Contacts of the strand formed by residues 198 - 205 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F VAL* 4.1 16.2 - - + -
70F ILE* 5.3 0.7 - - + -
78F LEU* 4.7 11.0 - - + -
127F ILE* 3.8 17.5 - - + +
128F ALA 2.8 16.6 + - - +
129F ILE* 4.2 16.2 - - + -
130F ALA* 2.9 24.3 + - - +
190F ALA* 3.8 26.9 - - + -
191F LEU 3.6 3.6 - - - +
192F LEU* 4.0 5.6 - - + +
196F GLY 4.1 0.4 + - - -
197F GLU* 1.3 68.7 - - - +
199F ILE* 1.3 60.0 + - - +
200F GLY 3.4 25.1 - - - +
201F ILE* 4.3 19.1 - - + -
221F SER* 3.4 18.7 + - - +
224F ALA* 5.5 0.9 - - + -
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Residues in contact with ILE 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ALA* 3.9 17.7 - - + -
131F ASP 5.7 0.4 - - - +
132F SER* 3.8 4.7 - - - -
135F LEU* 3.9 39.9 - - + -
140F PHE 4.9 1.8 - - - +
141F ALA* 4.1 17.0 - - + -
159F VAL* 4.2 8.1 - - + -
176F ILE* 3.2 15.1 - - - +
191F LEU* 2.8 45.6 + - + +
192F LEU 3.9 7.4 - - - +
193F ASN* 4.0 21.1 - - + +
197F GLU 3.4 0.8 + - - +
198F LEU* 1.3 76.6 - - - +
200F GLY* 1.3 57.4 + - - +
220F PRO* 3.6 0.2 - - - +
221F SER* 2.9 25.6 + - - +
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Residues in contact with GLY 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ILE* 4.3 4.5 - - - -
190F ALA 3.8 0.2 - - - -
191F LEU* 2.8 39.9 + - - +
198F LEU* 3.4 11.9 - - - +
199F ILE* 1.3 82.1 - - - +
201F ILE* 1.3 61.3 + - - -
218F ALA* 4.3 1.6 - - - -
219F ILE 3.1 14.1 - - - -
221F SER* 3.7 6.5 - - - -
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Residues in contact with ILE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F VAL* 3.5 35.9 - - + -
78F LEU* 4.2 20.2 - - + -
79F THR 4.6 7.6 - - - +
80F ASN* 4.0 14.4 - - - +
113F ILE* 5.3 2.7 - - + -
188F GLY* 3.6 29.2 - - - +
189F GLY 3.4 2.0 - - - +
198F LEU* 4.3 12.3 - - + -
200F GLY* 1.3 73.7 - - - +
202F ASN* 1.3 61.8 + - - +
203F THR* 2.9 10.3 + - - +
218F ALA* 3.1 2.1 - - - -
219F ILE* 2.7 44.1 + - + +
224F ALA* 4.2 20.6 - - + -
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Residues in contact with ASN 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ASN* 2.8 3.1 - - - +
143F ALA* 4.0 7.8 - - - +
144F VAL 4.1 3.5 - - - +
182F ILE* 3.6 40.5 - - + +
186F ASN* 3.8 17.9 - - - +
187F SER* 3.5 2.8 - - - -
188F GLY* 2.8 27.8 + - - -
189F GLY 3.0 9.5 + - - +
190F ALA 3.0 25.3 + - - +
191F LEU* 3.4 26.5 - - - +
201F ILE* 1.3 69.2 - - - +
203F THR* 1.3 58.2 + - - +
217F PHE 3.8 4.2 + - - -
218F ALA* 3.8 7.5 - - - +
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Residues in contact with THR 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ASN* 3.2 28.5 + - - +
82F HIS* 3.3 20.1 + - - -
112F ASP* 3.5 17.9 - - - +
170F GLU* 3.6 14.6 - - - +
175F PHE* 4.0 15.0 - - + -
182F ILE* 5.7 1.7 - - - +
187F SER* 4.2 6.0 - - - -
201F ILE 2.9 15.9 + - - -
202F ASN* 1.3 71.9 - - - +
204F ALA* 1.3 59.2 + - + +
217F PHE 2.9 14.0 + - - -
219F ILE* 3.2 18.8 - - + +
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Residues in contact with ALA 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F LEU* 3.9 37.9 - - + -
170F GLU* 5.3 1.3 - - - +
175F PHE* 5.0 1.8 - - + -
182F ILE* 4.7 2.0 - - - +
203F THR* 1.3 85.4 - - + +
205F ILE* 1.3 67.5 + - - +
217F PHE* 2.8 37.4 + - + +
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Residues in contact with ILE 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 5.1 5.2 - - - +
182F ILE* 3.4 50.0 - - + +
183F ASN* 4.6 10.5 - - - -
184F ARG* 5.2 3.8 - - + +
204F ALA* 1.3 84.7 - - - +
206F LEU* 1.4 68.3 + - - +
207F ALA* 3.6 26.7 + - + -
210F GLY 4.6 7.6 - - - +
211F GLY 4.3 1.6 - - - -
212F SER* 4.1 14.1 - - - +
215F ILE 3.4 13.9 - - - +
216F GLY* 4.2 2.0 - - - -
217F PHE* 4.2 4.5 - - - -
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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