Contacts of the strand formed by residues 224 - 232 (chain C) in PDB entry 1IVH
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 LEU 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C ALA* 3.6 31.6 - - + -
163C ASN* 2.8 26.8 - - - +
164C LYS* 2.8 26.9 + - + -
167C ILE* 3.7 26.5 - - + -
170C GLY* 4.5 1.1 - - - -
176C LEU* 3.6 22.4 - - + -
178C VAL* 4.5 2.5 - - + -
205C PHE* 3.7 17.7 - - + -
206C SER 3.8 3.1 - - - -
207C THR* 4.2 6.5 - - + -
222C CYS* 4.1 12.6 - - - -
223C GLU* 1.3 79.5 - - - +
225C ILE* 1.3 61.0 + - - +
226C PHE* 4.0 14.4 - - + -
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Residues in contact with ILE 225 (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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162C GLY 3.9 3.8 - - - +
163C ASN* 4.5 4.0 - - + -
204C GLY 3.1 4.9 - - - +
205C PHE* 3.3 3.1 - - - -
206C SER* 2.8 59.6 + - - +
207C THR 5.1 0.9 - - - -
208C SER* 3.7 24.2 - - - +
223C GLU* 4.2 19.3 - - + +
224C LEU* 1.3 78.3 - - - +
226C PHE* 1.3 63.7 + - - +
227C GLU* 3.9 29.6 - - + +
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Residues in contact with PHE 226 (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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149C LEU* 4.2 20.2 - - + -
160C LEU* 3.7 31.9 - - + +
161C ASN* 3.4 3.3 - - - +
162C GLY 2.8 42.4 + - - +
163C ASN* 5.0 0.7 - - - -
164C LYS* 4.7 0.7 - - + -
178C VAL* 4.0 14.6 - - + -
198C VAL* 3.9 30.1 - - + -
204C GLY 3.4 2.9 - - - -
205C PHE* 3.4 38.4 - + + -
224C LEU* 4.0 22.0 - - + -
225C ILE* 1.3 76.9 - - - +
227C GLU* 1.3 66.7 + - - +
229C CYS* 3.5 26.2 - - + -
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Residues in contact with GLU 227 (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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161C ASN* 3.5 4.7 - - - -
204C GLY* 2.8 27.5 + - - +
206C SER* 4.9 3.1 + - - -
225C ILE* 3.9 21.6 - - + +
226C PHE* 1.3 78.1 - - - +
228C ASP* 1.3 74.5 + - - +
229C CYS 3.2 0.8 + - - +
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Residues in contact with ASP 228 (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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152C GLU* 5.3 0.3 - - - +
159C ILE* 3.5 32.0 - - + +
160C LEU 3.0 1.0 + - - -
161C ASN* 2.7 34.2 + - - -
203C PRO 4.2 3.3 - - - +
204C GLY* 4.8 0.2 - - - -
227C GLU* 1.3 75.9 - - - +
229C CYS* 1.3 64.8 + - - +
230C LYS* 3.2 5.9 + - - +
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Residues in contact with CYS 229 (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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158C TYR 3.2 5.0 - - - +
159C ILE* 3.4 0.6 - - - -
160C LEU* 2.8 36.9 + - + +
202C MET* 4.0 15.7 - - - -
203C PRO 3.3 20.9 - - - +
204C GLY* 4.1 6.7 - - - -
205C PHE* 3.5 28.0 - - - -
226C PHE* 3.5 28.9 - - + -
227C GLU 3.2 1.0 - - - -
228C ASP* 1.3 73.6 - - - +
230C LYS* 1.3 63.6 + - - +
231C ILE* 3.5 10.7 + - - -
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Residues in contact with LYS 230 (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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154C LYS* 5.2 6.9 - - - +
157C HIS* 3.7 44.0 + - + +
158C TYR 3.4 3.4 - - - -
159C ILE* 3.3 27.1 - - + +
202C MET* 4.8 9.5 - - - +
203C PRO* 4.0 8.2 + - + +
228C ASP 3.2 5.9 + - - +
229C CYS* 1.3 72.7 - - - +
231C ILE* 1.3 61.2 + - - +
232C PRO* 3.9 6.2 - - - +
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Residues in contact with ILE 231 (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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157C HIS* 3.2 3.5 - - - -
158C TYR* 2.7 45.5 + - + +
160C LEU* 3.5 27.8 - - + -
196C PHE* 3.7 30.3 - - + -
197C ILE 4.9 0.7 - - - +
198C VAL* 3.4 35.7 - - + -
202C MET* 4.3 14.8 - - + -
226C PHE* 4.9 2.2 - - + -
229C CYS* 4.5 5.4 - - - +
230C LYS* 1.3 75.8 - - - +
232C PRO* 1.3 80.9 - - + +
235C ASN* 3.8 13.5 - - + -
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Residues in contact with PRO 232 (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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156C ASN* 4.4 2.5 - - - +
157C HIS* 3.4 23.5 - - + +
158C TYR* 4.7 0.7 - - - -
202C MET* 4.4 13.5 - - + -
230C LYS 3.9 6.7 - - - +
231C ILE* 1.3 92.4 - - + +
233C ALA* 1.3 59.8 + - - +
234C ALA* 4.2 9.0 - - + +
235C ASN* 2.8 48.1 + - - +
236C ILE 4.3 0.3 + - - -
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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