Contacts of the strand formed by residues 203 - 207 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ALA* 5.0 0.2 - - + -
161D MET 3.2 4.9 - - - +
162D HIS* 3.4 49.4 - - + +
166D LEU* 3.8 21.3 - - + +
168D PRO* 4.6 0.4 - - + -
175D TYR* 3.5 17.7 - - + +
184D HIS* 3.4 6.1 - - - -
185D VAL* 3.0 37.6 + - + -
186D ALA* 3.3 8.2 + - + +
201D GLY 3.1 5.9 + - - -
202D GLY* 1.3 78.4 - - - +
204D LEU* 1.3 62.8 + - - +
205D LEU* 4.0 13.0 - - + -
255D PHE* 3.6 27.1 - - + -
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG* 6.0 0.4 - - - +
159D ILE* 3.9 1.0 - - - +
160D ALA* 3.6 0.5 - - - -
161D MET* 2.9 56.1 + - + +
182D PRO* 4.6 7.6 - - + -
183D PHE 3.9 2.5 - - - +
184D HIS* 3.7 36.8 - - + +
200D VAL* 3.7 29.6 - - + +
201D GLY 5.7 0.4 - - - -
202D GLY 4.3 0.2 - - - -
203D ILE* 1.3 75.1 - - - +
205D LEU* 1.3 63.4 + - - +
206D LEU* 3.8 10.7 - - + +
231D PHE* 3.6 36.8 - - + -
235D ILE* 4.5 2.9 - - + -
242D LEU* 4.4 10.3 - - + -
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 5.0 0.4 - - + -
158D TYR* 3.9 14.1 - - + -
159D ILE 3.2 6.3 - - - +
160D ALA* 3.7 24.7 - - + -
174D ASP 4.2 4.3 - - - +
175D TYR* 3.7 42.8 - - + +
176D GLY 3.9 4.9 - - - +
178D PRO* 4.0 11.1 - - + +
182D PRO* 3.2 6.1 - - - +
183D PHE* 2.8 45.9 + - + +
185D VAL* 3.6 27.6 - - + -
203D ILE* 4.0 8.7 - - + -
204D LEU* 1.3 77.3 - - - +
206D LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D TYR* 3.2 1.7 - - - +
159D ILE* 2.9 36.9 + - + +
161D MET* 3.9 20.0 - - + -
178D PRO* 3.8 8.1 - - - -
182D PRO* 3.9 25.4 - - + -
204D LEU* 3.8 26.5 - - + +
205D LEU* 1.3 81.7 - - - +
207D SER* 1.3 68.1 - - - +
210D HIS* 4.2 8.1 - - + +
211D TYR* 3.9 30.1 - - + +
214D CYS* 4.6 4.0 - - - -
231D PHE* 3.7 23.8 - - + -
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Residues in contact with SER 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D TYR* 3.7 9.9 - - - -
159D ILE* 5.8 0.2 - - - -
177D PHE* 3.8 27.1 - - - -
178D PRO* 3.7 17.1 + - - +
179D GLU* 5.2 3.1 + - - -
206D LEU* 1.3 75.8 - - - +
208D LYS* 1.3 66.0 + - - +
209D GLN* 3.9 9.3 + - - +
210D HIS* 3.2 34.4 + - - +
211D TYR* 3.0 21.0 + - - +
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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