Contacts of the strand formed by residues 202 - 209 (chain E) in PDB entry 5IYB
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 ARG 202 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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965A VAL* 4.9 17.6 - - - +
1036A ASN* 3.2 52.0 + - + +
1039A LEU* 4.1 23.7 - - + +
194E ILE* 4.2 22.8 - - + +
195E ARG 3.5 10.8 - - - +
196E PRO* 5.6 0.2 - - + -
197E SER* 4.3 1.3 - - - -
200E ALA* 3.2 11.9 + - - +
201E GLY* 1.3 80.0 - - - +
203E TYR* 1.3 64.9 + - - +
204E ILE* 4.8 5.8 - - + -
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Residues in contact with TYR 203 (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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887A VAL 4.7 1.2 + - - -
888A GLN* 3.4 15.9 - - + +
889A LEU* 3.1 39.5 + - + +
890A ARG* 4.8 2.7 - - + -
893A GLU* 3.1 64.2 - - + +
1036A ASN* 4.6 2.0 - - - +
1403A ASP* 5.5 0.4 - - - -
193E ILE 4.0 0.9 - - - +
194E ILE* 3.9 1.0 - - - +
195E ARG* 3.0 65.9 + - + +
197E SER* 4.3 6.7 - - - -
202E ARG* 1.3 75.7 - - - +
204E ILE* 1.3 79.6 + - - +
205E THR* 4.1 15.0 + - - -
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Residues in contact with ILE 204 (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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889A LEU* 4.3 13.7 - - - +
1032A GLN* 3.4 29.2 - - - +
1033A ALA* 5.7 2.0 - - - -
1036A ASN* 3.4 28.5 - - + +
192E LYS* 4.0 22.4 - - + -
193E ILE 3.6 4.0 - - - +
194E ILE* 4.5 20.4 - - + -
202E ARG* 4.8 6.7 - - + -
203E TYR* 1.3 95.8 + - - +
205E THR* 1.3 63.9 + - - +
206E TYR* 3.8 27.8 - - + +
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Residues in contact with THR 205 (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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889A LEU* 4.8 6.5 - - - +
1372A GLU* 4.4 0.7 - - - +
171E PRO* 4.5 10.4 - - - +
192E LYS* 3.6 4.0 - - - +
193E ILE* 2.8 61.9 + - + +
195E ARG* 3.8 28.1 + - - +
203E TYR* 4.1 19.7 + - - -
204E ILE* 1.3 74.7 - - - +
206E TYR* 1.3 80.5 + - - +
207E ARG* 5.0 3.3 + - - +
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Residues in contact with TYR 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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889A LEU* 4.0 28.0 - - + +
1029A LEU* 3.9 19.0 - - + +
1032A GLN* 5.9 0.3 + - - -
151E MET* 3.9 20.4 - - + -
159E LEU* 3.6 50.6 - - + +
163E TYR* 4.9 2.6 + + - -
170E LEU* 4.9 12.1 - - + -
171E PRO* 3.7 19.8 - - + +
190E VAL* 4.2 8.3 - - + -
191E VAL 3.5 4.5 - - - -
192E LYS* 3.8 26.9 - - + +
204E ILE* 3.8 21.4 - - + +
205E THR* 1.3 83.1 + - - +
207E ARG* 1.3 74.6 + - - +
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Residues in contact with ARG 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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1371A ILE* 3.2 44.5 - - - +
1372A GLU* 2.7 27.7 + - - -
1375A ARG* 6.0 1.6 - - - +
1406A THR* 4.0 18.5 + - - -
1407A CYS* 5.4 0.9 - - - -
170E LEU* 5.2 0.7 - - - -
171E PRO* 3.4 22.8 - - - +
172E ARG 2.8 24.0 + - - +
173E ILE* 4.0 14.4 - - + +
190E VAL* 3.3 6.9 - - - -
191E VAL* 2.8 53.1 + - + +
193E ILE* 3.4 22.7 - - + -
195E ARG* 4.1 9.3 - - - +
205E THR* 5.0 3.9 + - + +
206E TYR* 1.3 83.1 - - - +
208E LEU* 1.3 60.8 + - - +
209E VAL 3.8 0.2 + - - -
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Residues in contact with LEU 208 (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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167E GLU* 3.8 41.1 - - + +
168E ASN* 4.8 4.5 - - - +
170E LEU* 4.5 9.2 - - + +
171E PRO 3.0 13.6 + - - +
172E ARG* 3.4 9.9 - - + +
173E ILE* 2.8 23.1 + - - -
188E GLY* 3.3 30.1 - - - +
189E GLN 3.7 4.3 - - - +
190E VAL* 3.9 14.1 - - + +
207E ARG* 1.3 71.9 - - - +
209E VAL* 1.3 74.2 + - - +
210E GLN* 3.5 22.3 + - + +
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Residues in contact with VAL 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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173E ILE* 3.6 22.0 - - + +
174E GLN 4.4 0.9 - - - +
175E ALA* 3.9 27.4 - - + -
180E ALA* 5.3 1.1 - - + -
185E ILE* 3.8 33.0 - - + +
186E LYS 4.1 5.6 - - - +
187E ARG* 3.9 17.6 - - - +
188E GLY* 3.1 27.1 + - - +
189E GLN 2.8 24.7 + - - +
191E VAL* 4.9 4.3 - - + -
207E ARG 4.8 2.7 - - - +
208E LEU* 1.3 73.6 - - - +
210E GLN* 1.3 67.7 + - - +
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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