Contacts of the strand formed by residues 224 - 232 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 3.4 32.8 - - + -
163B ASN* 2.8 26.5 - - - +
164B LYS* 2.9 26.1 + - + -
167B ILE* 4.0 20.9 - - + -
170B GLY* 4.4 2.2 - - - -
176B LEU* 3.8 23.1 - - + -
178B VAL* 4.2 10.3 - - + -
205B PHE* 3.6 14.6 - - + -
206B SER 3.8 2.2 - - - -
207B THR* 4.0 15.9 - - + -
222B CYS* 4.2 6.1 - - - -
223B GLU* 1.3 78.1 - - - +
225B ILE* 1.3 60.6 - - - +
226B PHE* 3.8 10.8 - - + -
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLY 3.8 4.0 - - - +
163B ASN* 4.3 4.0 - - + -
204B GLY 3.4 1.8 - - - +
205B PHE* 3.2 6.6 - - - -
206B SER* 2.9 53.1 + - - +
207B THR 4.5 5.4 - - - +
208B SER* 3.6 20.6 - - - +
223B GLU* 4.0 21.5 - - + +
224B LEU* 1.3 80.3 - - - +
226B PHE* 1.3 66.0 + - - +
227B GLU* 3.8 28.5 - - + +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 3.9 21.3 - - + -
160B LEU* 3.8 35.7 - - + +
161B ASN* 3.4 3.6 - - - +
162B GLY* 2.8 43.4 + - - +
163B ASN* 4.7 0.2 - - - -
164B LYS* 4.5 0.7 - - + -
178B VAL* 3.8 26.5 - - + -
198B VAL* 3.9 20.6 - - + -
204B GLY 4.0 2.5 - - - -
205B PHE* 3.9 29.6 - + + -
224B LEU* 3.8 25.4 - - + -
225B ILE* 1.3 76.5 - - - +
227B GLU* 1.3 65.8 + - - +
229B CYS* 3.8 22.0 - - + -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU 4.0 0.2 + - - -
161B ASN* 3.7 5.4 - - - -
204B GLY* 3.3 30.1 + - - +
206B SER* 5.2 2.3 + - - -
225B ILE* 3.8 23.1 - - + +
226B PHE* 1.3 77.2 - - - +
228B ASP* 1.3 77.5 + - - +
229B CYS 3.1 1.5 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 5.2 1.0 - - - +
159B ILE* 3.4 25.3 - - + +
160B LEU 3.1 3.9 + - - -
161B ASN* 3.0 28.5 + - - +
203B PRO 4.5 2.0 - - - +
227B GLU* 1.3 76.8 - - - +
229B CYS* 1.3 64.4 + - - +
230B LYS* 3.0 9.7 + - - +
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B TYR 3.2 4.2 - - - +
159B ILE* 4.4 0.2 - - - -
160B LEU* 2.9 31.0 + - + +
202B MET* 4.1 15.9 - - - -
203B PRO 3.4 22.0 - - - +
204B GLY 4.3 1.3 - - - -
205B PHE* 3.8 27.6 - - - +
226B PHE* 3.8 28.0 - - + -
227B GLU 3.1 2.0 - - - -
228B ASP* 1.3 74.0 - - - +
230B LYS* 1.3 61.7 + - - +
231B ILE* 3.4 17.5 + - - +
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LYS* 5.4 5.5 - - - +
157B HIS* 3.5 44.2 + - + +
158B TYR 3.4 4.3 - - - -
159B ILE* 3.4 24.9 - - + +
202B MET* 5.0 7.4 - - - +
203B PRO* 4.1 7.5 + - - +
228B ASP 3.0 8.1 + - - +
229B CYS* 1.3 73.4 - - - +
231B ILE* 1.3 59.9 + - - +
232B PRO* 3.8 6.6 - - - +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B HIS* 3.1 2.1 - - - -
158B TYR* 2.7 43.3 + - + +
160B LEU* 3.5 33.0 - - + -
196B PHE* 3.9 26.5 - - + -
197B ILE 4.3 3.1 - - - +
198B VAL* 3.5 25.8 - - + -
202B MET* 4.6 7.4 - - - -
229B CYS* 4.0 19.5 - - - +
230B LYS* 1.3 74.4 - - - +
232B PRO* 1.3 78.2 - - + +
235B ASN* 3.7 20.0 - - + +
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Residues in contact with PRO 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASN 3.6 2.0 - - - +
157B HIS* 3.4 26.9 - - + +
158B TYR* 4.7 0.2 - - - -
202B MET* 4.3 8.5 - - + -
230B LYS 3.8 7.2 - - - +
231B ILE* 1.3 91.7 - - + +
233B ALA* 1.3 58.1 + - - +
234B ALA* 3.0 10.8 - - + +
235B ASN* 2.8 51.4 + - - +
236B ILE* 4.4 1.0 + - - +
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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