Contacts of the strand formed by residues 228 - 232 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138T VAL* 3.7 36.8 - - + +
141T PHE* 3.7 38.8 - + - -
142T TYR* 3.8 40.2 - + + -
200T VAL* 3.9 14.9 + - - +
226T LYS* 4.6 10.5 + - + -
227T VAL* 1.4 75.4 - - - +
229T PHE* 1.4 61.2 + - - +
230T HIS 3.9 0.7 + - - -
250T ASP* 3.9 9.2 - - + +
251T LEU* 4.2 3.1 - - + -
274T PRO* 3.7 33.1 - - + +
275T ARG 4.8 1.3 + - - -
276T VAL* 3.6 28.3 - - + -
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Residues in contact with PHE 229 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T VAL* 3.9 8.1 - - + -
202T VAL* 3.8 23.6 - - + -
203T MET 5.0 0.2 - - - -
215T ILE* 4.4 14.6 - - + -
218T ILE* 3.4 34.5 - - + -
219T GLY* 4.4 15.3 - - - -
222T CYS* 3.6 29.2 - - + -
227T VAL 4.4 0.2 - - - -
228T TYR* 1.4 73.4 - - - +
230T HIS* 1.4 78.1 + - - +
231T THR* 3.3 22.6 + - + -
248T LYS 4.2 13.5 - - - +
249T ILE* 4.2 13.7 - - + -
250T ASP* 3.2 22.7 + - - +
251T LEU* 3.2 25.7 + - - +
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Residues in contact with HIS 230 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130T SER 4.2 1.6 + - - -
131T ASN* 3.2 43.6 + - + -
134T ALA* 3.2 34.0 - - + +
135T ILE* 3.6 23.3 - - + +
138T VAL* 5.3 1.7 - - + +
155T GLU* 5.4 0.4 - - - -
199T LEU* 5.0 6.7 - - + -
200T VAL 3.2 16.9 + - - +
201T SER* 3.7 13.7 + - - -
202T VAL 3.1 13.7 + - - +
228T TYR 3.9 1.8 + - - -
229T PHE* 1.4 79.9 - - - +
231T THR* 1.4 76.2 + - - +
232T ASP* 4.4 9.2 - - + -
251T LEU* 3.9 20.6 - - + +
252T MET 4.8 0.9 - - - -
253T SER* 4.4 5.7 + - - -
268T ILE* 5.9 0.2 - - - +
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Residues in contact with THR 231 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202T VAL 3.4 4.3 - - - +
203T MET* 3.6 5.8 - - - +
204T THR* 3.2 39.3 - - - +
215T ILE* 3.8 14.8 - - + -
229T PHE* 3.3 25.3 - - + -
230T HIS* 1.4 84.6 + - - +
232T ASP* 1.4 56.9 + - - +
233T ALA* 3.3 6.3 + - - -
249T ILE* 3.6 24.2 - - + +
251T LEU 3.3 3.9 + - - -
252T MET* 3.5 7.1 - - - +
253T SER 3.4 17.3 + - - -
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Residues in contact with ASP 232 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127T ALA* 4.3 0.3 - - - +
131T ASN* 3.5 30.9 + - - +
156T HIS* 3.8 10.4 + - - -
201T SER* 6.1 1.1 - - - +
202T VAL 3.7 7.2 + - - +
203T MET* 3.4 33.1 - - + +
204T THR 3.1 16.8 + - - -
205T VAL 3.9 6.4 - - - +
230T HIS* 4.4 4.6 - - + -
231T THR* 1.4 68.9 - - - +
233T ALA* 1.4 58.4 + - - +
234T ALA* 3.1 25.6 + - - +
235T GLN* 3.2 19.2 - - - +
253T SER* 3.4 14.2 + - - -
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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