Contacts of the strand formed by residues 190 - 194 (chain E) in PDB entry 1SMR
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 TRP 190 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E THR* 3.4 36.0 + - - +
123E MET 3.2 18.7 + - - -
124E GLY* 4.0 4.6 - - - -
125E PHE* 3.5 24.1 - + - -
128E GLN* 5.3 0.6 + - - +
151E PHE* 3.9 8.8 - + - -
184E LEU* 3.9 19.7 - - + -
189E SER* 1.4 67.0 + - - +
191E GLN* 1.3 56.5 + - - +
213E VAL* 3.3 7.7 - - + +
214E VAL* 2.8 43.3 + - - +
313E PHE* 3.8 22.0 - + + -
314E ASP 3.8 39.0 - - - -
315E ARG* 3.4 38.1 - - + -
319E ARG 3.9 5.8 - - - -
320E ILE* 3.9 21.8 - - + -
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Residues in contact with GLN 191 (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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184E LEU* 3.1 11.9 - - - +
185E SER* 2.8 23.2 + - - +
186E LYS* 3.7 29.6 + - + +
189E SER* 2.8 29.4 + - - +
190E TRP* 1.3 75.0 - - - +
192E ILE* 1.3 67.8 + - - +
211E GLU* 2.9 43.3 + - - +
212E VAL 3.3 14.4 - - - +
213E VAL* 4.0 7.4 - - + +
295E THR 5.5 2.2 + - - +
298E VAL* 4.3 11.2 - - - +
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Residues in contact with ILE 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E VAL* 4.3 21.1 - - + +
183E SER 3.7 19.3 - - - +
184E LEU* 4.1 13.0 - - + -
185E SER* 3.5 13.2 - - - +
191E GLN* 1.3 81.2 - - - +
193E THR* 1.3 59.8 + - - +
211E GLU* 3.7 3.3 - - - +
212E VAL* 3.0 41.8 + - + +
214E VAL* 4.2 17.7 - - + -
262E LEU* 3.7 34.8 - - + -
301E LEU* 5.3 0.2 - - + -
320E ILE* 4.2 13.2 - - + -
322E PHE* 4.4 8.7 - - + -
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Residues in contact with THR 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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182E VAL* 5.2 3.8 - - - +
183E SER 5.1 1.2 + - - -
185E SER* 3.1 18.0 + - - -
192E ILE* 1.3 77.1 - - - +
194E MET* 1.3 68.8 - - - +
195E LYS* 4.1 18.7 + - + +
209E GLY* 4.3 8.5 - - - -
210E CYS 3.5 12.6 - - - +
211E GLU* 2.9 22.1 + - - +
261E ASN 4.4 2.9 - - - +
262E LEU* 4.5 5.0 - - - +
263E GLY 4.6 8.7 + - - -
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Residues in contact with MET 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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192E ILE 3.9 0.8 + - - -
193E THR* 1.3 73.3 - - - +
195E LYS* 1.3 61.0 + - - +
196E GLY 3.5 19.1 + - - +
197E VAL* 3.5 14.4 - - + -
206E CYS* 3.6 2.3 - - + +
209E GLY* 3.3 2.1 - - - -
210E CYS* 2.7 50.0 + - + +
212E VAL* 4.1 15.3 - - + -
260E PHE* 3.4 33.4 - - + -
261E ASN 3.5 9.9 - - - +
262E LEU* 3.9 15.0 - - + -
299E TRP* 3.5 46.9 - - + -
301E LEU* 5.4 1.6 - - + -
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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