Contacts of the strand formed by residues 188 - 195 (chain D) in PDB entry 3IU3
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 VAL 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D LYS 5.3 0.4 - - - +
147D VAL* 3.5 4.7 - - - +
148D ASP* 2.7 48.9 + - - +
149D ASN 5.5 1.3 - - - +
187D LYS* 1.3 82.6 - - + +
189D TYR* 1.3 68.8 + - - +
190D ALA* 4.9 5.6 - - + +
205D SER* 4.6 14.1 - - - +
206D PHE 3.8 4.7 - - - +
207D ASN* 3.7 29.2 - - - +
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Residues in contact with TYR 189 (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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114D ILE* 4.2 2.9 - - - +
129D VAL* 4.6 13.9 - - + -
145D TRP* 5.5 4.7 - + + -
146D LYS 4.0 1.3 - - - -
147D VAL* 3.6 35.5 - - + +
176D LEU* 4.9 4.3 - - + -
178D LEU* 4.1 11.9 - - + +
182D ASP 4.0 3.3 + - - -
183D TYR* 2.5 68.9 + + - -
186D HIS* 4.0 19.0 - - + +
187D LYS 3.7 11.9 - - - -
188D VAL* 1.3 75.4 - - - +
190D ALA* 1.3 61.1 + - - +
205D SER* 3.3 3.6 - - - -
206D PHE* 3.1 63.1 + + + -
208D ARG* 4.6 2.0 - - + -
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Residues in contact with ALA 190 (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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145D TRP* 3.4 16.6 - - - -
146D LYS* 3.0 50.0 + - + +
188D VAL* 5.1 6.3 - - + -
189D TYR* 1.3 75.1 - - - +
191D CYS* 1.3 59.9 - - - +
192D GLU* 3.9 1.6 - - + +
203D THR* 3.9 13.7 - - - +
204D LYS 3.7 3.4 - - - -
205D SER* 3.8 13.2 - - - -
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Residues in contact with CYS 191 (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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112D VAL* 4.9 0.2 - - - -
114D ILE* 3.9 10.7 - - + +
131D CYS* 2.0 51.6 - - + -
143D VAL* 3.8 22.0 - - - -
144D GLN 3.9 2.5 - - - -
145D TRP* 4.4 6.7 - - + -
190D ALA* 1.3 72.0 - - - +
192D GLU* 1.3 57.8 + - - +
193D VAL* 3.9 9.8 + - - +
202D VAL 3.8 0.9 - - - +
203D THR* 3.3 3.2 - - - -
204D LYS* 2.7 48.9 + - + +
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Residues in contact with GLU 192 (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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142D LYS 3.6 1.0 - - - +
143D VAL* 3.4 4.7 - - - -
144D GLN* 2.9 71.7 + - + +
146D LYS* 3.3 35.7 + - + +
190D ALA* 3.9 2.5 - - + +
191D CYS* 1.3 71.8 - - - +
193D VAL* 1.3 63.4 + - - +
194D THR* 4.8 3.9 + - - -
201D PRO* 4.0 32.1 - - + +
202D VAL 3.6 5.8 - - - +
203D THR* 4.3 12.1 - - - +
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Residues in contact with VAL 193 (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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110D PRO* 4.7 3.6 - - + -
112D VAL* 3.9 22.7 - - + -
133D LEU* 3.5 48.2 - - + -
142D LYS 3.5 4.7 - - - +
143D VAL* 4.3 2.5 - - + -
191D CYS* 3.9 15.7 - - - +
192D GLU* 1.3 76.5 - - - +
194D THR* 1.3 70.4 + - - +
195D HIS* 4.8 0.2 - - + -
198D LEU* 4.1 23.3 - - + +
200D SER* 4.3 0.2 - - - -
201D PRO* 3.4 2.9 - - - +
202D VAL* 2.7 39.4 + - + +
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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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141D ALA* 3.5 3.8 - - - +
142D LYS* 2.8 57.8 + - + +
192D GLU* 4.8 4.9 + - - -
193D VAL* 1.3 75.0 - - - +
195D HIS* 1.3 68.0 + - - +
200D SER* 3.6 17.9 - - - +
201D PRO* 3.5 16.7 - - + +
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Residues in contact with HIS 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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108D ALA 3.5 15.5 - - - -
110D PRO* 3.5 29.8 - - + +
136D PHE* 3.5 16.2 - + - -
137D TYR 3.3 22.0 - - - -
138D PRO* 3.0 29.1 + - + +
140D GLU 3.1 25.8 - - - -
141D ALA* 3.9 7.9 - - + -
193D VAL* 4.2 3.2 + - + -
194D THR* 1.3 76.5 - - - +
196D GLN* 1.3 66.2 + - - +
197D GLY 3.1 24.7 + - - +
198D LEU* 3.0 17.9 + - + +
200D SER* 2.7 24.2 + - - -
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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