Contacts of the strand formed by residues 208 - 215 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178K LYS* 3.7 11.6 - - - -
179K VAL* 3.6 17.0 - - - +
180K ASP 3.9 8.3 - - - +
182K ILE* 4.2 17.4 - - + +
203K ALA 3.8 1.2 + - - -
204K ARG* 2.9 51.5 + - + +
205K ASP 5.0 1.6 - - - +
206K LYS 3.8 0.2 - - - -
207K TRP* 1.3 73.3 - - - +
209K LYS* 1.3 72.1 + - - +
210K PRO* 3.8 1.0 - - - +
212K GLY* 3.8 28.3 - - - +
213K LEU 4.0 9.4 - - - +
214K MET* 3.9 19.5 - - + -
281K TYR* 4.7 4.9 - - + -
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Residues in contact with LYS 209 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113K LYS* 3.9 17.4 - - - +
178K LYS* 3.6 18.6 - - + -
179K VAL 3.1 19.3 + - - +
180K ASP* 2.8 36.8 + - - +
207K TRP 3.4 1.4 + - - -
208K LEU* 1.3 80.3 - - - +
210K PRO* 1.3 82.9 - - + +
211K GLY 3.3 4.7 + - - -
212K GLY* 2.8 38.4 + - - +
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Residues in contact with PRO 210 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D PRO* 5.2 15.0 - - + -
178K LYS* 4.9 9.6 - - + -
208K LEU 3.8 2.2 - - - +
209K LYS* 1.3 97.9 - - + +
211K GLY* 1.3 59.9 + - - +
212K GLY 3.4 0.2 + - - -
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Residues in contact with GLY 211 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209K LYS* 3.3 7.4 + - - -
210K PRO* 1.3 72.9 - - - +
212K GLY* 1.3 66.8 + - - +
213K LEU* 3.9 11.1 + - - +
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Residues in contact with GLY 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K ASP 3.4 14.1 - - - -
208K LEU* 3.8 15.1 - - - +
209K LYS* 2.8 26.2 + - - -
210K PRO 3.2 1.0 + - - -
211K GLY* 1.3 84.1 - - - +
213K LEU* 1.3 62.7 + - - +
281K TYR* 3.6 15.9 - - - -
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Residues in contact with LEU 213 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109K VAL* 3.3 34.8 - - + -
113K LYS* 6.5 0.2 - - + -
180K ASP 3.2 6.8 + - - +
181K ILE* 3.3 13.3 - - + +
182K ILE 2.9 25.2 + - - -
208K LEU* 4.0 1.7 - - - +
211K GLY 4.0 8.7 - - - +
212K GLY* 1.3 78.6 - - - +
214K MET* 1.3 67.0 + - - +
215K PHE* 4.2 11.2 - - + -
281K TYR* 3.9 3.6 - - - +
317K LYS* 3.7 43.5 - - + -
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Residues in contact with MET 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K ILE* 3.3 25.1 - - + +
200K VAL* 3.6 31.6 - - + -
204K ARG* 3.7 41.1 - - + -
208K LEU* 3.9 11.0 - - + -
213K LEU* 1.3 79.8 - - - +
215K PHE* 1.3 70.3 + - - +
216K PRO* 3.5 12.5 - - - +
217K ASP* 3.1 29.7 - - + +
280K ILE* 3.7 21.1 - - + +
281K TYR* 3.4 24.3 + - + -
315K PHE* 5.3 0.5 - - - -
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Residues in contact with PHE 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K TYR* 4.0 3.5 - - + -
102K SER* 3.5 41.3 - - - -
103K MET* 4.7 2.2 - - + -
106K ASN* 5.6 0.7 - - + -
109K VAL* 4.3 16.6 - - + -
110K PHE* 3.9 26.2 - + - -
181K ILE* 3.9 17.3 - - + -
182K ILE* 2.9 7.3 + - - +
183K ILE* 3.4 19.7 - - + -
184K SER* 3.1 25.5 + - - +
213K LEU* 4.2 18.6 - - + -
214K MET* 1.3 83.3 - - - +
216K PRO* 1.3 62.6 - - - +
315K PHE* 3.7 16.6 - + + -
317K LYS* 4.8 11.7 - - + -
318K CYS* 4.0 15.9 - - - -
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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