Contacts of the strand formed by residues 172 - 182 (chain Y) in PDB entry 1IRA
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 GLY 172 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142Y LYS* 4.6 0.7 - - - -
143Y ASP* 3.7 15.3 - - - -
170Y HIS 3.5 2.4 + - - -
171Y ARG* 1.3 75.9 - - - +
173Y ASN* 1.3 61.6 + - - -
174Y TYR* 3.4 14.1 - - - -
195Y PHE 3.0 24.0 + - - -
401Y NAG 3.5 22.6 - - - +
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Residues in contact with ASN 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y TYR* 3.1 32.4 + - + +
107Y ILE* 3.6 8.4 - - - +
143Y ASP* 2.8 41.7 + - - +
144Y CYS 4.5 0.7 + - - -
172Y GLY* 1.3 70.8 - - - -
174Y TYR* 1.3 59.9 + - - +
175Y THR* 4.1 1.4 + - - +
192Y VAL* 4.3 5.8 - - + -
193Y ILE 3.4 3.9 - - - +
194Y GLU* 3.1 27.4 + - - +
401Y NAG 1.5 57.9 + - - +
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Residues in contact with TYR 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Y LEU* 4.4 9.0 - - + -
140Y TRP* 4.2 15.3 - + + -
141Y TYR 3.1 15.0 - - - +
142Y LYS* 3.4 29.0 - - + +
147Y LEU* 3.8 16.2 - - + -
154Y PHE* 4.0 13.0 - + - -
161Y LEU* 3.7 31.4 - - + -
163Y VAL* 5.3 1.0 - - + +
170Y HIS* 2.7 39.3 + - - +
172Y GLY 3.4 17.3 - - - -
173Y ASN* 1.3 75.9 - - - +
175Y THR* 1.3 61.9 + - - +
191Y ARG 3.8 0.3 - - - +
192Y VAL* 3.5 3.1 - - - +
193Y ILE* 2.7 39.6 + - + +
195Y PHE* 3.8 18.6 - + + -
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Residues in contact with THR 175 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Y CYS* 4.1 16.7 - - - +
102Y TYR* 4.1 21.3 - - + -
140Y TRP* 3.5 4.2 - - - -
141Y TYR* 3.0 40.9 + - - +
144Y CYS 4.8 1.4 + - - -
173Y ASN 5.0 0.4 - - - +
174Y TYR* 1.3 80.0 - - - +
176Y CYS* 1.3 59.5 + - - +
177Y HIS* 3.2 29.6 + - - +
190Y THR* 5.4 4.7 - - - -
191Y ARG 3.3 7.4 - - - +
192Y VAL* 3.9 24.2 - - + -
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Residues in contact with CYS 176 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Y CYS* 2.0 57.5 - - + -
125Y MET* 6.1 0.2 - - - +
138Y LEU* 4.6 5.2 - - + -
139Y GLN 3.7 4.3 - - - +
140Y TRP* 3.9 28.0 - - + +
174Y TYR 4.3 0.2 - - - -
175Y THR* 1.3 73.0 - - - +
177Y HIS* 1.3 61.3 + - - +
189Y ILE 3.6 0.7 - - - +
190Y THR* 3.1 25.3 - - - -
191Y ARG* 3.1 24.4 + - - -
193Y ILE* 4.4 2.2 - - - -
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Residues in contact with HIS 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Y CYS* 5.3 11.8 + - - +
137Y LYS 3.9 0.3 - - - +
138Y LEU* 3.1 9.9 - - - -
139Y GLN* 2.9 50.7 + - + +
141Y TYR* 3.2 34.9 - + - -
175Y THR* 3.2 38.8 + - - +
176Y CYS* 1.3 76.1 - - - +
178Y ALA* 1.3 61.5 + - - +
189Y ILE 3.2 4.9 - - - +
190Y THR* 3.4 22.9 - - + +
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Residues in contact with ALA 178 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Y MET* 3.8 17.7 - - + -
136Y PRO* 3.9 13.2 - - + -
137Y LYS 4.2 7.2 - - - +
138Y LEU* 3.3 23.3 - - + -
139Y GLN* 5.2 1.8 + - - -
177Y HIS* 1.3 75.6 - - - +
179Y SER* 1.3 67.2 + - - +
180Y TYR 4.2 0.2 - - - -
188Y PRO* 3.4 3.8 - - - +
189Y ILE* 2.8 35.6 + - + +
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Residues in contact with SER 179 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Y PRO* 4.1 16.6 - - - +
137Y LYS 5.0 1.4 + - - -
139Y GLN* 5.5 2.6 + - - -
178Y ALA* 1.3 79.4 + - - +
180Y TYR* 1.3 62.2 + - - +
181Y THR* 4.1 3.1 + - - -
186Y GLN* 3.5 33.5 + - - -
187Y TYR 3.3 5.6 - - - -
188Y PRO* 4.7 3.8 - - - +
189Y ILE* 4.9 0.4 - - - -
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Residues in contact with TYR 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Y ILE* 3.9 23.1 - - + -
62Y TRP* 4.1 20.7 - + - -
127Y PHE 4.7 2.9 + - - -
128Y PHE* 3.7 44.0 - + + -
129Y LYS 4.5 11.7 + - - -
130Y ASN* 5.0 5.1 - - + -
136Y PRO* 5.4 3.8 - - + -
178Y ALA 4.2 0.8 - - - -
179Y SER* 1.3 72.6 - - - +
181Y THR* 1.3 73.7 + - - +
182Y TYR* 3.5 29.0 + + + -
186Y GLN* 3.5 2.1 - - - -
187Y TYR* 2.8 38.3 + - - +
189Y ILE* 3.7 21.7 - - + +
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Residues in contact with THR 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179Y SER 4.1 3.2 + - - -
180Y TYR* 1.3 88.1 - - - +
182Y TYR* 1.3 58.5 + - - +
183Y LEU 4.0 1.2 + - - -
184Y GLY* 3.7 21.8 - - - +
185Y LYS 3.2 15.9 - - - +
186Y GLN* 4.2 14.6 + - + +
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Residues in contact with TYR 182 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Y ILE* 4.0 11.2 - - + -
50Y GLN* 3.1 28.3 + - - -
55Y HIS* 2.7 42.6 + + - -
57Y HIS* 3.9 14.1 + + - +
62Y TRP* 4.0 20.5 - + - -
64Y VAL* 3.5 26.9 - - + -
180Y TYR* 3.5 22.5 + + + -
181Y THR* 1.3 72.8 - - - +
183Y LEU* 1.3 88.5 - - + +
184Y GLY 3.4 0.4 - - - -
185Y LYS* 2.8 19.5 + - - +
187Y TYR* 3.7 24.8 + - + -
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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