Contacts of the strand formed by residues 203 - 207 (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 ILE 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ALA* 5.2 0.2 - - + -
161B MET 3.2 4.0 - - - +
162B HIS* 3.3 44.2 - - + +
166B LEU* 3.8 22.2 - - + +
168B PRO* 5.0 0.7 - - + -
175B TYR* 3.3 26.5 - - + +
184B HIS* 3.3 6.3 - - - -
185B VAL* 3.1 34.6 + - + -
186B ALA* 3.3 9.8 + - + +
201B GLY 3.1 4.6 + - - -
202B GLY* 1.3 79.2 - - - +
204B LEU* 1.3 61.8 + - - +
205B LEU* 4.0 8.7 - - + -
255B PHE* 3.8 26.7 - - + -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.0 1.0 - - - +
160B ALA* 3.5 0.5 - - - -
161B MET* 3.0 54.4 + - + +
182B PRO* 4.5 2.2 - - + -
183B PHE 3.6 16.8 - - - +
184B HIS* 3.8 18.6 - - + +
200B VAL* 3.8 30.3 - - + +
201B GLY 5.6 0.2 - - - -
203B ILE* 1.3 76.1 - - - +
205B LEU* 1.3 70.8 + - - +
206B LEU* 3.7 9.7 + - + +
217B MET* 6.0 0.2 - - + -
231B PHE* 3.7 35.9 - - + -
235B ILE* 4.4 3.4 - - + -
242B LEU* 4.4 11.0 - - + -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 5.1 0.7 - - + -
158B TYR* 4.0 13.2 - - + -
159B ILE 3.2 13.7 - - - +
160B ALA* 3.8 17.3 - - + -
174B ASP 4.3 4.5 - - - +
175B TYR* 3.8 44.2 - - + +
176B GLY 4.1 4.3 - - - +
178B PRO* 4.1 11.6 - - + +
182B PRO* 3.2 5.0 - - - +
183B PHE* 2.8 44.6 + - + +
185B VAL* 3.7 25.1 - - + -
203B ILE* 4.0 9.6 - - + -
204B LEU* 1.3 78.7 - - - +
206B LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.3 2.5 - - - +
159B ILE* 2.9 33.9 + - + +
161B MET* 4.1 10.5 - - + -
178B PRO* 3.9 9.6 - - - -
182B PRO* 3.8 27.1 - - + -
204B LEU* 3.7 24.2 + - + +
205B LEU* 1.3 83.1 - - - +
207B SER* 1.3 68.7 + - - +
210B HIS* 4.0 8.1 - - + +
211B TYR* 3.8 30.5 - - + +
214B CYS* 4.6 4.3 - - - -
231B PHE* 3.7 32.1 - - + -
235B ILE* 4.9 0.4 - - + -
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASP 4.3 0.4 - - - -
158B TYR* 3.6 11.4 - - - -
177B PHE* 3.8 27.8 - - - -
178B PRO* 3.8 10.8 - - - +
179B GLU* 6.0 0.2 - - - -
206B LEU* 1.3 76.2 - - - +
208B LYS* 1.3 60.3 + - - +
209B GLN* 3.6 10.2 + - - +
210B HIS* 2.8 41.0 + - - +
211B TYR* 2.8 25.5 + - - +
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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
------------------------------------------------------------
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