.9 5.2 - - + -
101B VAL* 3.9 32.3 - - + +
102B THR* 5.0 6.3 - - - -
103B ASN* 3.9 15.0 - - - +
136B ILE* 3.8 25.8 - - + -
212B GLY* 3.1 13.5 - - - +
213B ALA* 5.0 0.2 - - - -
221B LEU* 3.6 35.7 - - + -
223B GLY* 1.3 75.8 - - - +
225B ASN* 1.3 74.7 + - - +
226B THR* 3.6 0.7 + - - -
241B ALA* 3.8 1.6 - - - -
242B ILE* 2.9 31.1 + - + +
247B VAL* 4.2 10.2 - - + +
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Residues in contact with ASN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 2.7 27.2 + - - -
166B ALA* 3.9 12.3 - - - +
201B THR* 4.3 13.3 - - - +
203B ALA 4.9 4.6 + - - -
210B ALA* 4.8 1.1 - - - -
211B GLY* 3.3 17.8 - - - +
212B GLY 2.3 43.6 + - - +
213B ALA 3.3 18.9 - - - +
214B LEU* 3.8 14.7 - - - +
224B ILE* 1.3 67.9 - - - +
226B THR* 1.3 53.5 + - - +
239B GLY* 4.9 3.0 - - - -
240B PHE 3.7 10.9 + - - +
241B ALA* 3.8 14.7 - - - +
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 3.7 7.2 - - - +
134B SER 4.2 3.5 + - - -
135B ASP* 2.6 29.3 + - - +
136B ILE* 6.4 0.2 - - - -
198B PHE* 3.6 27.3 - - + -
210B ALA* 3.0 17.8 - - - +
224B ILE* 4.5 2.7 - - - -
225B ASN* 1.3 76.0 - - - +
227B ALA* 1.3 78.0 + - - +
228B ILE* 4.2 4.5 + - + +
235B ASN* 6.1 0.9 - - - +
240B PHE* 2.7 43.8 + - + +
241B ALA* 4.3 3.1 - - - -
242B ILE* 4.6 4.9 - - + +
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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