Contacts of the strand formed by residues 213 - 219 (chain G) in PDB entry 1QZW
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 ASP 213 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89G ASN 4.7 3.1 - - - +
90G VAL 5.4 3.3 - - - +
97G PHE* 3.8 15.9 - - + -
98G ILE 2.6 22.3 + - - +
99G ILE* 3.4 23.9 - - + -
100G MET 3.0 11.3 + - - -
212G ASP* 1.3 78.5 - - - +
214G VAL* 1.3 65.1 + - - +
215G ILE* 3.2 26.4 - - - +
239G ILE* 5.1 4.6 - - - +
241G SER* 5.2 0.3 + - - -
268G LYS* 3.3 28.3 + - - -
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Residues in contact with VAL 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G MET* 3.4 37.0 - - + +
102G VAL* 4.1 15.0 - - + -
202G MET* 5.3 3.8 - - + -
206G TYR* 3.8 19.3 - - + -
211G PRO* 3.7 21.1 - - + +
212G ASP 4.0 2.6 + - - +
213G ASP* 1.3 83.0 + - - +
215G ILE* 1.3 74.5 + - - +
233G PHE* 5.0 11.2 - - + -
237G SER* 5.6 2.5 - - - -
239G ILE* 4.2 10.9 + - + +
240G GLY* 3.7 10.0 - - - -
241G SER 3.3 18.4 + - - +
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Residues in contact with ILE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ILE* 4.3 15.5 - - + -
100G MET 2.9 12.6 + - - +
101G LEU* 3.4 16.4 - - + +
102G VAL* 2.8 37.4 + - - +
213G ASP* 3.2 28.0 - - - +
214G VAL* 1.3 88.8 - - - +
216G LEU* 1.3 79.4 + - - +
217G VAL* 4.1 8.7 - - + -
233G PHE* 5.2 1.3 - - - -
241G SER* 2.9 22.2 - - - +
242G VAL* 3.2 11.9 - - - -
243G ILE* 4.6 6.1 - - + -
268G LYS* 5.3 6.1 - - + -
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Residues in contact with LEU 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G VAL* 2.9 23.3 - - + +
103G GLY* 5.4 0.4 - - - -
104G VAL* 4.6 6.3 - - + -
198G LEU* 5.4 5.8 - - + -
215G ILE* 1.3 83.7 - - - +
217G VAL* 1.3 110.1 + - - +
218G ILE* 3.4 19.1 - - + -
229G LEU* 3.5 31.9 - - + -
230G ALA* 4.0 16.8 - - + -
233G PHE* 4.0 15.3 - - + -
242G VAL* 2.8 27.6 - - + +
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Residues in contact with VAL 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G LEU* 4.2 22.7 - - + -
102G VAL 3.7 3.7 + - - +
103G GLY* 4.7 7.2 - - - -
104G VAL* 4.2 11.3 + - - +
107G SER 4.7 5.6 - - - +
109G LYS* 4.9 7.9 - - - +
112G THR* 4.9 13.7 - - + -
215G ILE* 4.1 10.3 - - + -
216G LEU* 1.3 95.3 - - - +
218G ILE* 1.3 76.9 + - - +
243G ILE* 3.3 24.5 - - + +
245G THR* 3.7 19.3 - - + -
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Residues in contact with ILE 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G VAL* 4.3 3.6 - - + -
107G SER* 5.2 2.2 - - - -
192G TYR* 3.9 15.7 - - - +
216G LEU* 3.4 13.7 - - + -
217G VAL* 1.3 94.4 - - - +
219G ASP* 1.3 55.8 + - - +
222G ILE* 4.1 12.6 - - + -
226G ALA* 4.7 11.7 - - + -
229G LEU* 3.4 31.0 - - + -
242G VAL* 4.6 6.7 - - + -
243G ILE 2.9 21.9 + - - +
244G ILE* 2.9 29.3 - - + +
245G THR* 2.3 35.2 + - - +
256G ALA* 6.1 1.8 - - + -
260G VAL* 5.8 4.3 - - + -
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Residues in contact with ASP 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G SER* 4.8 12.0 + - - -
192G TYR* 4.8 3.0 + - - +
218G ILE* 1.3 75.2 - - - +
220G ALA* 1.3 70.7 + - - +
221G SER* 2.6 40.9 + - - -
222G ILE* 2.7 28.8 + - + +
244G ILE* 3.8 0.7 - - - -
245G THR* 2.6 25.4 + - - +
246G LYS* 3.0 39.9 + - - +
249G GLY 3.2 12.9 - - - +
250G THR* 3.3 3.5 + - - -
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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