Contacts of the strand formed by residues 198 - 205 (chain K) in PDB entry 3STJ
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 LEU 198 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K VAL* 4.1 16.6 - - + -
70K ILE* 5.2 1.1 - - + -
78K LEU* 4.8 7.9 - - + -
127K ILE* 3.7 18.3 - - + +
128K ALA 2.7 17.0 + - - +
129K ILE* 4.3 15.3 - - + -
130K ALA* 2.9 23.7 + - - +
190K ALA* 3.7 27.8 - - + -
191K LEU 3.5 4.0 - - - +
192K LEU* 4.1 5.6 - - + +
196K GLY 4.1 0.2 + - - -
197K GLU* 1.3 67.9 - - - +
199K ILE* 1.3 60.3 + - - +
200K GLY 3.3 25.4 - - - +
201K ILE* 3.6 22.7 - - + -
221K SER* 3.3 18.2 + - - +
224K ALA* 5.5 0.4 - - + -
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Residues in contact with ILE 199 (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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130K ALA* 3.9 10.1 - - + -
131K ASP 5.7 0.4 - - - +
132K SER* 3.9 3.8 - - - -
135K LEU* 3.9 39.7 - - + -
140K PHE 4.8 2.0 - - - +
141K ALA* 4.1 17.3 - - + -
159K VAL* 4.2 8.3 - - + -
176K ILE* 3.1 21.3 - - - +
191K LEU* 2.7 45.0 + - + +
192K LEU 3.9 8.3 - - - +
193K ASN* 3.8 33.4 - - + +
197K GLU 3.3 0.9 + - - +
198K LEU* 1.3 75.6 - - - +
200K GLY* 1.3 57.1 + - - +
221K SER* 3.1 22.2 + - - -
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Residues in contact with GLY 200 (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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176K ILE* 4.3 1.3 - - - -
190K ALA 3.7 0.2 - - - -
191K LEU* 2.7 40.7 + - - +
198K LEU* 3.3 11.6 - - - +
199K ILE* 1.3 80.4 - - - +
201K ILE* 1.3 62.9 + - - -
218K ALA* 4.2 4.5 - - - -
219K ILE 3.0 14.1 - - - -
221K SER* 3.8 6.8 - - - -
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Residues in contact with ILE 201 (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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68K VAL* 4.4 8.5 - - + -
78K LEU* 3.6 31.4 - - + -
79K THR 4.5 7.6 - - - +
80K ASN* 3.6 25.6 - - - +
113K ILE* 5.2 2.0 - - + -
188K GLY* 3.8 23.6 - - - +
189K GLY 3.3 7.6 - - - +
198K LEU* 3.6 30.1 - - + -
200K GLY* 1.3 71.4 - - - +
202K ASN* 1.4 53.7 + - - +
203K THR* 2.6 26.0 + - - +
218K ALA* 3.6 2.4 - - - +
219K ILE* 2.8 34.6 + - + +
224K ALA* 3.9 11.9 - - + -
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Residues in contact with ASN 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K ASN* 3.3 1.4 - - - +
143K ALA* 3.7 11.3 - - - +
144K VAL 4.1 3.8 - - - +
178K THR* 4.8 0.2 - - - +
182K ILE* 3.5 36.2 - - + +
186K ASN* 3.6 19.6 - - + +
187K SER* 3.4 3.2 - - - -
188K GLY* 2.8 31.2 + - - -
189K GLY 2.8 15.4 + - - +
190K ALA 3.0 24.8 - - - +
191K LEU* 3.6 24.0 - - - +
201K ILE* 1.4 67.8 - - - +
203K THR* 1.3 56.6 + - - +
217K PHE 3.8 3.6 - - - -
218K ALA* 3.7 8.0 - - - +
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Residues in contact with THR 203 (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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80K ASN* 3.3 20.1 + - - +
82K HIS* 3.3 20.8 + - - -
112K ASP* 3.7 17.9 - - - +
170K GLU* 3.8 13.7 - - - +
175K PHE* 4.2 15.0 - - + -
182K ILE* 5.4 2.6 - - - +
187K SER* 4.1 7.0 + - - +
201K ILE 2.6 23.1 + - - -
202K ASN* 1.3 71.7 + - - +
204K ALA* 1.3 58.5 + - + +
217K PHE 2.8 12.9 + - - -
219K ILE* 3.2 24.7 + - + +
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Residues in contact with ALA 204 (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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169K LEU* 3.9 37.2 - - + -
170K GLU* 5.2 1.6 - - - +
175K PHE* 4.8 2.5 - - + -
182K ILE* 4.7 1.5 - - - +
203K THR* 1.3 84.0 - - + +
205K ILE* 1.3 66.2 - - - +
217K PHE* 2.7 39.4 + - + +
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Residues in contact with ILE 205 (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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169K LEU* 4.9 5.5 - - - +
182K ILE* 3.4 49.6 - - + +
183K ASN* 4.6 10.3 - - - -
184K ARG* 5.1 4.7 - - + +
204K ALA* 1.3 82.4 - - - +
206K LEU* 1.3 68.2 + - - +
207K ALA* 3.7 26.4 + - + -
210K GLY 4.5 8.3 - - - +
211K GLY 4.3 1.6 - - - -
212K SER* 4.1 13.9 - - - +
215K ILE 3.4 9.2 - - - +
216K GLY* 4.0 6.7 - - - -
217K PHE* 4.3 4.7 - - - -
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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