Contacts of the strand formed by residues 215 - 224 (chain A) in PDB entry 1QSV
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 LEU 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A GLU* 4.3 23.6 - - + +
209A ALA 3.8 11.7 - - - +
210A THR* 3.5 24.3 - - + +
214A HIS* 1.3 88.4 + - - +
216A TYR* 1.3 71.3 + - - +
217A LYS* 3.0 25.6 + - + +
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Residues in contact with TYR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 4.8 0.4 - - - -
132A GLY 2.8 40.0 + - - -
133A ARG* 3.8 14.1 - - + -
134A PRO* 3.5 21.3 - - + -
135A PHE* 3.8 17.7 - - + -
138A MET* 6.4 2.2 - - + -
209A ALA 2.9 38.3 + - - +
211A VAL* 3.9 8.7 - - + -
212A ASN* 3.6 22.6 + - - -
214A HIS* 3.1 49.0 + + - -
215A LEU* 1.3 78.7 - - - +
217A LYS* 1.3 65.8 + - - +
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.9 5.0 - - - -
138A MET* 4.1 10.6 - - - +
139A TYR* 3.7 23.9 - - + +
206A THR* 4.3 8.7 - - + -
207A CYS 3.2 13.9 - - - +
208A GLU* 4.2 12.8 - - + -
215A LEU* 3.0 41.8 + - + +
216A TYR* 1.3 79.4 - - - +
218A THR* 1.3 68.2 + - - +
219A ASN* 4.3 13.7 - - - +
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Residues in contact with THR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.8 37.2 - - + -
137A GLU 4.4 0.2 - - - +
138A MET* 3.9 7.9 - - + -
139A TYR* 2.9 37.5 + - - +
158A CYS* 4.1 1.3 - - + -
206A THR* 3.6 1.5 - - - -
207A CYS* 2.9 30.6 + - + +
217A LYS* 1.3 78.4 - - - +
219A ASN* 1.3 63.1 + - - +
220A TYR* 3.1 35.0 + - + +
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TYR* 3.2 42.6 + - + +
143A PRO* 3.7 24.4 - - + +
144A GLU 3.1 18.7 + - - -
204A LEU* 4.1 13.7 - - + +
205A LEU 3.5 4.4 + - - +
206A THR* 2.9 34.5 + - - +
217A LYS* 4.3 7.0 - - - +
218A THR* 1.3 75.6 + - - +
220A TYR* 1.3 71.7 + - - +
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 3.8 6.3 + - + +
138A MET* 4.4 2.3 - - - -
139A TYR 5.2 1.8 - - - -
144A GLU* 3.5 45.3 - - + -
146A ILE* 4.1 10.8 - - + -
156A ILE* 3.6 28.3 - - + -
157A PRO* 2.8 34.1 + - + -
158A CYS* 3.3 11.0 - - + +
203A GLY 3.5 0.2 - - - +
204A LEU* 4.3 1.8 - - - -
205A LEU* 2.9 43.1 + - + +
207A CYS* 3.7 19.1 - - - -
218A THR* 3.1 43.4 + - + +
219A ASN* 1.3 75.0 - - - +
221A LEU* 1.3 62.1 + - - +
222A THR* 3.4 3.2 + - - +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PRO* 3.9 14.7 - - + +
144A GLU 2.9 7.7 + - - +
145A ILE* 3.5 29.4 - - + -
146A ILE 2.9 25.7 + - - -
203A GLY* 3.6 11.9 - - - +
204A LEU* 4.3 13.7 - - + -
220A TYR* 1.3 69.6 - - - +
222A THR* 1.3 62.6 + - - +
223A HIS* 3.3 26.3 + - + +
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.7 13.9 - - + -
148A MET* 3.8 7.7 - - - +
154A LEU* 4.2 10.5 - - + -
156A ILE* 3.8 25.1 - - + -
201A GLU 2.9 25.1 + - - +
202A ILE* 3.7 13.5 - - - +
203A GLY 2.8 38.6 + - - -
205A LEU* 3.1 18.9 - - + +
220A TYR 4.1 3.1 - - - +
221A LEU* 1.3 72.9 - - - +
223A HIS* 1.3 60.7 + - - +
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Residues in contact with HIS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 4.3 13.9 - - + -
146A ILE 2.9 10.5 + - - +
147A HIS* 3.4 31.0 + + - -
148A MET* 2.9 27.9 + - - +
202A ILE* 5.5 0.2 - - - -
221A LEU* 3.3 18.1 + - + +
222A THR* 1.3 71.7 - - - +
224A ARG* 1.3 87.5 + - - +
225A GLN* 3.1 6.9 + - - -
226A THR* 4.4 14.6 + - + +
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Residues in contact with ARG 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A MET* 3.8 11.4 - - + +
149A THR* 5.6 0.7 - - - -
150A GLU* 5.7 0.7 - - + +
202A ILE* 4.6 27.3 - - + +
222A THR 3.9 3.2 + - - -
223A HIS* 1.3 86.9 + - - +
225A GLN* 1.3 69.7 + - - +
226A THR* 3.7 3.3 + - - +
228A THR* 3.1 29.0 + - - +
229A ILE* 3.5 44.9 - - - +
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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