Contacts of the strand formed by residues 208 - 215 (chain G) in PDB entry 5DST
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 LEU 208 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178G LYS* 3.5 13.4 - - - -
179G VAL* 3.8 6.1 - - - +
180G ASP 3.7 14.1 - - - +
181G ILE 4.3 0.4 - - - +
182G ILE* 4.0 15.6 - - + +
203G ALA 3.7 1.6 + - - -
204G ARG* 2.9 45.6 + - + +
205G ASP 4.8 1.6 - - - +
207G TRP* 1.3 78.8 - - - +
209G LYS* 1.3 72.7 + - - +
210G PRO* 4.5 0.2 - - - +
212G GLY* 3.7 31.9 - - - +
213G LEU 3.8 10.1 - - - +
214G MET* 3.9 21.1 - - + -
281G TYR* 4.8 5.2 - - + -
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Residues in contact with LYS 209 (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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113G LYS* 3.9 18.4 - - - +
178G LYS* 3.6 17.5 - - + -
179G VAL 3.1 20.9 + - - +
180G ASP* 2.8 35.3 + - - +
207G TRP 3.3 1.0 + - - -
208G LEU* 1.3 79.4 - - - +
210G PRO* 1.3 88.1 - - + +
211G GLY 3.2 4.4 + - - -
212G GLY* 2.9 32.1 + - - +
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Residues in contact with PRO 210 (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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178G LYS* 4.8 9.4 - - + -
208G LEU 4.0 1.8 - - - +
209G LYS* 1.3 99.8 - - + +
211G GLY* 1.3 60.6 + - - +
212G GLY 3.3 0.3 + - - -
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Residues in contact with GLY 211 (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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209G LYS* 3.2 7.1 + - - -
210G PRO* 1.3 71.4 - - - +
212G GLY* 1.3 66.6 + - - +
213G LEU* 4.0 11.3 - - - +
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Residues in contact with GLY 212 (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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180G ASP 3.3 15.0 - - - -
208G LEU* 3.7 14.5 - - - +
209G LYS* 2.9 26.5 + - - -
210G PRO 3.1 2.0 + - - -
211G GLY* 1.3 85.2 - - - +
213G LEU* 1.3 62.6 + - - +
281G TYR* 3.6 15.9 - - - -
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Residues in contact with LEU 213 (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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109G VAL* 3.3 36.6 - - + -
113G LYS* 6.5 0.4 - - + -
180G ASP 3.2 6.2 + - - +
181G ILE* 3.4 12.8 - - + -
182G ILE 3.0 23.4 + - - -
208G LEU* 3.8 1.7 - - - +
211G GLY 4.0 9.2 - - - +
212G GLY* 1.3 80.2 - - - +
214G MET* 1.3 69.2 + - - +
215G PHE* 4.3 11.9 - - + -
281G TYR* 3.8 3.8 - - + +
317G LYS* 3.8 42.4 - - + -
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Residues in contact with MET 214 (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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182G ILE* 3.3 25.8 - - + +
200G VAL* 3.6 31.6 - - + -
204G ARG* 3.9 36.8 - - + -
208G LEU* 3.9 9.4 - - + -
213G LEU* 1.3 81.2 - - - +
215G PHE* 1.3 71.8 + - - +
216G PRO* 3.6 13.1 - - - +
217G ASP* 3.3 26.6 - - + +
280G ILE* 3.6 24.7 - - + +
281G TYR* 3.2 25.2 + - + -
315G PHE* 5.2 1.0 - - - -
317G LYS* 5.0 0.3 - - - +
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Residues in contact with PHE 215 (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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99G TYR* 3.9 4.2 - - + -
102G SER* 3.3 44.2 - - - +
103G MET* 4.6 2.2 - - + -
106G ASN* 5.5 0.7 - - + -
109G VAL* 4.3 17.3 - - + -
110G PHE* 3.8 27.1 - + - -
181G ILE* 4.0 15.9 - - + -
182G ILE 2.9 8.1 + - - +
183G ILE* 3.4 18.9 - - + -
184G SER* 3.0 26.0 + - - +
213G LEU* 4.3 18.6 - - + -
214G MET* 1.3 83.0 - - - +
216G PRO* 1.3 63.3 - - - +
315G PHE* 3.6 15.3 - + + -
317G LYS* 4.8 11.7 - - + -
318G CYS* 4.1 12.6 - - - -
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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