Contacts of the strand formed by residues 218 - 222 (chain G) in PDB entry 5N9G
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 LYS 218 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172G VAL 3.7 4.3 - - - +
173G ASN* 3.8 36.1 - - + +
213G ILE* 4.0 1.2 - - - +
214G PHE* 3.0 34.9 + - + +
216G SER* 3.4 21.2 + - - +
217G GLY* 1.3 79.7 - - - +
219G MET* 1.3 61.9 + - - +
220G VAL* 6.5 0.2 - - + -
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Residues in contact with MET 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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171G THR* 3.3 6.9 - - - +
172G VAL* 2.8 58.1 + - + +
174G LEU* 4.4 21.1 - - + -
211G ALA* 4.3 2.7 - - + -
212G LEU 3.3 12.8 - - - +
213G ILE* 3.9 19.7 - - + -
214G PHE* 5.0 0.2 - - - -
218G LYS* 1.3 78.2 - - - +
220G VAL* 1.3 72.5 + - - +
221G CYS* 5.0 4.0 - - + -
234G ALA* 3.3 36.1 - - + +
237G TYR* 3.6 28.7 - - + -
238G ALA 4.5 1.3 - - - +
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Residues in contact with VAL 220 (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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169G VAL* 3.9 26.0 - - + -
170G SER 3.4 4.9 - - - +
171G THR* 4.0 15.0 - - + -
210G THR 3.9 0.5 - - - +
211G ALA* 3.2 5.5 - - - +
212G LEU* 2.8 50.2 + - + +
214G PHE* 4.5 16.2 - - + -
219G MET* 1.3 75.8 - - - +
221G CYS* 1.3 60.8 + - - +
222G THR* 4.0 13.3 + - + +
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Residues in contact with CYS 221 (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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168G ILE 3.3 4.7 - - - +
169G VAL* 3.4 2.1 - - - +
170G SER* 2.8 48.0 + - - +
171G THR 6.4 0.2 - - - -
209G THR* 4.4 9.9 - - - -
210G THR 3.7 2.9 - - - -
211G ALA* 4.5 0.9 - - - +
219G MET* 4.3 5.8 - - + -
220G VAL* 1.3 71.7 - - - +
222G THR* 1.3 62.5 + - - +
230G SER* 3.8 28.0 - - - -
233G ALA* 3.9 18.8 - - - -
234G ALA* 4.1 14.8 - - + -
237G TYR* 4.2 13.0 - - + -
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Residues in contact with THR 222 (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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167G ASN* 4.6 2.0 - - - -
168G ILE 3.5 5.8 - - - -
169G VAL* 3.9 20.9 - - + -
209G THR* 3.3 10.0 - - - -
210G THR* 2.8 52.6 + - - +
212G LEU* 5.8 6.0 - - + +
220G VAL* 4.0 17.7 - - + +
221G CYS* 1.3 77.6 - - - +
223G GLY* 1.3 60.7 + - - +
224G ALA 3.4 3.1 - - - -
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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