Contacts of the strand formed by residues 139 - 142 (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 GLN 139 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137Y LYS 5.4 2.2 - - - +
138Y LEU* 1.3 73.6 - - - +
140Y TRP* 1.3 64.7 + - - +
141Y TYR* 3.2 29.2 + - + -
149Y LEU* 5.5 2.5 - - - -
176Y CYS* 4.6 0.2 - - - -
177Y HIS* 2.9 54.6 + - + +
178Y ALA* 5.2 1.4 + - - -
179Y SER* 5.5 2.8 + - - -
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Residues in contact with TRP 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120Y LEU* 4.1 10.3 - - + -
122Y CYS* 3.8 38.8 - - + -
138Y LEU* 4.1 19.7 + - + +
139Y GLN* 1.3 75.1 - - - +
141Y TYR* 1.3 70.4 + - - +
146Y PRO* 4.3 0.3 - - - +
147Y LEU* 3.3 40.9 + - + +
149Y LEU* 4.2 24.4 - - + +
156Y GLY* 4.9 3.9 - - - -
158Y LYS 5.5 1.0 + - - -
159Y ASP 4.0 7.6 - - - -
160Y ARG 4.0 8.0 + - - +
161Y LEU* 3.7 50.0 - - + +
174Y TYR* 4.2 18.6 - - + -
175Y THR 3.5 3.6 - - - -
176Y CYS* 3.9 19.1 - - + -
193Y ILE* 3.8 21.5 - - + -
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Residues in contact with TYR 141 (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* 6.3 0.2 - - - -
139Y GLN* 3.2 40.1 + - + -
140Y TRP* 1.3 78.6 - - - +
142Y LYS* 1.3 59.4 + - - +
143Y ASP 4.1 0.2 - - - -
144Y CYS* 4.2 12.3 - - - -
145Y LYS 3.4 13.2 - - - +
146Y PRO* 3.5 37.2 - - + -
147Y LEU* 4.1 5.2 - - - -
174Y TYR* 3.1 11.4 - - - +
175Y THR* 3.0 39.6 + - - +
177Y HIS* 3.2 41.1 - + - -
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Residues in contact with LYS 142 (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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141Y TYR* 1.3 73.5 - - - +
143Y ASP* 1.3 89.7 + - - +
145Y LYS* 2.9 26.9 + - - +
147Y LEU* 3.7 23.9 - - + +
154Y PHE* 5.5 2.5 - - + -
169Y LYS 4.0 15.0 + - - -
170Y HIS* 3.8 4.3 - - - +
171Y ARG 3.5 22.7 + - - -
172Y GLY* 4.9 0.4 - - - -
173Y ASN 3.9 2.5 - - - -
174Y TYR* 3.4 39.5 - - + +
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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