Contacts of the strand formed by residues 190 - 200 (chain B) in PDB entry 2RFQ
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 ASN 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ARG* 4.9 1.6 + - - +
32B ARG* 5.6 0.2 - - - +
138B TRP 3.5 1.9 + - - -
139B SER* 2.9 32.2 + - - -
142B CYS* 3.7 7.0 - - - -
143B ASP* 3.2 22.0 - - - +
175B ILE* 3.7 16.6 - - + +
176B ASP 3.2 10.1 - - - +
177B ASP* 3.5 16.3 + - - +
178B VAL* 2.9 28.5 - - - +
179B TRP* 3.0 22.0 - - - +
188B GLY* 2.9 18.1 + - - +
189B SER* 1.3 72.3 - - - +
191B THR* 1.3 64.6 + - - +
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Residues in contact with THR 191 (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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135B ALA* 4.0 15.5 - - + +
136B TRP 3.3 16.4 - - - +
137B ALA* 3.5 19.0 - - + +
138B TRP 4.6 0.2 + - - -
174B ARG 3.4 1.6 - - - +
175B ILE* 3.3 6.1 - - - -
176B ASP* 2.8 43.0 + - + +
178B VAL* 3.4 20.4 - - - +
190B ASN* 1.3 77.3 - - - +
192B VAL* 1.3 63.5 + - - +
193B VAL* 3.7 19.0 + - + -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 4.7 3.8 - - - +
134B GLY 3.9 1.2 - - - +
135B ALA* 3.5 0.7 - - - -
136B TRP* 2.8 41.5 + - - +
139B SER* 4.0 26.7 - - - +
142B CYS* 4.3 12.6 - - + -
148B ALA* 4.6 4.5 - - + -
150B LEU* 4.0 31.0 - - + -
173B TYR* 3.6 42.8 - - + -
174B ARG 3.5 3.1 - - - -
175B ILE* 4.6 2.9 - - + -
191B THR* 1.3 72.6 - - - +
193B VAL* 1.3 62.3 + - - +
194B VAL* 3.9 1.7 + - + -
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Residues in contact with VAL 193 (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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134B GLY 3.6 8.1 - - - +
135B ALA* 4.4 10.5 - - + -
173B TYR* 3.3 6.1 - - - +
174B ARG* 2.8 61.4 + - + +
176B ASP* 3.5 26.0 - - - +
191B THR* 3.9 17.9 - - + +
192B VAL* 1.3 75.5 - - - +
194B VAL* 1.3 61.3 + - - +
195B GLU* 3.7 28.0 + - + +
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Residues in contact with VAL 194 (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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132B VAL* 3.5 31.9 - - + +
133B ASN* 3.3 3.6 - - - +
134B GLY 2.8 40.2 + - - +
136B TRP* 3.9 7.9 - - + -
150B LEU* 3.7 30.5 - - + -
168B ILE* 3.9 9.4 - - + -
172B ASP 4.6 3.1 - - - +
173B TYR* 4.0 13.5 - - + -
192B VAL* 4.1 3.6 - - + -
193B VAL* 1.3 77.2 - - - +
195B GLU* 1.3 67.1 + - - +
197B VAL* 3.6 21.8 - - + -
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Residues in contact with GLU 195 (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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133B ASN* 3.5 5.2 - - - +
134B GLY 5.4 0.2 - - - +
172B ASP 4.9 1.0 + - - -
174B ARG* 3.9 16.0 + - - -
193B VAL* 3.7 24.9 + - + +
194B VAL* 1.3 81.0 - - - +
196B ASP* 1.3 74.7 - - + +
197B VAL* 3.3 11.8 + - - +
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Residues in contact with ASP 196 (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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131B THR* 3.3 19.7 - - - +
132B VAL 3.2 4.0 + - - -
133B ASN* 2.8 24.0 + - - +
195B GLU* 1.3 73.6 - - + +
197B VAL* 1.3 60.0 + - - +
198B PHE 4.0 1.2 + - - -
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Residues in contact with VAL 197 (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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130B TYR 3.5 0.3 - - - +
131B THR* 3.4 4.6 - - - -
132B VAL* 2.8 34.0 + - + +
168B ILE* 4.2 7.0 - - + -
172B ASP* 3.3 49.8 - - + +
194B VAL* 3.6 20.9 - - + -
195B GLU 3.5 16.2 - - - +
196B ASP* 1.3 75.5 - - - +
198B PHE* 1.3 77.3 + - - +
199B VAL* 3.6 11.5 + - + -
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Residues in contact with PHE 198 (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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126B VAL* 3.9 12.1 - - + -
127B ASP 3.7 20.0 - - - -
128B GLY* 3.4 25.1 - - - -
129B GLY* 3.8 14.4 - - - -
130B TYR 3.4 12.1 - - - -
131B THR* 4.8 2.9 - - - +
172B ASP* 4.6 5.7 - - - +
196B ASP 4.0 2.4 + - - -
197B VAL* 1.3 82.6 - - - +
199B VAL* 1.3 59.2 + - - +
200B PRO* 3.8 27.7 - - + +
203B ARG* 5.8 0.7 + - - -
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Residues in contact with VAL 199 (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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129B GLY* 3.3 0.7 - - - -
130B TYR* 2.9 39.6 + - + +
132B VAL* 3.6 26.2 - - + -
166B PHE* 4.5 2.7 - - + -
167B LEU 3.7 23.1 - - - +
168B ILE* 3.7 26.5 - - + -
197B VAL* 4.1 7.0 - - + -
198B PHE* 1.3 78.8 - - - +
200B PRO* 1.3 73.9 - - + +
203B ARG* 4.0 4.7 - - + +
204B VAL* 3.7 25.1 - - + -
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Residues in contact with PRO 200 (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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128B GLY 3.4 10.1 - - - +
198B PHE* 3.8 24.2 - - + +
199B VAL* 1.3 91.4 - - + +
201B THR* 1.3 67.3 + - - +
202B HIS* 3.6 32.1 - - + +
203B ARG* 2.9 46.2 + - - +
204B VAL* 3.7 5.4 - - - +
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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