Contacts of the strand formed by residues 219 - 226 (chain K) in PDB entry 6G2T
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 VAL 219 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158K VAL* 5.1 11.7 - - + -
177K ARG* 3.4 58.1 - - + +
178K VAL 3.5 12.8 - - - +
179K ALA* 4.8 6.5 - - + -
213K TYR* 4.9 1.1 - - - -
214K ASP* 3.8 25.9 + - - +
217K SER* 3.1 24.5 + - - +
218K LYS* 1.3 79.6 - - - +
220K TYR* 1.3 67.0 + - - +
221K LEU* 3.8 3.2 + - + +
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Residues in contact with TYR 220 (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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176K ALA 3.7 1.4 - - - +
177K ARG* 3.4 5.4 - - - -
178K VAL* 2.8 45.1 + - + +
180K GLY* 4.0 22.8 - - - -
185K LYS 5.1 1.7 - - - -
186K PRO* 3.9 29.4 - - + +
187K PRO* 3.6 25.6 - - + -
212K SER 4.0 4.7 - - - +
213K TYR* 3.2 47.5 - + + -
218K LYS 5.3 0.2 - - - -
219K VAL* 1.3 74.6 - - - +
221K LEU* 1.3 61.1 + - - +
222K PHE* 3.8 25.4 + + + -
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Residues in contact with LEU 221 (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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159K MET* 6.3 0.2 - - - -
175K SER* 3.9 24.7 - - - +
176K ALA 4.2 0.4 - - - +
177K ARG* 3.7 35.0 - - + +
210K HIS* 4.1 1.0 - - - +
211K ASP* 3.8 1.4 - - - -
212K SER* 3.2 48.7 + - - +
219K VAL* 3.8 3.8 + - + +
220K TYR* 1.3 71.2 - - - +
222K PHE* 1.3 67.2 + - - +
223K GLU* 3.4 28.0 - - + +
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Residues in contact with PHE 222 (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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175K SER* 3.1 5.4 - - - -
176K ALA* 2.8 44.8 + - + +
178K VAL* 3.6 34.3 - - + -
186K PRO* 6.2 0.2 - - + -
187K PRO* 3.4 29.4 - - + -
189K VAL* 3.6 35.4 - - + -
191K TRP* 4.1 7.0 - - + +
211K ASP* 3.2 30.1 - - + +
212K SER 5.3 1.6 - - - -
220K TYR* 3.8 27.8 - + + -
221K LEU* 1.3 79.2 - - - +
223K GLU* 1.3 61.4 + - - +
241K VAL* 4.1 13.7 - - + -
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Residues in contact with GLU 223 (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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173K THR* 4.5 7.1 - - + +
174K PHE 3.4 4.5 - - - +
175K SER* 3.7 15.9 - - - +
191K TRP* 4.2 6.1 + - - -
209K LEU* 3.8 9.0 - - - +
210K HIS* 3.0 49.0 + - - +
211K ASP* 4.2 1.5 + - - +
221K LEU* 3.4 29.0 - - + +
222K PHE* 1.3 79.7 - - - +
224K LEU* 1.3 61.2 + - - +
225K HIS* 3.1 34.7 + - + +
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Residues in contact with LEU 224 (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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172K ILE 4.0 0.5 - - - +
173K THR* 3.4 6.9 - - - +
174K PHE* 2.7 51.1 + - + +
191K TRP* 3.6 34.8 - - + -
199K LEU* 3.7 20.6 - - + -
207K LEU* 3.9 23.3 - - + -
208K GLN 3.9 2.7 - - - +
209K LEU* 3.4 24.5 - - + -
223K GLU* 1.3 74.6 - - - +
225K HIS* 1.3 65.2 + - - +
226K ILE* 4.6 15.9 - - + -
237K TYR* 4.6 2.2 - - + -
252K PHE* 4.3 10.8 - - + -
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Residues in contact with HIS 225 (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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172K ILE 3.9 1.1 - - - -
173K THR* 3.1 33.5 + - + +
206K HIS 3.9 0.2 - - - +
207K LEU* 3.4 7.1 - - - +
208K GLN* 2.8 59.9 + - + +
210K HIS* 4.2 22.5 - - + +
223K GLU* 3.1 30.7 + - + +
224K LEU* 1.3 76.7 - - - +
226K ILE* 1.3 65.0 + - - +
227K THR* 5.1 8.1 - - + -
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Residues in contact with ILE 226 (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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171K SER* 3.2 6.5 - - - -
172K ILE* 2.9 54.8 + - + +
174K PHE* 4.3 11.9 - - + -
206K HIS 3.6 6.3 - - - +
207K LEU* 4.7 11.7 - - + -
224K LEU* 4.6 13.0 - - + -
225K HIS* 1.3 77.6 - - - +
227K THR* 1.3 65.1 + - - +
229K ALA* 4.4 13.0 - - + -
233K PHE* 4.2 25.6 - - + -
237K TYR* 3.9 16.8 - - + +
254K LEU* 3.4 28.9 - - + -
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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