Contacts of the strand formed by residues 187 - 195 (chain D) in PDB entry 3RBQ
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 LYS 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D VAL* 4.6 10.5 - - + -
148D GLU* 2.6 42.2 + - + +
149D PHE 3.5 9.4 - - - +
150D THR* 4.1 17.2 - - + +
183D ILE* 5.6 1.7 - - - +
186D SER* 1.3 83.9 + - - +
188D ASN* 1.3 69.4 + - - +
189D THR* 4.6 7.9 - - + +
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Residues in contact with ASN 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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148D GLU* 3.2 6.2 - - - +
149D PHE* 2.7 57.1 + - + +
151D VAL* 3.2 16.0 - - - +
181D PHE 3.9 5.4 - - - +
182D CYS* 3.5 5.4 - - - -
183D ILE* 2.9 54.7 + - - +
186D SER* 3.2 20.8 + - - -
187D LYS* 1.3 76.7 + - - +
189D THR* 1.3 67.6 + - - +
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Residues in contact with THR 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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146D THR* 5.5 5.6 - - + -
147D VAL 3.3 7.6 - - - -
148D GLU* 3.8 25.4 - - + +
149D PHE* 4.3 4.5 - - - -
180D GLY 6.0 0.2 + - - -
187D LYS* 4.6 9.2 - - + +
188D ASN* 1.3 81.6 - - - +
190D CYS* 1.3 63.0 + - - +
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Residues in contact with CYS 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 ALA 3.8 0.5 - - - +
146D THR* 3.6 5.4 - - - +
147D VAL* 2.9 38.5 + - + +
149D PHE* 4.4 1.3 - - + -
178D HIS 4.8 3.6 - - - -
179D PHE* 3.6 43.3 - - + -
180D GLY 4.7 4.9 - - - +
189D THR* 1.3 78.2 - - - +
191D GLU* 1.3 72.9 + - - +
192D HIS* 3.8 24.7 - - - -
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Residues in contact with GLU 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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94D ARG* 2.7 40.6 + - - -
96D MET* 5.3 1.2 - - - +
145D ALA 3.3 14.1 - - - +
146D THR* 4.6 6.2 + - + +
190D CYS* 1.3 80.0 - - - +
192D HIS* 1.3 63.5 + - - +
193D ILE* 3.9 28.9 + - + +
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Residues in contact with HIS 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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91D PHE* 5.7 3.8 - - - -
143D VAL 3.9 0.3 - - - +
144D GLY* 3.6 0.5 - - - -
145D ALA* 2.7 47.3 + - + +
147D VAL* 4.4 13.7 - - + +
161D MET* 4.0 21.6 - - + +
177D PHE* 3.7 47.3 - + + +
178D HIS 5.8 1.1 - - - -
179D PHE* 3.5 43.1 + + - -
190D CYS* 3.8 18.2 - - + -
191D GLU* 1.3 71.5 - - - +
193D ILE* 1.3 61.3 + - - +
194D TYR* 3.9 12.9 + - + -
220D TYR* 5.9 0.2 - + - -
502J ALA* 6.2 3.5 - - + +
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Residues in contact with ILE 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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96D MET* 4.4 14.4 - - + -
142D GLN* 3.6 35.0 - - + +
143D VAL 3.7 0.7 - - - -
144D GLY* 3.7 23.1 - - - -
175D PHE* 5.0 1.2 - - - -
177D PHE* 3.5 17.9 - - - -
191D GLU* 3.9 29.4 + - + +
192D HIS* 1.3 74.8 - - - +
194D TYR* 1.3 60.8 + - - +
195D ASP* 3.7 7.8 + - - +
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Residues in contact with TYR 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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91D PHE* 5.0 3.7 - + - -
142D GLN* 3.3 6.4 - - - -
143D VAL* 2.8 53.1 + - + +
145D ALA* 3.7 24.5 - - + -
161D MET* 3.7 9.0 - - - +
163D GLU* 2.6 37.5 + - - -
175D PHE* 3.6 43.1 - + + -
177D PHE* 3.8 13.7 - + - -
192D HIS* 3.9 19.1 + - + -
193D ILE* 1.3 71.9 - - - +
195D ASP* 1.3 61.0 + - - +
196D PHE* 3.6 2.4 + - - -
500J DAO 3.7 39.0 - - + +
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Residues in contact with ASP 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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141D ARG* 3.7 8.3 + - - +
142D GLN* 2.9 35.8 + - - +
173D LYS* 2.7 36.7 + - - +
175D PHE* 3.4 11.8 - - - -
193D ILE* 3.7 9.7 + - - +
194D TYR* 1.3 69.0 - - - +
196D PHE* 1.3 62.2 + - - +
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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