Contacts of the strand formed by residues 193 - 199 (chain E) in PDB entry 5LS6
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 ILE 193 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E TYR* 3.7 20.2 - - - +
149E THR* 4.5 1.0 - - + +
166E ALA* 3.7 24.8 - - + +
167E GLY* 3.1 11.9 + - - +
170E GLY* 3.1 41.3 - - - +
171E ILE 3.6 3.1 - - - +
172E ILE* 4.2 7.9 - - + -
189E HIS* 4.0 22.0 - - + +
191E ASN 4.1 2.0 - - - +
192E ALA* 1.3 72.2 - - - +
194E ASN* 1.3 61.4 + - - +
195E GLU* 3.1 29.4 - - - +
196E LEU* 3.7 17.0 - - + -
208E SER* 4.3 6.3 - - - -
209E VAL 3.2 12.8 - - - +
210E SER* 4.8 0.2 - - - -
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Residues in contact with ASN 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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148E TYR* 4.2 14.0 - - - -
149E THR* 4.1 2.4 - - - -
192E ALA* 3.8 8.7 + - - +
193E ILE* 1.3 75.3 - - - +
195E GLU* 1.3 54.7 + - - +
209E VAL 2.9 6.1 + - - -
211E LYS* 4.1 10.3 - - - +
238E GLU* 3.4 21.5 + - - +
239E VAL 3.4 16.1 + - - +
240E LEU* 3.2 42.6 - - - +
364E TRP* 5.4 1.3 - - - -
365E TYR* 2.7 28.5 + - + -
367E ARG* 2.7 24.8 + - - -
7R M3L 4.8 5.7 - - - -
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Residues in contact with GLU 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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149E THR* 3.4 17.5 + - - +
193E ILE* 3.1 16.6 - - - +
194E ASN* 1.3 78.7 - - - +
196E LEU* 1.3 80.3 + - - +
197E LYS* 3.8 15.7 - - + -
207E LEU 4.2 0.2 - - - +
209E VAL* 3.2 27.4 + - + +
240E LEU 3.7 7.0 - - - +
241E SER* 2.6 30.6 + - - -
242E ALA 3.2 12.1 + - - +
313E ARG* 2.9 23.8 + - - -
367E ARG* 3.6 19.1 + - - +
415E GLN* 4.2 8.5 + - - -
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Residues in contact with LEU 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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100E GLN* 5.2 1.2 - - - +
149E THR* 3.3 19.6 + - + +
150E CYS 4.9 1.5 - - - +
151E ALA* 4.3 17.8 - - + +
164E ALA* 4.1 11.4 - - + +
165E VAL* 3.7 15.9 - - - +
166E ALA* 3.5 35.9 - - + +
172E ILE* 4.4 9.9 - - + -
193E ILE* 3.7 7.2 - - + -
195E GLU* 1.3 82.9 - - - +
197E LYS* 1.3 78.0 + - - +
206E LEU* 4.0 15.0 - - + -
207E LEU 3.4 5.2 - - - +
208E SER* 3.5 33.2 - - - -
209E VAL* 6.3 0.2 - - - -
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Residues in contact with LYS 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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100E GLN* 5.6 5.4 - - - +
151E ALA* 4.7 4.3 - - - -
195E GLU* 3.7 16.1 + - + -
196E LEU* 1.3 86.6 - - - +
198E PHE* 1.3 62.8 + - - +
206E LEU* 3.1 8.0 - - - +
207E LEU* 2.7 45.6 + - + +
209E VAL* 6.4 0.7 - - + -
242E ALA* 2.6 39.2 + - + +
243E ASP* 3.3 24.6 + - - +
244E TYR* 3.9 19.7 - - + -
313E ARG* 3.6 26.4 - - - +
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Residues in contact with PHE 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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104E HIS* 5.7 1.8 - - + +
151E ALA* 3.6 30.9 - - + +
152E TRP 3.7 22.7 - - - +
153E THR* 3.5 26.2 - - + +
164E ALA* 3.6 17.9 - - + -
174E ILE* 4.8 2.7 - - + -
197E LYS* 1.3 77.8 - - - +
199E HIS* 1.3 66.4 + - - +
200E PRO* 3.5 4.2 - - - +
203E PRO 3.5 28.9 - - - -
205E LEU 3.8 11.4 - - - -
206E LEU* 3.7 35.0 - - + -
220E ILE* 4.0 12.8 - - + -
244E TYR* 3.3 13.8 - - - -
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Residues in contact with HIS 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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104E HIS* 6.1 0.7 - - - -
198E PHE* 1.3 75.0 - - - +
200E PRO* 1.4 70.2 - - - +
201E ARG* 3.4 17.4 + - + -
202E ASP* 3.2 45.3 + - + +
203E PRO* 4.2 2.8 - - - +
205E LEU* 2.9 38.8 + - + +
217E LEU* 5.8 0.4 - - + -
244E TYR* 3.4 29.3 - + + -
247E LEU 4.6 0.2 - - - -
248E GLY* 2.9 36.1 + - - -
265E ILE* 4.0 10.5 - - + +
274E ILE* 5.9 1.0 - - - +
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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