Contacts of the strand formed by residues 142 - 150 (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 GLN 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D ASP* 3.8 4.9 + - - +
96D MET* 3.1 53.0 + - + +
97D ASP* 4.6 1.7 + - - -
140D LEU 3.7 1.0 - - - -
141D ARG* 1.3 114.6 + - - +
143D VAL* 1.3 68.6 + - - +
193D ILE* 3.6 25.8 - - + +
194D TYR 3.3 9.4 - - - +
195D ASP* 2.9 27.7 + - - +
196D PHE* 4.4 1.3 - - - -
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 4.7 7.4 - - + -
94D ARG 3.1 13.0 - - - +
95D ASP* 4.4 0.9 - - - -
96D MET* 3.9 2.9 - - - -
102D LEU* 3.6 15.5 - - + -
137D PHE* 4.6 2.2 - - + -
140D LEU* 3.6 29.6 - - + -
142D GLN* 1.3 80.4 - - - +
144D GLY* 1.4 58.2 + - - +
145D ALA 4.0 0.2 + - - -
192D HIS 3.9 0.5 - - - +
193D ILE* 3.7 1.9 - - - -
194D TYR* 2.8 57.1 + - + +
196D PHE* 3.6 19.9 - - + -
500J DAO 4.1 16.8 - - + -
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Residues in contact with GLY 144 (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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92D LYS 3.6 1.6 - - - +
93D ILE* 3.3 3.1 - - - -
94D ARG* 2.8 46.7 + - - +
96D MET* 3.7 14.5 - - - +
143D VAL* 1.4 73.0 - - - +
145D ALA* 1.3 60.8 + - - -
191D GLU* 4.7 0.2 - - - -
192D HIS 3.6 4.5 - - - -
193D ILE* 3.7 17.7 - - - -
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Residues in contact with ALA 145 (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* 3.8 15.5 - - + -
92D LYS 3.2 4.5 - - - -
93D ILE* 3.5 20.4 - - + -
143D VAL 4.0 0.4 - - - -
144D GLY* 1.3 73.4 - - - -
146D THR* 1.3 61.5 + - - +
147D VAL* 4.0 0.9 - - + -
190D CYS 3.8 0.3 - - - +
191D GLU* 3.3 8.1 - - - +
192D HIS* 2.7 48.1 + - + +
194D TYR* 3.7 19.1 - - + -
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Residues in contact with THR 146 (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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90D ARG* 3.9 22.1 - - - +
91D PHE* 3.4 5.1 - - - -
92D LYS* 2.7 65.7 + - - +
94D ARG* 4.1 10.6 + - - -
145D ALA* 1.3 73.9 - - - +
147D VAL* 1.3 69.6 + - - +
148D GLU* 4.9 2.7 - - + -
189D THR* 5.5 4.5 - - - -
190D CYS 3.6 9.2 - - - +
191D GLU* 4.6 5.9 + - + +
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Residues in contact with VAL 147 (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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88D PHE* 3.3 32.5 - - + -
90D ARG 3.2 11.7 - - - +
91D PHE* 4.2 9.4 - - + -
145D ALA* 4.0 1.3 - - + -
146D THR* 1.3 77.0 - - - +
148D GLU* 1.3 68.7 + - - +
149D PHE* 4.2 5.4 - - + -
179D PHE* 3.9 27.8 - - + -
189D THR* 3.3 4.3 - - - -
190D CYS* 2.9 45.2 + - + +
192D HIS* 4.4 12.6 - - + +
502J ALA* 4.0 15.3 - - + -
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Residues in contact with GLU 148 (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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88D PHE* 3.5 2.3 - - - -
89D VAL* 2.8 34.1 + - + +
90D ARG* 2.6 68.4 + - + +
146D THR* 4.9 2.9 - - + -
147D VAL* 1.3 80.2 - - - +
149D PHE* 1.3 62.6 + - - +
187D LYS* 2.6 36.4 + - + -
188D ASN 3.2 9.2 - - - +
189D THR* 3.8 16.9 - - + +
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Residues in contact with PHE 149 (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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86D ILE* 3.9 14.1 - - + -
87D ASP 3.2 14.6 - - - +
88D PHE* 3.6 20.9 - + + -
89D VAL* 4.2 0.9 - - - +
147D VAL* 4.2 12.6 - - + -
148D GLU* 1.3 78.8 - - - +
150D THR* 1.3 60.1 + - - +
151D VAL* 3.7 22.0 - - + -
159D PHE* 3.7 15.7 - + - -
179D PHE* 3.8 32.8 - + + -
182D CYS* 4.0 14.8 - - - -
186D SER 3.9 0.2 - - - +
187D LYS* 4.3 2.0 - - - +
188D ASN* 2.7 72.0 + - + +
189D THR 4.1 10.8 - - - -
190D CYS* 4.4 0.9 - - + -
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Residues in contact with THR 150 (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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85D LYS 4.0 2.2 + - - -
86D ILE* 3.4 5.5 - - - +
87D ASP* 2.9 52.3 + - - +
89D VAL* 4.4 16.1 - - + +
149D PHE* 1.3 75.5 - - - +
151D VAL* 1.3 66.6 + - - +
186D SER 3.3 7.6 - - - +
187D LYS* 4.1 20.4 - - + +
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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