Contacts of the strand formed by residues 183 - 189 (chain D) in PDB entry 6IY6
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 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D LYS* 3.6 9.9 - - - +
122D ILE* 4.6 10.8 - - + -
142D LEU* 4.2 14.8 - - + -
146D PHE* 4.0 29.6 - - + -
147D ARG 3.2 4.7 + - - +
148D VAL* 3.3 15.6 - - + -
149D LEU* 3.0 26.0 + - - +
181D TYR* 4.4 2.5 - - - +
182D GLN* 1.3 91.5 - - + +
184D GLY* 1.3 65.0 + - - +
199D PHE* 5.0 18.4 - - + -
220D LEU* 4.4 16.8 - - + -
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Residues in contact with GLY 184 (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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120D LYS 2.9 15.6 + - - +
121D ASP* 3.2 19.3 - - - -
122D ILE* 2.6 32.6 + - - +
149D LEU* 3.7 12.6 - - - -
183D LEU* 1.3 75.8 - - - +
185D PHE* 1.3 58.3 + - - +
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Residues in contact with PHE 185 (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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121D ASP* 3.5 0.6 + - - -
122D ILE* 3.4 17.5 - - + -
124D ILE* 3.4 31.6 - - + -
135D LEU* 4.3 11.0 - - + -
136D LEU* 5.8 1.6 - - + -
139D HIS* 3.4 38.1 - + + -
142D LEU* 4.4 14.8 - - + -
148D VAL* 3.6 20.6 - - + -
149D LEU 3.3 9.0 + - - -
150D SER* 3.3 2.3 - - - -
151D THR 3.0 26.1 + - - +
169D PHE* 3.7 25.5 - + - -
184D GLY* 1.3 71.3 - - - +
186D THR* 1.3 59.4 + - - +
187D LEU* 4.4 13.9 - - + -
217D LEU* 4.1 19.3 - - + -
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Residues in contact with THR 186 (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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340B LEU* 5.7 0.2 - - + -
384B TYR* 4.0 22.7 - - + -
601B PO4 4.7 3.9 + - - +
121D ASP* 2.7 31.0 + - - -
122D ILE 2.8 10.1 + - - -
123D VAL* 3.4 5.7 - - + +
124D ILE 2.9 25.7 + - - -
149D LEU 5.4 0.3 + - - -
151D THR* 3.5 12.7 + - - +
153D HIS* 3.8 29.8 - - + +
185D PHE* 1.3 70.2 + - - +
187D LEU* 1.3 58.8 + - - +
188D ILE* 3.6 15.4 + - + -
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Residues in contact with LEU 187 (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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124D ILE* 3.5 31.2 - - + +
126D ALA* 4.0 17.3 - - + -
132D PRO* 5.3 3.1 - - + -
135D LEU* 6.0 0.9 - - + -
136D LEU* 3.9 24.2 - - + -
151D THR 3.0 7.4 + - - +
152D VAL* 3.3 6.4 - - + +
153D HIS 3.0 25.6 + - - +
168D CYS* 3.9 15.3 - - - -
169D PHE* 4.0 22.0 - - + -
185D PHE* 3.7 9.2 + - + -
186D THR* 1.3 69.6 - - - +
188D ILE* 1.3 60.6 + - - +
189D TRP* 3.8 34.8 - - + +
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Residues in contact with ILE 188 (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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340B LEU* 4.0 24.2 - - + -
384B TYR* 3.6 25.4 - - + +
123D VAL* 3.9 17.5 - - + -
124D ILE 2.9 8.7 + - - +
125D ASN* 3.4 23.6 - - - +
126D ALA 3.0 24.4 + - - -
153D HIS* 3.5 14.6 - - + +
155D HIS* 3.9 30.3 - - + +
186D THR* 4.0 19.5 - - + +
187D LEU* 1.3 76.1 - - - +
189D TRP* 1.3 62.3 - - - +
190D LYS* 3.5 2.3 + - + -
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Residues in contact with TRP 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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126D ALA* 3.3 24.0 - - + -
127D ASN 3.7 8.3 - - - -
128D PRO* 3.5 31.6 - - + -
131D PRO* 4.0 14.8 - - + -
132D PRO* 3.8 26.0 - - + -
136D LEU* 5.2 6.3 - - + -
152D VAL* 3.6 17.1 - - + +
153D HIS 2.9 20.5 + - - +
154D THR* 4.5 3.8 - - - +
155D HIS* 2.8 31.7 + - - +
158D VAL* 3.1 8.0 - - - +
161D VAL* 4.1 31.9 - - + -
165D LEU* 3.2 42.5 + - + -
166D LEU* 5.0 1.1 - - - -
168D CYS* 4.7 3.6 - - - -
187D LEU* 3.8 26.0 - - + +
188D ILE* 1.3 68.4 - - - +
190D LYS* 1.3 55.3 + - - +
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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