Contacts of the strand formed by residues 175 - 182 (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 MET 175 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224R ILE 5.8 0.4 - - - +
227R LEU* 4.3 29.8 - - + -
228R GLY 5.9 0.9 - - - -
231R ARG* 5.0 3.4 - - - +
8S SER* 4.3 22.2 - - - +
10S VAL 5.8 2.2 - - - +
12S VAL* 3.6 8.6 - - - +
40S GLY 4.7 5.2 - - - +
43S GLY* 4.0 30.3 - - - +
44S ASN* 4.6 5.8 - - - +
169T VAL* 3.9 0.9 - - - +
170T ASP* 2.9 31.4 + - + +
173T GLU* 3.2 26.0 - - + +
174T GLN* 1.3 85.1 - - - +
176T ALA* 1.3 69.3 + - - +
177T ARG* 3.3 2.9 + - + +
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Residues in contact with ALA 176 (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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10S VAL* 4.1 20.0 + - + +
12S VAL* 3.7 11.7 - - + +
167T ILE* 3.7 25.4 - - + -
168T TRP 3.8 5.8 - - - -
169T VAL* 4.6 0.9 - - - +
175T MET* 1.3 78.3 - - - +
177T ARG* 1.3 60.5 + - - +
178T PHE 5.0 0.2 - - - +
193T MET* 3.4 34.4 - - + +
194T GLN* 5.3 1.4 - - - +
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Residues in contact with ARG 177 (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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227S SER 5.1 1.0 + - - -
229S PHE 5.4 0.2 - - - -
230S GLY* 4.1 22.8 - - - +
232S GLU* 4.5 14.1 + - - -
233S CYS* 4.4 18.1 - - - -
236S GLU* 5.2 2.0 + - - -
130T LYS* 5.8 0.4 - - - +
131T ILE* 3.8 14.5 - - + +
168T TRP 2.9 9.8 + - - +
170T ASP* 3.5 43.5 + - + +
175T MET* 3.3 4.9 + - - +
176T ALA* 1.3 75.3 - - - +
178T PHE* 1.3 93.0 + - + +
193T MET* 2.9 23.8 + - - +
194T GLN* 3.8 19.1 + - - +
230T GLU* 2.6 36.8 + - - -
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Residues in contact with PHE 178 (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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131T ILE* 4.1 27.1 - - + -
167T ILE* 3.6 7.6 - - - +
168T TRP* 2.7 50.0 + - + +
176T ALA 3.7 0.2 - - - -
177T ARG* 1.3 105.2 - - + +
179T LEU* 1.3 62.2 + - - +
190T LEU* 4.2 31.4 - - + -
191T LEU 3.3 7.9 - - - +
192T PRO* 3.8 19.1 - - + -
193T MET* 4.1 4.1 - - - +
225T VAL* 4.4 7.0 - - + -
230T GLU* 3.7 26.2 - - + -
233T ILE* 4.8 9.2 - - + -
234T CYS* 4.1 22.9 - - - -
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Residues in contact with LEU 179 (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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148T PRO* 3.7 28.9 - - + -
164T VAL* 4.2 13.0 - - + -
166T ASP 3.6 4.3 - - - +
167T ILE* 3.6 30.7 - - + -
178T PHE* 1.3 77.7 - - - +
180T GLU* 1.3 60.8 + - - +
181T VAL* 3.6 11.0 + - + +
190T LEU* 3.5 3.3 - - - -
191T LEU* 3.0 35.7 + - + +
193T MET* 3.6 23.3 - - + -
196T VAL* 3.9 26.0 - - + -
198T VAL* 4.8 0.2 - - + -
203T VAL* 4.2 15.0 - - + -
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Residues in contact with GLU 180 (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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133T PRO* 4.8 2.3 - - - +
135T LYS* 5.8 1.6 - - - +
164T VAL* 3.3 7.1 - - - +
165T VAL* 2.8 45.8 + - + +
166T ASP* 2.7 29.8 + - + +
168T TRP* 2.9 40.7 + - + +
178T PHE 4.2 0.4 - - - -
179T LEU* 1.3 71.5 - - - +
181T VAL* 1.3 57.4 + - - +
188T THR* 3.0 34.6 + - - +
189T ARG 3.5 6.1 - - - +
190T LEU* 3.8 11.2 - - + -
219T ILE* 6.4 0.4 - - - -
222T PRO* 5.0 6.4 - - - +
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Residues in contact with VAL 181 (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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153T VAL* 3.5 40.2 - - + -
162T GLY* 4.2 3.8 - - - -
163T LYS 3.3 11.7 - - - +
164T VAL* 4.7 2.2 - - + -
179T LEU* 3.9 13.2 - - + +
180T GLU* 1.3 79.3 - - - +
182T GLU* 1.3 67.8 + - - +
183T LEU* 3.8 3.5 + - + +
188T THR* 3.2 4.6 - - - -
189T ARG* 2.8 40.6 + - + +
191T LEU* 3.6 32.1 - - + -
203T VAL* 6.4 0.4 - - + -
213T PHE* 4.6 11.4 - - + -
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Residues in contact with GLU 182 (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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162T GLY* 3.0 25.8 - - - -
163T LYS* 2.8 40.0 + - + +
165T VAL* 3.7 28.7 - - + +
180T GLU 4.2 0.4 - - - -
181T VAL* 1.3 72.7 - - - +
183T LEU* 1.3 70.7 + - - +
186T GLY* 3.7 31.2 - - - +
187T SER 3.4 4.0 - - - +
188T THR* 4.0 10.0 - - + +
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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