Contacts of the strand formed by residues 201 - 210 (chain B) in PDB entry 2QC8
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 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 5.0 2.5 - - + -
137B TYR 3.2 19.5 - - - +
138B THR* 3.6 17.3 + - - +
195B ALA* 4.0 0.7 - - - +
196B GLU* 2.8 46.0 + - + +
197B VAL 3.9 1.0 + - - -
198B MET* 2.9 46.1 + - + +
199B PRO 3.1 0.6 - - - -
200B ALA* 1.3 76.7 - - - +
202B TRP* 1.3 64.9 + - - +
242B PRO* 5.3 1.6 - - - +
248B ASN* 4.0 15.4 + - - +
249B GLY* 3.3 30.5 + - - +
250B ALA* 3.7 11.4 - - - +
601B P3S 4.5 1.5 + - - -
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Residues in contact with TRP 202 (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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136B GLU* 3.4 6.1 - - - +
137B TYR* 2.9 51.8 + - + +
139B LEU* 4.0 16.5 - - + +
170B ALA* 4.0 24.5 - - + -
171B TYR 2.9 30.0 + - - +
173B ARG* 3.8 40.6 - - + -
176B VAL* 3.3 30.7 - - + -
194B ASN* 3.7 9.0 - - - -
195B ALA* 3.3 41.7 - - + -
196B GLU* 3.9 3.5 - - - +
200B ALA* 3.4 16.0 + - - +
201B GLN* 1.3 80.7 + - - +
203B GLU* 1.3 64.3 + - - +
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU* 3.1 11.5 - - + +
135B GLN 3.3 14.1 - - - +
136B GLU* 3.2 7.1 - - + +
137B TYR* 3.9 5.5 + - - -
176B VAL* 5.3 1.6 - - - +
193B THR* 3.3 7.4 - - - +
194B ASN* 3.0 43.4 + - - +
196B GLU* 2.9 9.0 - - + +
202B TRP* 1.3 79.2 - - - +
204B PHE* 1.3 69.5 + - - +
205B GLN* 3.0 8.3 + - - +
401B MN 2.0 35.3 + - - -
403B MN 2.1 29.2 + - - -
501B ADP 3.0 6.1 + - - -
601B P3S 3.0 0.5 + - - -
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Residues in contact with PHE 204 (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 MET 3.8 0.2 - - - +
134B GLU 3.8 0.5 - - - -
135B GLN* 2.9 59.4 + - + +
137B TYR* 3.6 24.0 - + - +
179B HIS* 3.4 31.9 - + + +
190B ILE* 4.0 8.3 - - + -
192B GLY 3.3 11.9 - - - +
193B THR* 3.7 11.9 - - + +
203B GLU* 1.3 77.0 - - - +
205B GLN* 1.3 61.3 + - - +
206B ILE* 3.6 36.6 - - + -
218B LEU* 3.9 4.0 - - + -
221B ALA* 3.7 22.4 - - + -
222B ARG* 4.6 4.3 - - + -
225B LEU* 4.1 10.5 - - + -
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Residues in contact with GLN 205 (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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43A LYS* 6.3 0.4 - - - +
44A THR 4.6 1.2 - - - +
60A TRP* 5.2 5.5 - - - -
133B MET 3.2 3.8 - - - +
134B GLU* 4.0 6.5 - - + -
190B ILE* 3.6 3.1 - - - +
191B ALA* 2.9 32.1 + - + +
192B GLY* 2.9 35.2 + - - +
193B THR* 3.7 3.1 + - - +
194B ASN* 3.0 26.9 + - - -
203B GLU* 3.0 18.8 + - - +
204B PHE* 1.3 75.0 - - - +
206B ILE* 1.3 69.0 + - - +
501B ADP 3.4 49.1 + - - +
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Residues in contact with ILE 206 (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 GLY* 3.2 3.1 - - - -
133B MET 2.7 35.9 + - - +
183B CYS* 5.5 0.4 - - - -
188B VAL* 3.8 23.1 - - + -
189B LYS 3.5 8.5 - - - +
190B ILE* 4.0 10.5 - - + -
204B PHE* 3.6 32.3 - - + -
205B GLN* 1.3 81.9 - - - +
207B GLY* 1.3 59.7 + - - +
209B CYS* 4.0 4.0 - - - -
214B MET* 3.7 25.1 - - + +
217B HIS* 3.8 24.7 - - + -
218B LEU* 4.0 14.6 - - + +
221B ALA* 3.9 4.7 - - + -
501B ADP 3.8 3.1 + - - -
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Residues in contact with GLY 207 (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 PHE 3.6 2.2 - - - -
189B LYS* 3.1 25.4 + - - +
191B ALA* 3.6 12.9 - - - +
205B GLN 4.2 0.8 - - - -
206B ILE* 1.3 75.8 - - - +
208B PRO* 1.3 77.2 - - - +
209B CYS* 3.5 9.4 - - - -
501B ADP 3.3 12.6 + - - -
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Residues in contact with PRO 208 (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 TRP* 3.9 36.0 - - + -
131B PHE 3.1 8.7 - - - +
189B LYS* 3.3 25.8 - - - +
207B GLY* 1.3 81.4 - - - +
209B CYS* 1.3 59.7 + - - +
210B GLU 4.2 0.7 + - - -
501B ADP 3.3 40.8 - - + +
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Residues in contact with CYS 209 (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 TRP* 3.5 2.3 - - - -
131B PHE* 2.8 32.1 + - - +
189B LYS* 4.1 12.8 - - - -
206B ILE* 4.0 20.0 - - - -
207B GLY* 3.9 17.3 - - - -
208B PRO* 1.3 74.3 - - - +
210B GLU* 1.3 63.1 + - - +
211B GLY 3.7 0.9 + - - -
213B SER* 3.6 8.5 - - - +
214B MET* 3.5 26.1 - - + +
217B HIS* 4.0 23.3 - - - -
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Residues in contact with GLU 210 (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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125B SER* 4.3 5.4 - - - +
128B HIS* 2.8 42.2 + - - +
129B PRO* 3.3 14.8 - - + +
130B TRP* 3.1 27.7 + - + +
208B PRO 4.2 1.0 + - - -
209B CYS* 1.3 70.7 - - - +
211B GLY* 1.3 67.9 + - - +
212B ILE* 3.5 0.5 + - - +
213B SER* 2.5 29.6 + - - +
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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