Contacts of the strand formed by residues 191 - 199 (chain E) in PDB entry 6I53
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 HIS 191 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E ASP 4.6 9.7 + - - -
175E VAL* 3.9 20.3 + - + -
178E VAL* 4.0 32.9 - - + +
179E GLU* 4.5 13.0 - - - -
190E GLU* 1.3 79.1 - - - +
192E ARG* 1.3 68.6 + - - +
193E LEU* 4.8 7.6 - - + -
210E LEU* 4.3 15.5 - - + -
211E SER 3.3 17.0 - - - +
212E PHE* 3.9 16.2 - - + -
1F NAG 5.0 0.7 - - - -
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Residues in contact with ARG 192 (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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190E GLU* 3.5 27.0 + - - -
191E HIS* 1.3 79.4 - - - +
193E LEU* 1.3 71.6 + - - +
194E VAL* 4.2 8.5 - - + -
209E SER 3.6 2.1 - - - +
210E LEU* 3.7 2.1 - - - +
211E SER* 3.3 37.4 + - - +
213E ARG* 4.2 6.1 - - - +
1F NAG 3.1 41.2 + - + +
2F NAG 2.8 33.8 + - - -
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Residues in contact with LEU 193 (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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168E TRP* 3.8 33.0 - - + +
171E GLY 3.3 26.5 - - - +
172E ASP* 3.9 30.1 + - - +
174E ALA* 4.1 13.0 - - + -
175E VAL* 3.7 17.9 - - + +
191E HIS* 4.8 6.5 - - + -
192E ARG* 1.3 83.9 - - - +
194E VAL* 1.3 62.3 - - - +
195E SER 4.2 0.5 + - - -
209E SER 3.8 1.8 - - - +
210E LEU* 3.7 20.6 - - + -
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Residues in contact with VAL 194 (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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168E TRP* 3.8 4.3 + - - +
192E ARG* 4.8 8.7 - - + -
193E LEU* 1.3 80.7 - - - +
195E SER* 1.3 65.9 + - - +
196E ARG* 4.6 9.8 - - + +
207E ARG 4.0 0.7 - - - +
208E LEU* 3.5 5.5 - - - -
209E SER* 3.1 46.4 + - - +
211E SER* 5.5 2.0 - - - +
1F NAG 4.6 2.5 - - - +
2F NAG 3.8 59.9 - - - +
3F BMA 4.2 13.9 - - - +
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Residues in contact with SER 195 (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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166E PHE 3.8 13.0 + - - -
167E TYR* 4.8 3.6 - - - +
168E TRP* 4.6 7.2 - - - -
193E LEU 4.2 1.2 + - - -
194E VAL* 1.3 73.6 - - - +
196E ARG* 1.3 64.8 + - - +
207E ARG 3.8 4.2 + - - -
208E LEU* 3.6 19.8 - - - +
3F BMA 3.5 17.6 + - - +
5F MAN 4.9 0.3 - - - +
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Residues in contact with ARG 196 (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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153E GLU* 4.2 6.9 + - - -
194E VAL* 4.6 9.1 - - + +
195E SER* 1.3 80.4 + - - +
197E ASN* 1.3 78.5 + - - +
198E VAL* 3.9 14.3 - - - +
206E PRO* 3.8 1.0 - - - +
207E ARG* 3.0 69.5 + - + +
209E SER* 5.7 2.2 + - - -
2F NAG 3.4 53.5 + - - +
3F BMA 3.8 3.6 - - - -
5F MAN 3.8 25.8 - - - -
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Residues in contact with ASN 197 (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 THR* 4.0 23.3 + - - +
196E ARG* 1.3 88.6 - - - +
198E VAL* 1.3 70.0 + - - +
199E VAL* 5.5 3.3 - - + +
204E ALA* 5.2 8.3 - - + -
205E TYR 3.4 7.6 - - - +
206E PRO* 3.4 20.6 - - - +
5F MAN 4.3 12.6 + - - +
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Residues in contact with VAL 198 (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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155E GLU* 3.6 14.1 - - - +
196E ARG* 3.9 20.9 - - - +
197E ASN* 1.3 79.0 - - - +
199E VAL* 1.3 64.6 + - - +
200E PHE* 3.9 6.9 + - + -
203E GLY 3.9 0.3 - - - +
204E ALA* 3.3 2.6 - - - -
205E TYR* 2.7 48.2 + - + +
207E ARG* 3.4 56.3 - - + +
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Residues in contact with VAL 199 (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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197E ASN* 5.5 2.2 - - + +
198E VAL* 1.3 79.6 - - - +
200E PHE* 1.3 78.4 + - - +
203E GLY 3.9 7.4 - - - +
204E ALA* 4.3 14.8 - - + +
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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