Contacts of the strand formed by residues 214 - 224 (chain D) in PDB entry 1QQW
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 GLY 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D PHE* 4.1 7.5 - - - -
148D ASN 3.4 8.7 - - - -
213D ASN* 1.3 74.5 - - - +
215D TYR* 1.3 68.6 + - - -
235D HIS* 3.5 0.9 - - - -
236D TYR* 2.8 60.6 + - - -
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Residues in contact with TYR 215 (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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147D GLY* 3.0 24.4 - - - -
148D ASN 2.9 10.4 + - - -
149D ASN 3.1 36.6 - - - -
150D THR 3.5 8.5 - - - +
151D PRO* 3.8 38.6 - - + +
198D PHE* 5.7 0.2 - - - -
203D ARG* 2.9 24.6 + - - -
213D ASN* 3.6 22.3 + - + +
214D GLY* 1.3 77.1 - - - -
216D GLY* 1.3 61.5 + - - +
217D SER* 3.0 10.4 + - - +
234D PHE 3.3 7.9 - - - +
235D HIS* 3.3 31.6 - + + +
236D TYR* 3.2 7.0 + - - -
237D LYS* 4.8 11.1 + - - -
305D HIS* 6.3 2.2 - + - -
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Residues in contact with GLY 216 (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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145D LEU* 4.4 18.2 - - - -
146D VAL 4.2 1.9 - - - +
147D GLY* 4.5 3.4 - - - -
215D TYR* 1.3 71.6 - - - +
217D SER* 1.3 56.7 + - - +
218D HIS* 2.7 25.7 + - - -
220D PHE* 4.0 9.8 - - - -
234D PHE* 3.0 28.1 + - - -
236D TYR* 4.0 3.8 - - - -
600D HEM 3.8 11.7 - - - +
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Residues in contact with SER 217 (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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148D ASN* 4.4 5.2 + - - +
150D THR 2.9 26.0 + - - -
151D PRO* 3.7 17.9 - - - +
152D ILE 4.2 2.4 + - - -
153D PHE* 6.4 0.2 - - - -
215D TYR* 3.0 10.3 + - - +
216D GLY* 1.3 77.8 - - - +
218D HIS* 1.3 66.0 + - - +
233D LYS* 3.3 25.5 + - - +
234D PHE 4.5 2.0 + - - +
299D LEU* 4.0 20.9 - - - +
600D HEM 4.0 19.4 - - - +
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Residues in contact with HIS 218 (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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216D GLY 2.7 17.3 + - - -
217D SER* 1.3 79.8 + - - +
219D THR* 1.3 61.2 + - - +
220D PHE* 3.3 33.0 + + + -
232D CYS 4.0 1.7 - - - +
233D LYS* 3.6 9.2 - - - +
234D PHE 5.1 0.2 + - - -
299D LEU* 3.6 30.6 - - + +
348D ASP* 2.8 23.0 + - - +
350D MET* 3.7 5.8 - - + -
351D LEU* 3.6 39.6 - - + +
354D ARG* 3.2 43.1 + - - -
600D HEM 4.4 8.8 - - + +
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Residues in contact with THR 219 (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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217D SER 3.9 0.2 + - - -
218D HIS* 1.3 71.9 - - - +
220D PHE* 1.3 62.7 + - - +
231D TYR* 3.9 16.2 - - + -
232D CYS 3.5 4.9 - - - +
233D LYS* 3.4 14.3 + - - +
296D PRO 2.6 23.6 + - - +
297D PHE* 3.8 25.6 - - + -
303D TRP* 3.5 33.0 - - + -
346D SER* 2.9 22.9 + - - -
348D ASP* 4.2 5.0 + - - -
351D LEU* 4.2 6.4 - - - +
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Residues in contact with PHE 220 (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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145D LEU* 4.3 13.9 - - + -
146D VAL 5.8 1.3 - - - -
216D GLY 4.0 11.7 - - - -
218D HIS* 3.3 44.6 - + + -
219D THR* 1.3 75.0 - - - +
221D LYS* 1.3 62.6 + - - +
231D TYR* 3.3 7.7 - - - +
232D CYS* 2.8 45.8 + - - -
234D PHE* 3.5 35.0 - + + -
336D PRO* 5.5 4.3 - - + -
339D MET* 4.2 16.2 - - + -
343D ILE* 5.0 4.9 - - + -
344D GLU 3.8 15.7 - - - +
346D SER* 4.5 2.0 - - - -
351D LEU* 3.8 31.4 - - + -
354D ARG* 5.4 3.1 - - - -
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Residues in contact with LYS 221 (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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220D PHE* 1.3 74.2 - - - +
222D LEU* 1.3 78.2 + - - +
223D VAL* 3.9 3.6 - - - -
229D ALA* 4.0 9.2 - - + -
230D VAL 3.6 6.7 - - - +
231D TYR* 4.1 17.9 - - + -
286D PHE* 4.6 0.4 - - + -
343D ILE* 3.7 1.6 - - - +
344D GLU* 2.6 67.4 + - - +
345D ALA 3.4 20.8 + - - +
421D HIS* 3.1 48.8 + - + +
423D ILE* 4.1 18.1 - - + +
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D ILE* 5.5 5.2 - - + -
94D TYR* 3.9 26.2 - - + +
95D SER* 3.7 19.3 - - - -
100D PHE* 5.4 3.4 - - + -
221D LYS* 1.3 80.1 - - - +
223D VAL* 1.3 64.4 + - - +
228D GLU 3.5 0.7 - - - +
229D ALA* 3.0 25.8 - - - +
230D VAL* 2.7 26.9 + - + +
232D CYS* 3.5 30.1 - - + -
234D PHE* 4.8 9.2 - - + -
281D ILE* 4.9 12.6 - - + -
283D VAL* 5.9 1.3 - - + -
342D GLY 3.5 14.4 - - - +
343D ILE* 3.8 19.1 - - + -
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Residues in contact with VAL 223 (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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94D TYR 3.3 3.4 - - - -
95D SER* 3.4 0.2 - - - -
96D LYS* 3.0 29.0 + - + +
221D LYS* 3.9 11.2 - - + -
222D LEU* 1.3 79.6 - - - +
224D ASN* 1.3 71.2 + - - +
227D GLY* 3.9 23.8 - - - +
228D GLU 3.3 2.5 - - - +
229D ALA* 4.4 1.3 - - + -
342D GLY* 2.9 26.6 + - - +
344D GLU* 3.7 26.7 - - + +
421D HIS* 3.8 21.1 - - + +
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Residues in contact with ASN 224 (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 THR 4.2 3.8 - - - +
93D LYS* 3.8 19.6 + - - +
94D TYR 3.0 22.9 + - - +
95D SER 4.1 0.2 - - - -
96D LYS* 3.6 10.2 - - - +
223D VAL* 1.3 81.8 - - - +
225D ALA* 1.3 61.7 + - - +
226D ASN* 2.8 24.2 + - - -
227D GLY 3.1 8.1 + - - -
228D GLU* 2.6 64.8 + - - +
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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