Contacts of the strand formed by residues 158 - 162 (chain B) in PDB entry 4IRQ
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 4.3 7.1 - - + +
94B ARG* 3.5 18.8 - - - -
95B LEU* 3.4 39.0 - - + +
96B ALA* 2.9 25.8 + - - +
124B ILE* 3.6 11.3 - - - +
156B THR* 3.6 1.4 - - - -
157B ASP* 1.3 93.5 - - - +
159B ILE* 1.3 69.3 + - - +
175B TYR 2.8 22.9 + - - -
176B GLY* 3.5 20.9 - - - -
177B PHE* 3.6 24.3 + + + -
178B PRO* 3.4 16.2 - - + -
205B LEU* 4.0 6.5 - - + -
206B LEU 3.3 12.8 - - - +
207B SER* 3.6 8.1 - - - -
208B LYS* 3.9 4.0 - - - +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.6 3.9 - - - +
96B ALA* 3.3 10.8 - - + -
98B LEU* 3.6 30.3 - - + -
145B ILE* 4.5 1.8 - - + -
149B PHE* 4.0 20.2 - - + -
158B TYR* 1.3 79.4 - - - +
160B ALA* 1.3 60.2 + - - +
161B MET* 4.0 22.4 - - + +
204B LEU 4.5 2.0 - - - +
205B LEU* 3.2 8.7 - - - +
206B LEU* 2.9 42.5 + - + +
207B SER 5.3 0.2 - - - +
208B LYS* 4.1 16.6 - - + -
211B TYR* 3.9 36.8 - - + -
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.6 23.6 - - + -
96B ALA 3.0 9.0 + - - +
97B VAL* 4.5 4.3 - - + -
98B LEU* 2.8 26.7 + - - -
159B ILE* 1.3 75.9 - - - +
161B MET* 1.3 66.6 + - - +
162B HIS* 3.2 16.0 + - + +
175B TYR* 5.2 1.3 - - + -
204B LEU 3.5 6.1 - - - -
205B LEU* 3.8 20.6 - - + -
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Residues in contact with MET 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.3 8.3 - - - -
141B ARG* 3.9 25.6 - - - +
145B ILE* 3.6 26.0 - - + -
159B ILE* 4.0 7.7 - - + +
160B ALA* 1.3 70.9 - - - +
162B HIS* 1.3 58.1 + - - +
202B GLY 3.5 3.1 - - - +
203B ILE* 3.2 5.7 - - - +
204B LEU* 3.0 57.2 + - + +
206B LEU* 4.1 8.1 - - + -
211B TYR* 3.9 16.4 - - + -
217B MET* 3.7 29.6 - - - +
231B PHE* 3.8 28.0 - - + -
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Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 3.8 18.2 - - + -
98B LEU 2.8 9.0 + - - +
99B VAL* 3.5 11.1 - - - +
100B PRO* 3.4 16.8 - - - +
111B PHE* 3.3 18.0 - + + -
115B MET* 3.6 19.0 - - + +
160B ALA* 3.7 12.6 - - + +
161B MET* 1.3 74.5 - - - +
163B ASP* 1.3 86.2 + - - +
164B VAL 3.5 0.9 + - - -
166B LEU 3.0 26.9 - - - -
168B PRO* 4.4 0.4 - - + -
175B TYR* 2.8 34.0 + + - -
202B GLY 3.6 1.6 - - - -
203B ILE* 3.3 28.4 - - + +
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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
------------------------------------------------------------
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