Contacts of the strand formed by residues 227 - 232 (chain F) in PDB entry 1XSK
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 LYS 227 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189E SER* 6.3 0.6 - - - -
133F GLN* 3.6 17.8 + - - -
136F ASN* 3.8 24.1 + - - +
153F ARG* 3.7 32.8 - - + +
154F LEU 3.5 10.1 - - - +
155F ASP* 3.0 26.2 + - - +
156F LEU* 4.2 6.1 - - - +
219F GLU 3.5 2.8 - - - +
221F GLY 3.0 23.4 + - - -
224F LYS* 3.1 26.4 + - + +
225F VAL 3.4 1.6 + - - -
226F SER* 1.3 96.2 + - - +
228F VAL* 1.3 63.9 + - - +
229F GLN 3.8 0.6 + - - -
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Residues in contact with VAL 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F GLU 3.7 1.6 - - - +
153F ARG* 3.4 1.7 - - - -
154F LEU 3.0 30.5 + - - +
156F LEU* 3.8 15.9 - - + -
162F VAL* 3.8 29.4 - - + -
200F TYR* 3.8 40.4 - - + +
218F PHE* 4.2 13.5 - - + -
219F GLU 3.6 2.7 - - - -
220F VAL* 4.2 25.4 - - + +
227F LYS* 1.3 74.8 - - - +
229F GLN* 1.3 60.8 + - - +
230F PHE* 3.9 5.9 - - + -
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Residues in contact with GLN 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET 3.1 19.0 + - - +
3F ILE* 4.0 13.4 - - + +
151F PHE* 4.4 7.2 - - + -
152F GLU 3.3 5.6 - - - +
153F ARG* 2.7 47.8 + - + +
217F SER 3.6 1.5 + - - +
218F PHE* 3.2 4.9 - - - +
219F GLU* 2.6 59.7 + - + +
223F GLU* 3.0 35.5 + - + +
224F LYS* 4.8 2.9 - - + +
227F LYS* 3.8 1.7 + - + +
228F VAL* 1.3 73.2 - - - +
230F PHE* 1.3 66.8 + - - +
231F SER* 4.8 4.0 + - - -
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Residues in contact with PHE 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F PHE* 3.3 3.8 - - - +
152F GLU* 2.9 63.8 + - + -
154F LEU* 3.9 22.4 - - + -
200F TYR* 4.5 5.2 - - - -
208F VAL* 4.6 3.4 - - + -
210F VAL* 3.5 33.7 - - + -
216F VAL* 4.1 7.2 - - + -
217F SER 3.3 6.1 - - - +
218F PHE* 3.8 26.7 - + + -
228F VAL* 3.9 12.6 - - + -
229F GLN* 1.3 77.8 - - - +
231F SER* 1.3 61.0 + - - +
237F LEU* 3.9 12.7 - - + +
239F TYR* 3.8 32.5 - + + -
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Residues in contact with SER 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.8 42.1 + - - +
3F ILE* 4.7 3.1 - - - -
149F TYR* 4.9 3.6 - - - -
150F MET 3.3 13.2 - - - -
151F PHE* 3.7 12.3 - - - -
215F CYS 4.5 0.2 - - - +
216F VAL* 3.8 4.1 - - - -
217F SER* 3.0 36.6 + - - -
229F GLN* 4.8 2.8 + - - -
230F PHE* 1.3 76.2 - - - +
232F VAL* 1.3 62.5 + - - +
237F LEU* 5.7 1.3 - - - -
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F TYR* 3.4 6.5 - - - -
150F MET* 3.1 23.3 + - + +
212F HIS* 3.7 38.6 - - + +
214F GLN* 3.5 27.8 - - + +
215F CYS 3.7 20.0 - - - +
216F VAL* 4.6 5.2 - - + -
231F SER* 1.3 76.0 - - - +
233F GLU* 1.3 61.0 + - - +
234F SER* 3.0 23.4 + - - -
236F TYR 4.2 2.5 - - - +
237F LEU* 4.0 12.1 - - + -
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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