Contacts of the helix formed by residues 203 - 213 (chain C) in PDB entry 4IYM
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 ASP 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ARG* 3.0 33.4 + - - -
35C LEU* 3.9 16.4 - - + +
36C ALA 5.3 1.7 - - - +
171C LYS* 4.3 2.9 - - - +
174C GLU* 3.8 18.2 - - - +
202C GLY* 1.3 75.2 - - - -
204C LYS* 1.3 66.5 + - - +
205C GLY* 2.9 18.7 + - - -
206C ALA* 3.1 11.9 + - - +
207C VAL* 3.2 18.9 + - - +
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Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ASP* 1.3 79.7 - - + +
205C GLY* 1.3 61.7 + - - +
207C VAL* 3.2 10.2 + - + +
208C ASP* 2.9 50.5 + - - +
230C TYR* 3.4 28.3 + - + -
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Residues in contact with GLY 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ARG* 6.1 1.1 - - - -
36C ALA 4.8 5.8 - - - -
38C ASP* 4.4 6.4 - - - +
203C ASP* 2.9 12.9 + - - -
204C LYS* 1.3 78.1 - - - +
206C ALA* 1.3 59.4 + - - +
208C ASP* 3.5 6.6 + - - +
209C ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ALA* 4.2 25.2 + - + +
37C SER 5.8 0.9 - - - -
41C LEU* 4.7 3.1 - - + +
171C LYS* 4.1 15.0 - - + -
200C VAL* 4.6 5.2 - - + -
201C ASN 4.5 0.2 - - - +
202C GLY* 4.0 21.3 - - - -
203C ASP* 3.1 12.4 + - - +
205C GLY* 1.3 72.6 - - - +
207C VAL* 1.3 61.2 + - - +
209C ALA* 3.3 8.1 + - - +
210C ILE* 2.9 33.9 + - + +
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE* 3.8 33.9 - - + -
171C LYS* 3.7 21.8 - - + +
203C ASP 3.4 15.5 - - - +
204C LYS* 3.2 12.2 + - + +
206C ALA* 1.3 75.9 - - - +
208C ASP* 1.3 60.1 + - - +
210C ILE* 3.1 11.3 + - - +
211C LEU* 2.9 47.6 + - + +
227C ILE* 6.1 1.8 - - + -
230C TYR* 5.0 4.3 - - + -
231C VAL* 4.3 10.5 - - + -
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Residues in contact with ASP 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LYS* 2.9 45.8 + - - +
205C GLY* 3.9 5.3 - - - +
207C VAL* 1.3 73.8 - - - +
209C ALA* 1.3 63.8 + - - +
211C LEU* 4.2 6.8 - - - +
212C THR* 2.9 36.9 + - + +
230C TYR* 2.5 34.5 + - - -
234C THR* 5.3 1.4 - - - +
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER 5.3 0.9 - - - +
38C ASP* 3.7 25.8 - - + +
41C LEU* 3.6 26.1 - - + +
205C GLY 3.1 14.7 + - - +
206C ALA* 3.5 11.2 - - - +
208C ASP* 1.3 75.8 - - - +
210C ILE* 1.3 61.2 + - - +
212C THR* 3.9 5.2 + - - -
213C HIS* 3.2 26.5 + - - +
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Residues in contact with ILE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.8 23.1 - - + -
142C ALA* 3.6 30.7 - - + -
144C ILE* 4.5 9.6 - - + -
169C ILE* 4.9 5.6 - - + -
171C LYS* 3.7 33.2 - - + +
200C VAL* 5.9 0.7 - - + -
206C ALA* 2.9 21.6 + - + +
207C VAL* 3.3 10.3 - - - +
209C ALA* 1.3 77.3 - - - +
211C LEU* 1.3 65.3 + - + +
212C THR 3.3 0.9 + - - -
213C HIS 3.4 5.5 + - - -
216C ILE* 3.7 19.2 - - + +
219C VAL* 4.3 19.3 - - + -
240C LYS* 3.4 12.8 - - - -
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE* 4.7 3.6 - - + -
207C VAL* 2.9 38.3 + - + +
208C ASP* 3.2 8.7 + - - +
210C ILE* 1.3 74.0 - - + +
212C THR* 1.3 59.2 + - + +
219C VAL* 4.1 20.0 - - + -
230C TYR* 4.0 15.0 - - + -
231C VAL* 3.9 35.9 - - + +
234C THR* 3.9 34.7 - - + +
235C ALA* 4.1 12.2 - - + +
238C ASN* 3.2 18.0 - - - +
240C LYS* 3.1 20.2 - - - +
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Residues in contact with THR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ASP* 2.9 24.7 + - + +
209C ALA* 3.9 5.4 + - - -
211C LEU* 1.3 81.1 - - + +
213C HIS* 1.3 63.9 + - - +
214C PRO* 3.4 9.2 - - - +
234C THR* 5.3 4.3 - - + -
238C ASN* 3.6 25.1 - - - +
240C LYS* 4.5 0.9 - - - -
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Residues in contact with HIS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.8 20.2 - - + -
42C ALA* 4.5 14.1 + - + +
45C VAL* 3.4 31.0 - - + +
46C GLU* 5.1 3.6 + - - -
209C ALA 3.2 16.2 + - - +
210C ILE 3.4 7.2 + - - +
212C THR* 1.3 76.1 - - - +
214C PRO* 1.3 71.6 - - + +
215C ASP* 3.1 47.3 + - - +
216C ILE* 3.2 15.9 + - + -
240C LYS* 2.7 25.8 + - - -
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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