Contacts of the strand formed by residues 198 - 205 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68G VAL* 4.1 11.4 - - + -
70G ILE* 5.3 1.3 - - + -
78G LEU* 4.8 10.8 - - + -
127G ILE* 3.7 19.2 - - + +
128G ALA 2.8 16.6 + - - +
129G ILE* 4.2 15.0 - - + -
130G ALA* 2.9 24.8 + - - +
190G ALA* 3.7 27.6 - - + -
191G LEU 3.6 3.8 - - - +
192G LEU* 4.0 5.2 - - + +
196G GLY 4.1 0.2 + - - -
197G GLU* 1.3 68.9 - - - +
199G ILE* 1.3 59.7 + - - +
200G GLY 3.4 24.9 - - - +
201G ILE* 3.9 24.7 - - + -
221G SER* 3.4 19.9 + - - +
224G ALA* 5.5 0.7 - - + -
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Residues in contact with ILE 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ALA* 3.9 17.5 - - + -
131G ASP 5.6 0.4 - - - +
132G SER* 3.8 4.7 - - - -
135G LEU* 3.9 40.8 - - + -
140G PHE 4.8 1.8 - - - +
141G ALA* 4.0 17.5 - - + -
159G VAL* 4.2 7.0 - - + -
176G ILE* 3.2 16.5 - - - +
191G LEU* 2.8 44.8 + - + +
192G LEU 3.9 7.9 - - - +
193G ASN* 3.9 19.5 - - + +
197G GLU 3.4 2.4 + - - +
198G LEU* 1.3 77.4 - - - +
200G GLY* 1.3 57.4 + - - +
220G PRO* 3.6 0.2 - - - +
221G SER* 3.0 25.5 + - - +
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Residues in contact with GLY 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G ILE* 4.5 0.4 - - - -
190G ALA 3.8 0.2 - - - -
191G LEU* 2.8 38.8 + - - +
198G LEU* 3.4 10.4 - - - +
199G ILE* 1.3 81.4 - - - +
201G ILE* 1.4 62.0 + - - -
218G ALA* 4.3 5.4 - - - -
219G ILE 3.1 14.4 - - - -
220G PRO* 4.3 0.2 - - - -
221G SER* 3.8 6.4 - - - +
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Residues in contact with ILE 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G VAL* 3.7 31.0 - - + -
78G LEU* 4.2 19.3 - - + -
79G THR 4.4 8.1 - - - +
80G ASN* 4.0 14.6 - - - +
113G ILE* 5.3 2.2 - - + -
188G GLY* 3.5 25.8 - - - +
189G GLY 3.4 2.0 - - - +
198G LEU* 3.9 22.0 - - + -
200G GLY* 1.4 69.1 - - - -
202G ASN* 1.3 61.4 + - - +
203G THR* 2.7 24.4 + - - +
218G ALA* 3.9 1.3 - - - -
219G ILE* 2.8 35.5 + - + +
224G ALA* 4.0 22.7 - - + -
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Residues in contact with ASN 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASN* 3.0 2.6 - - - +
143G ALA* 3.6 13.2 - - - +
144G VAL 4.3 2.1 + - - +
178G THR* 4.8 0.2 - - - +
182G ILE* 3.6 33.5 - - + +
186G ASN* 3.6 21.9 - - - +
187G SER* 3.4 3.0 - - - -
188G GLY 2.9 29.8 + - - -
189G GLY 3.0 8.4 + - - +
190G ALA 3.0 25.4 + - - +
191G LEU* 3.5 22.4 - - - +
200G GLY 4.0 0.2 - - - -
201G ILE* 1.3 67.8 - - - +
203G THR* 1.4 55.8 + - - +
217G PHE 3.8 3.8 + - - -
218G ALA* 3.6 10.3 - - - +
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Residues in contact with THR 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASN* 3.1 30.4 + - - +
82G HIS* 3.3 10.1 - - + -
112G ASP* 3.5 17.7 - - - +
170G GLU* 3.7 14.1 - - - +
175G PHE* 4.1 14.1 - - + -
182G ILE* 5.6 1.9 - - - +
187G SER* 3.2 19.9 + - - -
201G ILE 2.7 22.3 + - - -
202G ASN* 1.4 69.9 - - - +
204G ALA* 1.3 59.7 + - + +
217G PHE 2.9 12.7 + - - -
219G ILE* 3.2 17.1 - - + +
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Residues in contact with ALA 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G LEU* 3.9 38.1 - - + -
170G GLU* 5.3 1.3 - - - +
175G PHE* 5.0 1.8 - - + -
182G ILE* 4.8 2.8 - - - +
203G THR* 1.3 86.5 - - + +
205G ILE* 1.3 65.7 + - - +
217G PHE* 2.7 39.0 + - + +
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Residues in contact with ILE 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G LEU* 5.0 4.9 - - - +
182G ILE* 3.4 50.0 - - + +
183G ASN* 4.5 10.3 - - - +
184G ARG* 5.1 3.6 - - + +
204G ALA* 1.3 82.7 - - - +
206G LEU* 1.3 67.3 + - - +
207G ALA* 3.6 28.2 + - + -
210G GLY 4.0 13.2 - - - +
212G SER* 4.2 9.9 - - - +
215G ILE 3.4 9.0 - - - +
216G GLY* 4.0 6.3 - - - -
217G PHE* 4.2 4.9 - - - -
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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