Contacts of the strand formed by residues 208 - 214 (chain E) in PDB entry 6GYK
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 208 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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864A ILE 5.2 0.5 + - - -
865A GLN* 4.1 10.0 - - + +
866A PHE* 3.4 31.3 + + - -
867A ILE* 4.4 19.0 + - + -
870A GLU* 3.6 50.0 - - + -
199E ILE* 3.7 3.1 - - - +
200E ARG* 2.9 81.9 + - + +
202E SER* 4.1 17.6 - - - +
205E SER* 4.2 3.3 + - - +
206E GLY 4.2 0.2 - - - -
207E ARG* 1.3 75.4 - - - +
209E ALA* 1.3 75.2 + - - +
210E SER* 4.3 3.4 - - - -
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Residues in contact with ALA 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A PHE* 4.1 7.3 - - - +
867A ILE* 5.9 0.5 - - - +
1013A ASP* 5.1 11.1 - - + +
197E LYS* 3.7 29.2 - - - +
198E ILE 3.5 4.7 - - - -
199E ILE* 4.7 4.0 - - + +
207E ARG* 4.2 2.6 + - + -
208E TYR* 1.3 96.3 + - - +
210E SER* 1.3 60.9 + - - +
211E TYR* 4.8 11.5 - - + +
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Residues in contact with SER 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A PHE* 3.8 15.8 - - - -
176E PRO* 5.1 3.6 - - - +
197E LYS* 3.3 10.7 - - - +
198E ILE* 2.9 40.0 + - - -
200E ARG* 3.4 28.4 + - - -
208E TYR* 4.3 2.0 - - - -
209E ALA* 1.3 75.8 - - - +
211E TYR* 1.3 77.3 + - - +
212E ARG* 4.5 10.6 + - - +
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Residues in contact with TYR 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A PHE* 3.7 26.8 - + + -
1006A ILE* 3.6 25.3 - - + +
156E LEU* 4.5 13.5 - - + -
160E GLU* 5.7 1.8 - - - -
164E LEU* 3.6 47.8 - - + -
168E TYR* 4.3 14.4 - - - -
175E LEU* 4.5 7.0 - - + +
176E PRO* 3.4 26.2 - - - +
195E VAL* 4.4 3.6 - - + -
196E VAL 3.4 4.5 - - - +
197E LYS* 3.8 46.4 + - + -
209E ALA* 4.8 7.9 - - + +
210E SER* 1.3 85.5 + - - +
212E ARG* 1.3 64.5 + - - +
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Residues in contact with ARG 212 (chain E).
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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1341A ILE* 4.2 21.4 - - - +
1342A GLU* 2.6 35.1 + - - -
1345A ARG* 5.4 7.1 - - - +
1376A THR* 3.8 28.9 + - - -
153E HIS* 6.2 0.2 - - - -
175E LEU* 5.1 1.6 - - - -
176E PRO* 3.2 26.1 - - + +
177E ARG 3.9 15.0 + - - -
178E ILE* 4.1 27.5 - - + +
195E VAL* 3.1 10.0 - - - +
196E VAL* 2.9 35.0 + - + -
198E ILE* 3.7 18.7 - - + +
200E ARG* 4.3 6.3 - - - +
210E SER* 4.5 8.6 + - - +
211E TYR* 1.3 78.8 - - - +
213E ILE* 1.3 62.1 + - - +
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Residues in contact with ILE 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LYS* 4.2 16.8 - - - +
172E GLU* 3.7 39.0 - - + +
175E LEU* 3.6 29.8 - - + +
176E PRO 3.1 5.9 + - - +
177E ARG* 3.2 8.9 - - + -
178E ILE* 2.8 25.8 + - - -
193E GLY* 4.4 11.7 - - - -
194E GLU 3.5 11.4 - - - +
195E VAL* 4.1 13.9 - - + -
212E ARG* 1.3 76.6 - - - +
214E CYS* 1.3 75.5 + - - +
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Residues in contact with CYS 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E ARG* 5.3 2.3 - - - +
178E ILE* 3.3 18.9 - - + +
179E GLN 4.8 0.4 - - - -
180E ARG* 4.2 29.8 - - - -
185E ALA* 5.7 1.3 - - - -
190E LEU* 4.9 13.2 - - + -
191E LYS* 3.3 33.7 - - - +
192E ARG* 4.4 3.6 - - - -
193E GLY 4.4 4.1 + - - +
194E GLU 3.3 9.4 + - - +
213E ILE* 1.3 94.0 - - - +
215E MET* 1.3 83.9 + - - +
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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