Contacts of the strand formed by residues 205 - 213 (chain E) in PDB entry 6A5T
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 GLY 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943A PHE* 4.5 13.7 - - - -
947A ILE* 5.6 1.2 - - - +
948A VAL* 4.3 18.9 - - - +
1019A LEU* 4.1 12.3 - - - +
199E ARG 3.3 3.1 - - - +
200E ARG* 3.6 5.0 - - - -
201E SER* 2.8 36.8 + - - -
203E THR 3.9 0.2 - - - -
204E SER* 1.3 75.2 - - - +
206E ARG* 1.3 58.7 + - - -
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Residues in contact with ARG 206 (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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943A PHE* 3.5 31.8 - - + -
947A ILE* 3.9 15.4 - - - +
1015A ASN* 2.7 59.1 + - - +
1016A ALA* 4.7 0.3 - - - -
1018A SER* 5.0 8.8 + - - +
198E ILE* 3.8 30.7 - - + +
199E ARG 3.7 2.5 - - - +
204E SER* 3.0 11.4 + - - -
205E GLY* 1.3 73.7 - - - +
207E TYR* 1.3 60.6 + - - +
208E ALA* 5.5 0.2 - - + -
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Residues in contact with TYR 207 (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 GLN* 3.3 11.4 - - + -
867A PHE* 2.4 45.5 + - + +
868A LEU* 3.2 21.3 + - + -
871A GLU* 3.2 58.3 - - + +
1015A ASN* 5.4 0.2 - - - -
1376A ASP* 5.8 1.1 - - - -
198E ILE* 3.6 2.0 - - - -
199E ARG* 2.9 73.7 + - + +
201E SER* 4.3 4.0 - - - -
204E SER* 4.8 1.1 - - - +
205E GLY 4.0 0.4 + - - -
206E ARG* 1.3 71.8 - - - +
208E ALA* 1.3 64.2 + - - +
209E SER* 3.6 9.1 + - - -
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Residues in contact with ALA 208 (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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867A PHE* 5.0 3.8 - - - +
1015A ASN* 4.4 24.9 - - + +
196E LYS* 4.6 13.0 - - - -
197E ILE 3.4 7.0 - - - +
198E ILE* 3.8 23.1 - - + -
206E ARG* 4.0 1.4 + - + +
207E TYR* 1.3 80.5 - - - +
209E SER* 1.3 62.9 + - - +
210E TYR* 3.8 15.8 - - + -
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Residues in contact with SER 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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867A PHE* 4.4 11.3 - - - -
1345A GLU* 6.4 1.1 - - - -
175E PRO* 5.6 1.7 - - - +
196E LYS* 3.7 4.7 - - - +
197E ILE* 2.9 40.5 + - - +
199E ARG* 3.1 34.3 + - - -
207E TYR* 3.6 7.2 + - - -
208E ALA* 1.3 74.6 - - - +
210E TYR* 1.3 70.8 + - - +
211E ARG* 4.1 9.7 + - - +
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Residues in contact with TYR 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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867A PHE* 3.3 41.5 - + + -
1008A LEU* 3.6 25.9 - - + +
155E LEU* 4.2 13.2 - - + -
163E LEU* 3.4 42.5 - - + +
167E TYR* 4.8 6.5 - - - -
174E LEU* 4.8 4.2 - - + +
175E PRO* 3.6 16.3 - - - +
194E VAL* 4.0 15.0 - - + -
195E VAL 3.8 2.2 - - - +
196E LYS* 3.7 39.2 + - + +
208E ALA* 3.8 16.8 - - + +
209E SER* 1.3 80.8 + - - +
211E ARG* 1.3 62.8 + - - +
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Residues in contact with ARG 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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1344A ILE* 3.5 31.8 - - - +
1345A GLU* 2.3 36.0 + - - -
1348A ARG* 5.1 4.2 - - - +
1376A ASP* 5.6 2.2 + - - -
1379A THR* 3.1 37.4 + - - -
1380A SER 4.4 2.2 + - - -
1382A GLY 4.6 0.6 - - - +
174E LEU* 5.2 0.2 - - - -
175E PRO* 3.9 14.8 - - + +
176E ARG 3.7 20.6 + - - +
177E ILE* 4.7 9.5 - - + +
194E VAL* 3.7 3.8 - - - +
195E VAL* 2.9 46.4 + - + +
197E ILE* 4.1 12.9 - - + +
209E SER* 4.1 9.2 + - - +
210E TYR* 1.3 75.9 - - - +
212E ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 212 (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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160E LYS* 5.3 0.2 - - - -
171E GLU* 3.1 37.5 - - + +
172E SER* 6.0 0.2 - - - -
174E LEU* 3.9 24.0 - - + +
175E PRO 2.9 24.0 + - - +
176E ARG* 3.2 17.6 - - + +
177E ILE* 2.5 36.8 + - - +
192E GLY* 5.0 10.1 - - - -
193E GLN 3.4 14.4 - - - +
194E VAL* 4.2 12.3 - - + +
210E TYR 4.3 0.4 + - - -
211E ARG* 1.3 73.0 - - - +
213E CYS* 1.3 71.4 + - - +
214E LEU* 5.3 1.1 - - + -
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Residues in contact with CYS 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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177E ILE* 3.4 22.2 - - + +
178E GLN 4.1 9.4 - - - -
179E ARG* 4.2 15.3 - - - -
184E ALA* 5.1 0.2 - - - -
189E LEU* 3.9 34.3 - - + -
190E LYS 4.4 9.4 - - - +
191E ARG* 5.2 0.3 - - - +
192E GLY 4.4 6.6 + - - -
193E GLN 3.1 13.2 + - - +
195E VAL* 5.3 0.4 - - - +
211E ARG 4.2 0.4 + - - -
212E ILE* 1.3 97.8 - - - +
214E LEU* 1.3 95.7 + - - +
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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