Contacts of the strand formed by residues 188 - 192 (chain T) in PDB entry 1RZZ
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 THR 188 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165T VAL* 4.3 10.1 - - + -
180T GLU* 3.0 32.6 + - - +
181T VAL 3.2 7.4 - - - -
182T GLU* 4.0 22.0 - - + +
186T GLY 4.3 3.8 - - - +
187T SER* 1.3 80.0 - - - +
189T ARG* 1.3 80.7 + - - +
218T THR* 4.6 4.7 - - - +
219T ILE* 5.9 4.7 - - - +
222T PRO* 6.0 1.6 - - - +
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Residues in contact with ARG 189 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179T LEU 3.6 0.3 - - - +
180T GLU* 3.5 5.0 - - - +
181T VAL* 2.8 34.1 + - - +
183T LEU* 3.6 23.0 - - + +
185T ASP* 4.9 4.2 + - - -
187T SER* 2.8 32.3 + - - -
188T THR* 1.3 89.2 + - - +
190T LEU* 1.3 64.4 + - - +
191T LEU* 4.3 4.9 - - + -
213T PHE 3.6 14.1 - - - +
214T ALA* 3.1 24.4 + - - +
216T ILE* 3.0 48.4 + - + -
217T PRO 4.2 3.6 - - - -
218T THR* 3.4 24.4 - - - +
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Residues in contact with LEU 190 (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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168T TRP* 3.5 50.9 - - + +
178T PHE* 4.2 21.1 - - + -
179T LEU 3.5 2.5 - - - +
180T GLU* 3.8 17.5 - - + -
189T ARG* 1.3 74.8 - - - +
191T LEU* 1.3 64.6 + - - +
192T PRO* 4.1 0.2 - - - +
216T ILE* 4.1 7.5 - - - +
217T PRO 5.5 0.8 + - - -
219T ILE* 4.3 15.5 - - + -
225T VAL* 4.1 31.9 - - + -
233T ILE* 3.2 41.0 - - + +
237T VAL* 5.0 0.2 - - - +
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Residues in contact with LEU 191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178T PHE* 3.3 4.8 - - - -
179T LEU* 3.0 34.8 + - + +
181T VAL* 3.6 30.7 - - + -
189T ARG* 4.2 5.8 - - + +
190T LEU* 1.3 81.0 - - - +
192T PRO* 1.3 77.0 - - + +
193T MET* 3.2 1.0 + - - -
195T MET 5.6 0.2 - - - +
196T VAL* 4.0 17.5 - - + -
205T VAL* 4.2 27.8 - - + -
208T LEU* 4.7 1.1 - - + -
213T PHE* 4.2 13.5 - - + -
216T ILE* 3.9 28.7 - - + -
237T VAL* 4.4 11.0 - - + -
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Residues in contact with PRO 192 (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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228S ARG 4.0 6.7 - - - +
178T PHE* 3.8 12.1 - - + -
190T LEU 4.1 3.1 - - - +
191T LEU* 1.3 85.0 - - + +
193T MET* 1.3 65.0 + - - +
194T GLN* 3.3 17.7 - - - +
195T MET* 3.0 30.7 + - + +
196T VAL* 3.4 11.6 - - - +
233T ILE* 4.4 2.2 - - + -
234T CYS* 3.7 35.7 - - - +
237T VAL* 3.8 28.0 - - + -
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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