Contacts of the strand formed by residues 193 - 198 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148K TYR* 3.7 9.4 - - - +
149K THR* 4.1 1.4 - - + +
166K ALA* 3.7 17.3 - - + -
167K GLY* 3.2 25.2 + - - +
170K GLY* 3.2 42.4 - - - +
171K ILE 3.6 3.8 - - - +
172K ILE* 3.7 20.2 - - + -
189K HIS* 4.0 23.8 - - + +
191K ASN 3.5 0.6 + - - -
192K ALA* 1.3 71.6 - - - +
194K ASN* 1.3 59.5 + - - +
195K GLU 3.2 30.1 - - - +
196K LEU* 3.7 16.6 - - + -
208K SER* 4.2 9.0 - - - -
209K VAL 3.4 7.9 - - - +
210K SER* 4.2 0.4 - - - -
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Residues in contact with ASN 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K TYR* 4.0 16.3 - - - -
149K THR* 3.8 5.6 - - - -
192K ALA* 3.6 5.3 + - - +
193K ILE* 1.3 74.3 - - - +
195K GLU* 1.3 56.5 + - - +
209K VAL 2.9 5.6 + - - +
211K LYS* 3.8 11.3 - - - +
238K GLU* 3.7 17.2 + - - +
239K VAL 3.2 26.1 + - - +
240K LEU* 3.5 33.3 - - - +
364K TRP* 5.4 0.9 - - - -
365K TYR* 2.9 28.2 + - + -
367K ARG* 2.6 27.0 + - - -
7T M3L 4.6 5.9 - - - -
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Residues in contact with GLU 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149K THR* 3.6 16.3 + - - +
193K ILE* 3.2 8.1 - - - +
194K ASN* 1.3 79.1 - - - +
196K LEU* 1.3 73.2 + - - +
197K LYS* 4.0 12.8 - - + -
207K LEU 4.1 0.4 - - - +
208K SER* 3.5 0.5 - - - -
209K VAL* 3.0 42.5 + - + +
240K LEU 3.7 2.7 - - - +
241K SER* 2.5 36.2 + - - -
242K ALA* 4.4 8.5 - - + +
313K ARG* 3.4 23.7 + - - -
367K ARG* 3.8 19.6 + - - +
415K GLN* 4.6 6.4 + - - -
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Residues in contact with LEU 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K THR* 3.6 22.1 + - + +
150K CYS* 4.7 0.9 - - - +
151K ALA* 3.5 21.6 - - + +
164K ALA* 3.7 25.8 - - + +
165K VAL 3.6 16.2 - - - +
166K ALA* 3.5 21.3 - - + -
172K ILE* 3.9 14.4 - - + -
193K ILE* 3.7 9.2 - - + -
195K GLU* 1.3 76.8 - - - +
197K LYS* 1.3 71.3 + - - +
206K LEU* 3.8 18.8 - - + -
207K LEU 3.4 2.2 - - - -
208K SER* 3.5 28.7 - - - -
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Residues in contact with LYS 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K GLN* 6.2 4.5 - - - +
151K ALA* 4.4 6.7 - - + -
195K GLU* 4.0 17.2 + - + -
196K LEU* 1.3 80.1 - - - +
198K PHE* 1.3 65.3 + - - +
206K LEU* 3.3 4.8 - - - +
207K LEU* 2.9 38.1 + - + +
242K ALA* 3.2 29.4 + - + +
243K ASP* 3.6 20.8 + - - +
244K TYR* 4.0 18.8 - - + -
313K ARG* 3.4 33.5 - - - +
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Residues in contact with PHE 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K HIS* 5.9 1.3 - - - +
151K ALA* 3.3 32.8 - - + +
152K TRP 3.5 21.1 - - - +
153K THR* 3.4 34.1 - - + +
164K ALA* 3.7 22.2 - - + -
174K ILE* 4.5 2.7 - - + -
197K LYS* 1.3 77.9 - - - +
199K HIS* 1.3 67.3 + - - +
200K PRO* 3.4 3.8 - - - +
203K PRO 3.4 20.6 - - - -
205K LEU 3.6 4.5 - - - -
206K LEU* 3.7 35.4 - - + -
220K ILE* 3.8 14.1 - - + -
244K TYR* 3.4 16.1 - - - -
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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