Contacts of the strand formed by residues 201 - 207 (chain G) in PDB entry 5DK3
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 TYR 201 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145G LEU* 3.7 36.6 - - + -
161G TRP* 4.4 4.5 - + + -
162G ASN* 3.6 5.8 - - - -
166G LEU* 3.6 33.7 - - + -
191G VAL* 3.7 33.1 - - + +
192G PRO* 4.4 2.8 - - - +
195G SER* 3.6 27.7 + - - -
196G LEU* 4.6 6.3 - - - -
199G LYS* 3.8 30.5 - - + +
200G THR* 1.3 79.3 - - - +
202G THR* 1.3 62.7 + - - +
217G ARG* 3.9 0.9 - - - -
218G VAL* 3.0 24.5 + - + +
219G GLU* 2.9 27.2 + - + +
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Residues in contact with THR 202 (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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161G TRP* 3.4 8.1 - - - -
162G ASN* 2.8 43.8 + - - -
200G THR* 3.8 7.4 - - - +
201G TYR* 1.3 70.8 - - - +
203G CYS* 1.3 65.2 + - - +
204G ASN* 3.7 20.1 + - - +
215G ASP* 4.0 16.6 - - + -
216G LYS 3.4 13.2 - - - +
217G ARG* 3.2 27.7 + - + +
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Residues in contact with CYS 203 (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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128G VAL* 3.9 6.3 - - - -
147G CYS* 2.0 51.1 - - + -
159G VAL* 4.1 5.8 - - + -
160G SER 3.3 10.8 - - - +
161G TRP* 3.7 21.2 - - + -
202G THR* 1.3 73.0 - - - +
204G ASN* 1.3 58.9 + - - +
205G VAL* 3.8 16.4 - - - -
214G VAL 3.4 1.9 - - - +
215G ASP* 3.4 2.6 - - - -
216G LYS* 3.0 36.6 + - - -
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Residues in contact with ASN 204 (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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158G THR* 3.4 2.1 + - - +
159G VAL* 3.3 4.3 - - - -
160G SER* 2.8 46.7 + - - +
162G ASN 3.7 1.0 + - - -
163G SER* 2.8 45.3 + - - +
202G THR* 3.7 14.3 - - - +
203G CYS* 1.3 74.0 - - - +
205G VAL* 1.3 61.2 + - - +
206G ASP* 4.1 0.6 + - - +
214G VAL 3.5 4.9 - - - -
215G ASP* 2.9 28.0 + - - +
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Residues in contact with VAL 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G PRO* 4.2 10.5 - - + -
128G VAL* 3.9 20.6 - - + -
149G VAL* 3.7 43.5 - - + -
157G VAL* 4.6 7.4 - - + -
158G THR 3.3 7.0 - - - +
159G VAL* 4.4 8.1 - - + -
203G CYS* 3.8 25.4 - - - -
204G ASN* 1.3 75.0 - - - +
206G ASP* 1.3 62.4 + - - +
207G HIS 4.3 0.4 - - - +
212G THR 4.0 0.5 - - - +
213G LYS* 3.5 4.7 - - - +
214G VAL* 2.8 40.7 + - + +
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Residues in contact with ASP 206 (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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156G PRO 4.3 0.5 - - - +
157G VAL* 3.3 7.2 - - - -
158G THR* 2.9 48.7 + - + +
204G ASN 4.1 0.8 + - - +
205G VAL* 1.3 74.4 - - - +
207G HIS* 1.3 66.4 + - - +
208G LYS* 3.5 35.7 + - - +
211G ASN* 5.3 0.9 - - - -
212G THR 3.1 16.0 + - - +
213G LYS* 3.3 31.0 - - + +
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Residues in contact with HIS 207 (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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124G LYS 3.2 24.9 + - - -
125G GLY* 3.8 2.4 - - - -
126G PRO* 3.6 15.7 - - + -
152G TYR* 3.8 3.7 - + + -
153G PHE 3.3 13.7 - - - -
154G PRO 2.7 24.4 + - - -
156G PRO 3.5 19.3 - - - -
157G VAL* 3.5 16.8 - - + -
205G VAL* 4.3 0.4 - - - +
206G ASP* 1.3 73.5 - - - +
208G LYS* 1.3 63.3 + - - +
209G PRO* 3.7 14.5 - - + +
210G SER* 2.8 31.5 + - - -
211G ASN 3.2 2.8 + - - -
212G THR* 3.0 40.4 + - - +
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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