Contacts of the strand formed by residues 193 - 199 (chain D) 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 ILE 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D VAL* 5.9 3.6 - - + -
147D MET* 3.4 33.7 - - + -
179D TYR* 3.6 25.6 - - + -
180D ALA 3.2 10.8 - - - +
181D LYS* 4.6 9.4 - - + -
189D ALA 4.7 1.1 - - - +
190D SER* 3.3 25.6 - - - +
191D ARG 3.6 1.2 - - - -
192D GLY* 1.3 79.0 - - - +
194D THR* 1.3 72.5 + - - +
241D ASN* 3.1 11.3 - - - +
243D GLY 3.0 21.5 + - - -
244D VAL* 3.4 26.0 - - + +
247D LEU* 3.9 12.1 - - + -
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Residues in contact with THR 194 (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* 5.9 0.2 - - - +
179D TYR* 3.4 1.4 - - - -
180D ALA 2.8 30.5 + - - +
182D THR* 2.6 41.1 + - + +
193D ILE* 1.3 75.2 - - - +
195D ALA* 1.3 72.2 + - - +
196D PHE* 3.7 16.7 - - + -
236D ILE* 3.9 13.9 - - + -
237D LEU 5.2 0.4 - - - +
239D HIS 3.9 5.2 - - - +
240D GLU* 3.5 23.3 - - + -
241D ASN 2.9 12.0 + - - +
243D GLY* 4.2 4.7 - - - -
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Residues in contact with ALA 195 (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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177D ILE* 4.4 8.5 - - + -
178D VAL 3.3 6.1 - - - +
179D TYR* 3.8 27.1 - - + -
194D THR* 1.3 76.0 - - - +
196D PHE* 1.3 57.1 + - - +
236D ILE* 3.2 10.9 - - - +
237D LEU* 2.8 48.4 + - + +
243D GLY* 4.4 4.4 - - - -
246D VAL* 3.9 11.4 - - + -
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Residues in contact with PHE 196 (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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151D ALA* 3.7 13.2 - - + -
158D TYR* 3.8 22.2 - + + -
160D LEU* 3.9 10.1 - - + -
176D LEU 3.4 1.6 - - - +
177D ILE* 3.5 4.1 - - - -
178D VAL* 2.7 41.8 + - + +
180D ALA* 3.6 28.3 - - + -
182D THR* 3.5 23.6 - - + -
194D THR* 3.7 20.9 - - + -
195D ALA* 1.3 72.9 - - - +
197D ILE* 1.3 63.6 + - - +
198D VAL* 3.5 3.4 + - + +
231D ILE* 4.0 33.4 - - + -
235D ASN 3.4 3.6 - - - +
236D ILE* 3.1 37.0 - - + -
237D LEU* 4.3 0.4 - - - +
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Residues in contact with ILE 197 (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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108D LEU* 3.9 20.2 - - + -
116D GLN* 3.9 30.3 - - + +
120D TYR* 3.7 35.7 - - + -
175D VAL* 3.5 31.6 - - + -
176D LEU 3.4 5.4 - - - +
177D ILE* 4.7 4.0 - - + +
196D PHE* 1.3 72.9 - - - +
198D VAL* 1.3 59.6 + - - +
199D GLU* 4.9 0.2 - - + -
202D MET* 4.6 0.2 - - - +
231D ILE* 4.2 4.7 - - - +
235D ASN* 2.7 54.0 + - - +
237D LEU* 4.2 17.5 - - + -
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Residues in contact with VAL 198 (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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160D LEU* 4.4 2.2 - - + -
175D VAL* 3.4 4.0 - - - +
176D LEU* 2.8 62.2 + - + +
178D VAL* 3.8 28.7 - - + -
196D PHE* 4.1 3.1 - - + +
197D ILE* 1.3 73.9 - - - +
199D GLU* 1.3 63.2 + - - +
202D MET* 3.8 10.3 - - - -
205D PHE* 4.4 9.6 - - + -
226D PHE* 4.0 24.7 - - + -
231D ILE* 3.3 25.6 - - + -
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Residues in contact with GLU 199 (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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119D LYS* 3.8 13.4 + - - -
120D TYR* 2.9 44.3 + - + +
129D TYR* 6.1 0.3 - - - -
174D ASP 3.2 11.2 - - - +
175D VAL* 4.8 3.1 - - + -
176D LEU* 4.9 0.4 - - - -
197D ILE 4.8 1.1 - - - +
198D VAL* 1.3 80.4 - - - +
200D LYS* 1.3 69.8 + - - +
201D GLY 3.3 0.3 + - - -
202D MET* 3.2 42.1 + - + +
205D PHE* 3.7 11.1 - - - -
235D ASN* 3.9 10.5 + - - -
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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