Contacts of the strand formed by residues 198 - 205 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D VAL* 4.1 11.7 - - + -
70D ILE* 5.3 1.3 - - + -
78D LEU* 4.8 11.0 - - + -
127D ILE* 3.8 17.9 - - + +
128D ALA 2.7 17.0 + - - +
129D ILE* 4.2 15.7 - - + -
130D ALA* 2.9 24.3 + - - +
190D ALA* 3.8 26.7 - - + -
191D LEU 3.6 3.6 - - - +
192D LEU* 4.1 5.4 - - + +
196D GLY 4.1 0.2 + - - -
197D GLU* 1.4 67.9 - - - +
199D ILE* 1.3 58.2 + - - +
200D GLY 3.4 24.2 - - - +
201D ILE* 3.9 24.5 - - + -
221D SER* 3.4 19.2 + - - +
224D ALA* 5.5 0.7 - - + -
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Residues in contact with ILE 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ALA* 3.9 17.7 - - + -
131D ASP 5.7 0.2 - - - +
132D SER* 3.8 4.2 - - - -
135D LEU* 3.8 41.3 - - + -
140D PHE 4.9 1.8 - - - +
141D ALA* 4.0 17.7 - - + -
159D VAL* 4.3 6.7 - - + -
176D ILE* 3.1 16.0 - - + +
191D LEU* 2.8 44.5 + - + +
192D LEU 3.9 8.1 - - - +
193D ASN* 3.9 20.0 - - + +
197D GLU 4.0 2.2 - - - +
198D LEU* 1.3 78.5 - - - +
200D GLY* 1.3 58.4 + - - +
220D PRO* 3.7 0.2 - - - +
221D SER* 3.0 25.9 + - - -
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Residues in contact with GLY 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ILE* 4.4 1.1 - - - -
190D ALA 3.8 0.2 - - - -
191D LEU* 2.8 38.0 + - - -
198D LEU* 3.4 13.8 - - - +
199D ILE* 1.3 81.2 - - - +
201D ILE* 1.3 63.3 + - - -
218D ALA* 4.3 5.2 - - - -
219D ILE 3.1 13.5 - - - -
220D PRO* 4.3 0.2 - - - -
221D SER* 3.8 6.1 - - - -
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D VAL* 3.6 33.7 - - + -
78D LEU* 4.3 17.7 - - + -
79D THR 4.8 6.3 - - - +
80D ASN* 3.8 16.6 - - - +
113D ILE* 5.6 2.5 - - + -
188D GLY* 3.7 30.1 - - - +
189D GLY 3.4 3.1 - - - +
198D LEU* 3.9 18.6 - - + -
200D GLY* 1.3 73.4 - - - +
202D ASN* 1.3 56.0 + - - +
203D THR* 2.8 14.6 + - - -
218D ALA* 3.7 2.5 - - - -
219D ILE* 2.8 43.9 + - + +
224D ALA* 4.1 22.4 - - + -
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Residues in contact with ASN 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.0 1.9 - - - +
143D ALA* 3.6 12.5 - - - +
144D VAL 4.1 3.8 - - - +
182D ILE* 3.7 36.7 - - + +
186D ASN* 3.6 21.3 - - - +
187D SER* 3.4 3.3 - - - -
188D GLY 2.9 29.1 + - - -
189D GLY 2.9 13.0 + - - +
190D ALA 3.2 21.0 + - - +
191D LEU* 3.5 25.7 - - - +
200D GLY 4.1 0.2 - - - -
201D ILE* 1.3 67.6 - - - +
203D THR* 1.3 58.5 + - - +
217D PHE 3.8 4.3 - - - -
218D ALA* 3.8 7.4 - - - +
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Residues in contact with THR 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.2 22.8 + - - +
82D HIS* 3.3 18.2 - - - -
112D ASP* 3.5 23.3 - - - +
170D GLU* 3.6 14.6 - - - +
175D PHE* 4.0 15.3 - - + -
182D ILE* 5.6 2.1 - - - +
187D SER* 3.5 7.9 + - - -
201D ILE 2.8 16.1 + - - -
202D ASN* 1.3 71.0 - - - +
204D ALA* 1.4 59.7 + - + +
217D PHE 2.9 13.8 + - - -
219D ILE* 3.2 17.6 - - + +
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 3.9 37.5 - - + -
170D GLU* 5.3 1.1 - - - +
175D PHE* 5.0 2.2 - - + -
182D ILE* 4.7 2.0 - - - +
203D THR* 1.4 85.4 - - + +
205D ILE* 1.3 66.8 + - - +
217D PHE* 2.8 38.2 + - + +
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Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 5.0 5.5 - - - +
182D ILE* 3.4 48.9 - - + +
183D ASN* 4.6 9.6 - - - -
184D ARG* 5.2 3.1 - - + +
204D ALA* 1.3 83.7 - - - +
206D LEU* 1.3 67.2 + - - +
207D ALA* 3.7 26.8 + - + -
210D GLY 4.5 8.7 - - - +
211D GLY 4.3 1.3 - - - -
212D SER* 4.1 13.2 - - - +
215D ILE 3.4 9.6 - - - +
216D GLY* 4.0 6.5 - - - -
217D PHE* 4.2 5.4 - - - -
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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
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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