Contacts of the strand formed by residues 142 - 150 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 3.8 4.9 - - - +
96B MET* 3.0 49.9 + - + +
97B ASP* 4.7 1.7 + - - +
140B LEU 3.7 0.6 - - - -
141B ARG* 1.3 116.8 + - - +
143B VAL* 1.3 65.7 + - - +
193B ILE* 3.3 32.3 - - + +
194B TYR 3.3 4.9 - - - +
195B ASP* 2.9 23.8 + - - +
196B PHE* 4.5 1.1 - - - -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.7 34.1 - - + -
94B ARG 3.2 10.1 - - - +
95B ASP* 4.6 0.4 - - - -
96B MET* 4.0 2.5 - - - -
102B LEU* 3.9 12.1 - - + -
137B PHE* 4.8 1.8 - - + -
140B LEU* 3.8 23.3 - - + -
142B GLN* 1.3 79.5 - - - +
144B GLY* 1.3 61.8 + - - +
145B ALA 3.8 0.9 + - - -
193B ILE* 3.7 1.9 - - - +
194B TYR* 2.9 42.8 + - + +
196B PHE* 3.5 29.4 - - + -
500H DAO 4.7 5.8 - - + -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 3.6 1.4 - - - +
93B ILE* 3.3 1.9 - - - -
94B ARG* 2.8 43.9 + - - +
96B MET* 3.7 21.2 - - - +
143B VAL* 1.3 72.8 - - - +
145B ALA* 1.3 60.2 + - - -
146B THR* 4.1 1.3 + - - -
191B GLU* 4.9 7.9 - - - -
192B HIS 3.7 4.9 - - - -
193B ILE* 3.9 9.6 - - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 4.1 13.2 - - + -
92B LYS 3.2 5.2 - - - +
93B ILE* 3.7 14.8 - - + -
143B VAL 3.8 0.8 + - - -
144B GLY* 1.3 71.9 - - - -
146B THR* 1.3 59.9 + - - +
147B VAL* 4.0 1.3 - - + +
190B CYS 3.8 0.7 - - - +
191B GLU* 3.3 5.5 - - - +
192B HIS* 2.8 43.4 + - + +
194B TYR* 3.7 29.6 - - + -
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.9 20.1 - - - +
91B PHE* 3.5 5.6 + - - -
92B LYS* 2.9 50.5 + - - +
144B GLY 4.1 1.9 + - - -
145B ALA* 1.3 70.8 - - - +
147B VAL* 1.3 62.7 + - - +
148B GLU* 5.0 1.3 - - + -
189B THR* 3.8 25.8 - - + -
190B CYS 3.5 3.6 - - - +
191B GLU* 2.4 30.5 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 3.3 37.2 - - + -
90B ARG 3.4 10.5 - - - +
91B PHE* 4.3 9.6 - - + -
145B ALA* 4.0 1.7 - - + +
146B THR* 1.3 75.2 - - - +
148B GLU* 1.3 64.8 + - - +
149B PHE* 4.4 4.8 - - + -
179B PHE* 4.1 18.4 - - + -
188B ASN 4.0 0.2 - - - +
189B THR* 3.3 5.2 - - - +
190B CYS* 2.8 56.2 + - + +
192B HIS* 4.7 7.0 - - - +
502H ALA* 4.2 11.4 - - + -
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.5 2.1 - - - -
89B VAL* 2.8 33.0 + - + +
90B ARG* 3.0 64.9 + - + +
146B THR* 5.0 1.1 - - + -
147B VAL* 1.3 76.8 - - - +
149B PHE* 1.3 63.9 + - - +
187B LYS* 3.0 35.2 + - + +
188B ASN 3.1 7.0 - - - +
189B THR* 3.4 25.5 + - + +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 4.1 9.4 - - + -
87B ASP 3.1 14.6 - - - +
88B PHE* 3.5 27.6 - + + -
89B VAL* 4.3 1.8 - - - +
147B VAL* 4.4 7.9 - - + -
148B GLU* 1.3 79.0 - - - +
150B THR* 1.3 64.6 + - - +
151B VAL* 3.6 29.6 - - + -
159B PHE* 3.8 13.0 - + - -
179B PHE* 3.9 21.8 - + + -
181B PHE 5.7 0.7 - - - -
182B CYS* 3.7 22.9 - - - -
187B LYS* 3.5 2.4 - - - +
188B ASN* 2.8 62.5 + - + +
189B THR 4.9 0.2 - - - -
190B CYS* 4.6 11.9 - - + -
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS 3.2 3.7 + - - +
86B ILE* 3.3 4.3 - - - -
87B ASP* 2.8 49.8 + - - +
89B VAL* 4.4 11.7 - - + +
149B PHE* 1.3 78.0 - - - +
151B VAL* 1.3 67.5 + - - +
185B SER 6.1 0.2 - - - -
186B SER 3.4 12.6 - - - +
187B LYS* 4.2 18.8 - - + +
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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