Contacts of the strand formed by residues 198 - 205 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68J VAL* 4.1 16.8 - - + -
70J ILE* 5.3 1.3 - - + -
78J LEU* 4.7 12.3 - - + -
127J ILE* 3.7 19.7 - - + +
128J ALA 2.8 17.4 + - - +
129J ILE* 4.2 16.4 - - + -
130J ALA* 2.9 26.7 + - - +
190J ALA* 3.7 27.6 - - + -
191J LEU 3.7 4.0 - - - +
192J LEU* 4.0 6.0 - - + +
196J GLY 4.1 0.2 + - - -
197J GLU* 1.3 69.4 - - - +
199J ILE* 1.3 59.8 + - - +
200J GLY 3.4 25.1 - - - +
201J ILE* 4.3 16.8 - - + -
221J SER* 3.4 18.8 + - - +
224J ALA* 5.5 0.9 - - + -
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Residues in contact with ILE 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ALA* 3.9 15.7 - - + -
131J ASP 5.7 0.4 - - - +
132J SER* 3.8 4.3 - - - -
135J LEU* 3.9 41.3 - - + -
140J PHE 4.9 1.3 - - - +
141J ALA* 4.1 10.3 - - + -
159J VAL* 4.3 6.7 - - + -
176J ILE* 3.1 16.0 - - - +
191J LEU* 2.9 46.6 + - + +
192J LEU 3.9 14.1 - - - +
193J ASN* 4.0 15.7 - - + +
197J GLU 3.4 7.8 + - - +
198J LEU* 1.3 77.6 - - - +
200J GLY* 1.3 59.0 + - - +
221J SER* 3.0 24.5 + - - +
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Residues in contact with GLY 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J ILE* 4.3 0.7 - - - -
190J ALA* 3.8 0.3 - - - -
191J LEU* 3.0 30.9 + - - -
198J LEU* 3.4 15.1 - - - +
199J ILE* 1.3 79.8 - - - +
201J ILE* 1.4 63.4 + - - -
202J ASN 4.0 0.9 - - - -
218J ALA* 4.2 9.0 - - - -
219J ILE 3.1 14.6 - - - -
220J PRO* 4.3 0.2 - - - -
221J SER* 3.8 5.3 - - - +
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Residues in contact with ILE 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J VAL* 3.6 31.2 - - + -
78J LEU* 4.2 26.7 - - + -
79J THR 4.6 7.0 - - - +
80J ASN* 3.7 24.9 - - - +
113J ILE* 5.3 2.9 - - + -
188J GLY* 3.7 22.4 - - - +
189J GLY 3.4 2.0 - - - +
198J LEU* 4.3 8.3 - - + -
200J GLY* 1.4 74.0 - - - +
202J ASN* 1.4 54.9 + - - +
203J THR* 2.6 25.3 + - - +
218J ALA* 3.8 2.0 - - - -
219J ILE* 2.8 34.4 + - + +
224J ALA* 4.1 21.8 - - + -
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Residues in contact with ASN 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J ASN* 3.0 1.9 - - - +
143J ALA* 3.6 14.4 - - - +
144J VAL 4.4 2.8 + - - +
178J THR* 4.7 0.2 - - - +
182J ILE* 3.6 37.8 - - + +
186J ASN* 4.1 14.5 - - + +
187J SER* 3.5 3.0 - - - -
188J GLY* 2.8 30.0 + - - -
189J GLY 2.8 15.1 + - - +
190J ALA 3.3 20.4 - - - +
191J LEU* 3.4 25.4 - - - +
200J GLY 4.0 0.2 - - - -
201J ILE* 1.4 69.6 - - - +
203J THR* 1.4 56.6 + - - +
217J PHE 3.8 2.9 - - - -
218J ALA* 3.5 10.5 - - - +
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Residues in contact with THR 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J ASN* 3.2 28.1 + - - +
82J HIS* 3.3 19.9 + - - -
112J ASP* 3.5 18.2 - - - +
170J GLU* 3.7 14.1 - - - +
175J PHE* 4.0 14.8 - - + -
182J ILE* 5.6 1.3 - - - +
187J SER* 4.2 6.8 + - - -
201J ILE 2.6 21.9 + - - -
202J ASN* 1.4 69.9 - - - +
204J ALA* 1.3 59.2 + - + +
217J PHE 2.9 13.2 + - - -
219J ILE* 3.2 18.8 - - + +
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Residues in contact with ALA 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J LEU* 3.9 38.4 - - + -
170J GLU* 5.3 0.7 - - - +
175J PHE* 5.0 1.3 - - + -
182J ILE* 4.8 1.8 - - - +
203J THR* 1.3 86.1 - - + +
205J ILE* 1.3 66.5 + - - +
217J PHE* 2.7 38.2 + - + +
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Residues in contact with ILE 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J LEU* 5.1 5.2 - - - +
182J ILE* 3.4 50.0 - - + +
183J ASN* 4.5 10.8 - - - -
184J ARG* 5.1 3.6 - - + +
204J ALA* 1.3 82.7 - - - +
206J LEU* 1.3 69.0 + - - +
207J ALA* 3.6 26.5 + - + -
210J GLY 4.5 8.1 - - - +
211J GLY 4.3 2.0 - - - -
212J SER* 4.2 12.8 - - - +
215J ILE 3.5 9.2 - - - +
216J GLY* 4.0 7.0 - - - -
217J PHE* 4.2 5.2 - - - -
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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