Contacts of the strand formed by residues 193 - 198 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H TYR* 3.5 23.6 - - - +
149H THR* 3.9 5.7 - - + +
166H ALA* 3.5 34.1 - - + -
167H GLY* 2.9 11.4 + - - +
170H GLY* 3.5 28.0 - - - +
172H ILE* 3.8 20.4 - - + -
189H HIS* 3.9 28.9 - - + +
191H ASN 3.5 0.2 + - - -
192H ALA* 1.3 72.3 - - - +
194H ASN* 1.3 61.4 + - - +
195H GLU 3.7 17.9 - - - +
196H LEU* 4.2 6.7 - - + -
208H SER* 4.6 1.1 - - - -
209H VAL 3.3 19.3 - - - +
210H SER* 4.2 0.4 - - - -
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Residues in contact with ASN 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H TYR* 4.1 13.8 - - - -
149H THR* 4.0 3.5 - - - -
192H ALA* 3.8 9.2 + - - +
193H ILE* 1.3 77.6 - - - +
195H GLU* 1.3 56.2 + - - +
209H VAL 3.0 5.7 + - - -
211H LYS* 4.0 7.7 - - - +
238H GLU* 3.5 22.0 + - - +
239H VAL 3.2 20.8 + - - +
240H LEU* 3.4 39.0 - - - +
364H TRP* 5.3 0.6 - - - -
365H TYR* 2.8 25.8 + - + -
367H ARG* 2.6 24.9 + - - -
7S M3L 4.8 5.9 - - - -
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Residues in contact with GLU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H THR* 3.6 11.7 + - - +
193H ILE* 3.6 4.8 - - - +
194H ASN* 1.3 80.9 - - - +
196H LEU* 1.3 75.6 + - - +
197H LYS* 4.1 12.0 + - + +
207H LEU 3.9 0.7 - - - +
208H SER* 3.8 0.3 - - - -
209H VAL* 3.1 39.0 + - + +
240H LEU 3.7 8.5 - - - +
241H SER* 2.5 35.2 + - - +
242H ALA 4.5 4.0 - - - +
313H ARG* 3.3 23.4 + - - -
367H ARG* 3.6 23.6 + - - +
415H GLN* 4.0 9.5 + - - -
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Residues in contact with LEU 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLN* 5.6 0.3 - - - +
149H THR* 3.0 25.9 + - + +
150H CYS 4.9 1.3 - - - +
151H ALA* 4.3 16.4 - - + +
164H ALA* 3.9 25.8 - - + +
165H VAL* 3.8 8.1 - - - +
166H ALA* 3.8 27.8 - - + +
172H ILE* 4.3 11.2 - - + -
193H ILE* 4.2 6.1 - - + -
195H GLU* 1.3 78.1 - - - +
197H LYS* 1.3 79.7 + - - +
206H LEU* 3.7 21.5 - - + -
207H LEU 3.3 2.5 - - - -
208H SER* 3.7 30.5 - - - -
209H VAL* 6.4 0.2 - - - -
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Residues in contact with LYS 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLN* 5.4 7.2 - - - -
151H ALA* 4.6 4.5 - - - -
195H GLU* 4.1 12.3 - - + -
196H LEU* 1.3 86.7 - - - +
198H PHE* 1.3 64.6 + - - +
206H LEU* 3.2 4.9 - - - +
207H LEU* 2.7 43.6 + - + +
209H VAL* 6.6 0.2 - - + -
242H ALA* 2.7 36.3 + - + +
243H ASP* 3.7 22.4 + - - +
244H TYR* 3.5 24.7 - - + -
313H ARG* 3.2 32.7 - - - +
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Residues in contact with PHE 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H HIS* 6.1 0.7 - - + +
151H ALA* 3.5 30.7 - - + +
152H TRP 3.9 9.9 - - - +
153H THR* 3.5 31.9 - - + +
164H ALA* 3.8 10.5 - - + -
174H ILE* 4.8 2.0 - - + -
197H LYS* 1.3 76.3 - - - +
199H HIS* 1.3 68.2 + - - +
200H PRO* 3.3 5.4 - - - +
203H PRO* 3.1 33.2 - - + -
204H ASN 4.4 0.2 - - - -
205H LEU 3.5 11.2 - - - -
206H LEU* 3.6 38.6 - - + -
220H ILE* 3.7 17.9 - - + -
244H TYR* 3.4 14.4 - - - +
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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
------------------------------------------------------------
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