Contacts of the strand formed by residues 228 - 232 (chain Q) in PDB entry 5KZ5
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 TYR 228 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q VAL* 4.2 20.6 - - + -
141Q PHE* 3.9 25.0 - + - -
142Q TYR* 3.8 42.9 - + + -
198Q SER 5.2 0.4 - - - +
199Q LEU* 4.0 3.6 - - - +
200Q VAL* 3.2 23.9 + - - +
226Q LYS* 4.8 8.5 - - + -
227Q VAL* 1.3 79.8 - - - +
229Q PHE* 1.3 59.0 + - - +
230Q HIS 4.1 0.8 + - - -
250Q ASP* 3.7 6.1 - - - +
251Q LEU* 4.2 3.6 - - + -
274Q PRO* 4.0 24.8 - - + +
275Q ARG 3.4 22.1 + - - -
276Q VAL* 3.6 28.3 - - + -
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Residues in contact with PHE 229 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200Q VAL* 3.6 9.0 - - + -
202Q VAL* 3.8 22.4 - - + -
203Q MET 5.2 0.4 - - - -
215Q ILE* 4.6 10.3 - - + -
218Q ILE* 3.6 34.3 - - + -
219Q GLY* 4.5 13.0 - - - -
222Q CYS* 3.8 25.1 - - + -
228Q TYR* 1.3 74.1 - - - +
230Q HIS* 1.4 78.1 + - - +
231Q THR* 3.3 25.3 + - + -
248Q LYS 4.2 5.6 - - - +
249Q ILE* 3.9 27.6 - - + -
250Q ASP* 3.2 19.7 + - - +
251Q LEU* 3.0 29.7 + - - +
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Residues in contact with HIS 230 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130Q SER 4.3 0.4 + - - -
131Q ASN* 3.2 45.6 + - + -
134Q ALA* 3.5 25.8 - - + +
135Q ILE* 3.7 16.6 - - + +
155Q GLU* 5.3 0.9 - - - -
199Q LEU* 4.1 15.8 - - + +
200Q VAL 3.1 15.3 + - - +
201Q SER* 3.6 15.8 + - - +
202Q VAL 3.3 12.0 - - - +
228Q TYR 4.1 0.6 + - - -
229Q PHE* 1.4 81.6 - - - +
231Q THR* 1.4 73.8 + - - +
232Q ASP* 4.9 2.5 - - + -
251Q LEU* 3.4 23.7 - - + +
252Q MET 4.6 0.6 - - - -
253Q SER* 3.6 17.6 + - - -
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Residues in contact with THR 231 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202Q VAL 3.3 5.2 - - - +
203Q MET 3.7 7.2 - - - +
204Q THR* 3.2 38.4 - - - +
215Q ILE* 4.1 5.2 - - + -
229Q PHE* 3.3 25.2 - - + -
230Q HIS* 1.4 81.4 + - - +
232Q ASP* 1.4 57.5 + - - +
233Q ALA 3.2 6.4 + - - -
249Q ILE* 3.4 32.4 - - + +
251Q LEU 3.2 4.6 + - - -
252Q MET* 3.5 6.0 - - - +
253Q SER 3.3 17.7 + - - -
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Residues in contact with ASP 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q ALA* 4.0 3.1 - - - +
131Q ASN* 3.3 23.0 + - - +
156Q HIS* 4.2 6.8 + - - -
201Q SER* 5.6 1.3 + - - +
202Q VAL 3.7 7.2 + - - +
203Q MET* 3.5 35.9 - - + +
204Q THR 3.0 19.1 + - - -
205Q VAL 3.8 6.8 - - - +
230Q HIS* 4.4 4.0 + - + -
231Q THR* 1.4 67.4 - - - +
233Q ALA* 1.4 56.6 + - - +
234Q ALA* 3.3 15.2 + - - +
235Q GLN* 3.1 22.9 - - - +
253Q SER* 3.0 27.9 + - - -
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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