Contacts of the strand formed by residues 203 - 207 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C MET 3.1 5.2 - - - +
162C HIS* 3.4 47.8 - - + -
166C LEU* 3.9 21.1 - - + +
168C PRO* 4.9 0.4 - - + -
175C TYR* 3.6 15.3 - - - +
184C HIS* 3.3 10.0 - - - -
185C VAL* 3.1 36.7 + - + -
186C ALA* 3.4 5.7 + - + +
201C GLY 3.2 3.8 + - - -
202C GLY* 1.3 82.2 - - - +
204C LEU* 1.3 63.3 + - - +
205C LEU* 3.8 13.5 - - + -
255C PHE* 3.7 27.6 - - + -
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ILE* 4.0 0.9 - - - +
160C ALA* 3.7 0.2 - - - -
161C MET* 2.9 49.4 + - + +
182C PRO* 4.6 3.8 - - + -
183C PHE 3.6 21.1 - - - +
184C HIS* 3.7 12.1 - - + +
200C VAL* 3.5 49.1 - - + +
201C GLY 5.6 0.2 - - - -
203C ILE* 1.3 76.1 - - - +
205C LEU* 1.3 63.7 + - - +
206C LEU* 3.9 11.5 - - + +
231C PHE* 3.6 34.8 - - + -
235C ILE* 4.5 1.1 - - + -
242C LEU* 4.1 8.1 - - + -
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 4.9 0.4 - - + -
158C TYR* 4.1 7.9 - - + -
159C ILE 3.3 6.5 - - - +
160C ALA* 3.5 26.0 - - + -
174C ASP 4.1 5.8 - - - +
175C TYR* 3.7 46.7 - - + +
176C GLY 4.0 7.6 - - - +
178C PRO* 4.0 12.9 - - + +
182C PRO* 3.3 6.1 - - - +
183C PHE* 2.8 44.7 + - + +
185C VAL* 3.8 13.9 - - + -
203C ILE* 3.8 19.5 - - + -
204C LEU* 1.3 76.4 - - - +
206C LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C TYR* 3.2 1.9 - - - +
159C ILE* 3.0 36.7 + - + +
161C MET* 3.9 20.4 - - + -
178C PRO* 3.7 8.7 - - - -
182C PRO* 3.7 29.4 - - + -
204C LEU* 3.9 23.6 - - + +
205C LEU* 1.3 83.0 - - - +
207C SER* 1.3 68.6 + - - +
210C HIS* 4.2 7.0 - - + +
211C TYR* 4.1 29.6 - - + +
214C CYS* 4.8 3.6 - - - -
231C PHE* 3.8 24.2 - - + -
235C ILE* 5.0 0.4 - - + -
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Residues in contact with SER 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PHE* 5.2 0.2 - - - -
157C ASP 4.3 0.2 - - - -
158C TYR* 3.7 10.3 - - - -
177C PHE* 3.8 28.9 - - - -
178C PRO* 3.7 12.6 + - - +
179C GLU* 5.7 0.7 - - - -
206C LEU* 1.3 77.3 - - - +
208C LYS* 1.3 63.8 + - - +
209C GLN* 3.5 10.4 + - - +
210C HIS* 3.0 36.1 + - - +
211C TYR* 3.0 21.5 + - - +
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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