Contacts of the strand formed by residues 214 - 224 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C PHE* 4.2 4.9 - - - -
148C ASN 3.6 7.2 - - - -
213C ASN* 1.3 76.6 - - - +
215C TYR* 1.3 66.4 + - - -
235C HIS* 3.4 2.6 - - - -
236C TYR* 2.7 63.7 + - - -
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Residues in contact with TYR 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLY* 3.1 22.3 - - - -
148C ASN 3.1 8.3 + - - -
149C ASN 3.3 26.7 - - - -
150C THR 3.5 18.2 - - - +
151C PRO* 3.9 36.8 - - + -
203C ARG* 3.1 22.8 + - - -
213C ASN* 3.6 28.6 + - + +
214C GLY* 1.3 77.7 - - - -
216C GLY* 1.3 64.8 + - - +
217C SER* 3.8 8.4 - - - +
234C PHE 3.1 8.1 - - - +
235C HIS* 3.2 31.9 - + + +
236C TYR* 3.6 6.9 + - - -
237C LYS* 5.5 9.7 + - + -
305C HIS* 6.3 1.1 - - - -
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Residues in contact with GLY 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU* 4.0 26.9 - - - -
146C VAL 4.1 2.4 - - - +
147C GLY* 4.6 1.8 - - - -
215C TYR* 1.3 71.9 - - - +
217C SER* 1.3 59.4 + - - +
218C HIS* 2.8 22.5 + - - -
220C PHE* 4.2 10.4 - - - -
234C PHE* 2.8 23.2 + - - +
236C TYR* 4.3 0.6 + - - -
600C HEM 3.6 12.4 - - - +
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Residues in contact with SER 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ASN* 4.7 3.5 + - - +
150C THR 2.9 26.0 + - - -
151C PRO 3.5 20.9 - - - +
152C ILE 4.0 4.9 + - - -
215C TYR* 3.0 8.1 + - - +
216C GLY* 1.3 79.8 - - - +
218C HIS* 1.3 63.0 + - - +
233C LYS* 3.4 25.0 + - - +
234C PHE 4.5 2.2 + - - +
299C LEU* 3.8 20.0 - - - +
600C HEM 3.8 19.2 - - - +
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Residues in contact with HIS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLY 2.8 19.0 + - - -
217C SER* 1.3 78.6 + - - +
219C THR* 1.3 62.3 + - - +
220C PHE* 3.5 22.8 + + + -
232C CYS 3.9 1.4 - - - +
233C LYS* 3.5 12.8 - - - +
299C LEU* 3.8 14.8 - - + +
348C ASP* 2.7 23.3 + - - +
350C MET* 3.6 18.2 - - + -
351C LEU* 3.4 44.8 - - + +
354C ARG* 2.7 41.3 + - - -
600C HEM 4.1 11.0 - - + +
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Residues in contact with THR 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C HIS* 1.3 73.8 - - - +
220C PHE* 1.3 67.5 + - - +
231C TYR* 4.1 15.0 - - + -
232C CYS 3.7 4.9 - - - -
233C LYS* 2.8 21.1 + - - +
296C PRO 2.7 24.8 + - - +
297C PHE* 3.6 32.2 - - + +
303C TRP* 3.5 8.8 - - + -
346C SER* 2.8 34.6 + - - +
348C ASP* 4.4 5.4 + - - -
351C LEU* 4.0 7.3 - - - +
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Residues in contact with PHE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU* 4.3 11.9 - - + -
146C VAL 5.8 1.3 - - - -
216C GLY* 4.2 13.7 - - - -
218C HIS* 3.6 30.5 - + + -
219C THR* 1.3 75.7 - - - +
221C LYS* 1.3 61.6 + - - +
231C TYR* 3.2 8.5 - - - +
232C CYS* 2.8 41.5 + - - +
234C PHE* 3.5 43.5 - + + -
336C PRO* 5.5 3.8 - - + -
339C MET* 4.4 18.4 - - - -
343C ILE* 5.0 4.0 - - + -
344C GLU 3.8 14.1 - - - +
346C SER* 4.5 1.6 - - - -
351C LEU* 3.7 33.2 - - + -
354C ARG* 5.4 2.2 - - - -
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Residues in contact with LYS 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN* 6.1 1.0 - - - +
220C PHE* 1.3 74.3 - - - +
222C LEU* 1.3 79.6 + - - +
223C VAL* 4.4 1.1 - - + -
229C ALA* 4.0 8.3 - - + -
230C VAL 3.6 9.0 - - - +
231C TYR* 4.1 20.0 - - + -
286C PHE* 4.5 0.9 - - + -
343C ILE* 3.7 1.2 - - - +
344C GLU* 2.9 54.9 + - + +
345C ALA 3.5 20.6 + - - +
421C HIS* 3.3 45.4 + - + -
423C ILE* 3.2 30.6 - - + +
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ILE* 4.9 10.1 - - + -
94C TYR* 3.7 24.9 - - + +
95C SER* 3.7 20.0 - - - -
100C PHE* 5.3 3.8 - - + -
221C LYS* 1.3 78.6 - - - +
223C VAL* 1.3 63.9 + - - +
228C GLU 3.6 0.5 - - - +
229C ALA* 3.0 6.8 - - - +
230C VAL* 2.6 47.5 + - + +
232C CYS* 3.4 27.8 - - + -
234C PHE* 4.9 7.0 - - + -
281C ILE* 5.1 9.9 - - + -
283C VAL* 6.0 0.7 - - + -
342C GLY 3.3 15.5 - - - +
343C ILE* 3.9 21.3 - - + -
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Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C TYR 3.4 4.0 - - - -
95C SER* 3.2 0.7 - - - -
96C LYS* 2.9 35.1 + - + +
221C LYS* 4.4 3.4 - - - -
222C LEU* 1.3 80.9 - - - +
224C ASN* 1.3 73.0 + - - +
227C GLY* 3.9 21.3 - - - +
228C GLU 3.3 4.9 - - - +
229C ALA* 4.2 7.4 - - + -
342C GLY* 2.9 18.3 + - - +
344C GLU* 4.1 21.8 - - + +
421C HIS* 3.8 29.4 - - + +
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Residues in contact with ASN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR 4.0 7.4 - - - +
93C LYS* 4.0 16.7 + - - +
94C TYR* 3.2 19.1 + - - +
95C SER 3.9 0.2 - - - -
96C LYS* 3.2 18.1 - - - +
223C VAL* 1.3 79.8 - - - +
225C ALA* 1.3 63.8 + - - +
226C ASN* 2.7 22.3 + - - -
227C GLY 3.3 7.4 + - - -
228C GLU* 2.7 64.7 + - - +
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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