Contacts of the strand formed by residues 198 - 205 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H VAL* 4.1 17.5 - - + -
70H ILE* 5.3 0.9 - - + -
78H LEU* 4.7 7.6 - - + -
127H ILE* 3.7 17.9 - - + +
128H ALA 2.8 16.8 + - - +
129H ILE* 4.3 15.0 - - + -
130H ALA* 2.9 24.6 + - - +
190H ALA* 3.8 26.9 - - + -
191H LEU 3.6 3.8 - - - +
192H LEU* 4.1 6.1 - - + +
196H GLY 4.1 0.4 + - - -
197H GLU* 1.3 69.0 - - - +
199H ILE* 1.3 60.3 + - - +
200H GLY 3.2 25.4 - - - +
201H ILE* 3.6 23.8 - - + -
221H SER* 3.4 17.4 + - - +
224H ALA* 5.5 0.4 - - + -
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Residues in contact with ILE 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H ALA* 3.9 18.2 - - + -
131H ASP 5.8 0.4 - - - +
132H SER* 3.8 4.3 - - - -
135H LEU* 3.9 37.9 - - + -
140H PHE 4.9 1.6 - - - +
141H ALA* 4.1 16.6 - - + -
159H VAL* 4.2 9.0 - - + -
176H ILE* 3.1 16.7 - - - +
191H LEU* 2.8 45.6 + - + +
192H LEU 3.9 7.6 - - - +
193H ASN* 4.0 16.8 - - + +
197H GLU 3.4 6.3 + - - +
198H LEU* 1.3 77.7 - - - +
200H GLY* 1.3 58.1 + - - +
221H SER* 3.0 24.0 + - - +
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Residues in contact with GLY 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ILE* 4.5 0.7 - - - -
190H ALA 3.8 0.2 - - - -
191H LEU* 2.9 34.3 + - - -
198H LEU* 3.2 12.5 - - - +
199H ILE* 1.3 81.2 - - - +
201H ILE* 1.3 66.2 + - - -
218H ALA* 4.3 4.9 - - - -
219H ILE 3.0 13.9 - - - -
221H SER* 3.7 7.5 - - - +
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Residues in contact with ILE 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H VAL* 4.6 7.0 - - + -
78H LEU* 3.6 37.2 - - + -
79H THR 4.7 7.4 - - - +
80H ASN* 3.7 25.1 - - - +
113H ILE* 5.2 2.9 - - + -
188H GLY* 3.9 24.2 - - - +
189H GLY 3.3 9.4 - - - +
198H LEU* 3.6 22.7 - - + -
200H GLY* 1.3 71.8 - - - +
202H ASN* 1.4 55.6 + - - +
203H THR* 2.8 14.0 + - - +
218H ALA* 3.1 2.8 - - - +
219H ILE* 2.8 42.2 + - + +
224H ALA* 3.7 14.4 - - + -
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Residues in contact with ASN 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ASN* 3.0 1.4 - - - +
143H ALA* 3.5 14.0 - - - +
144H VAL 4.2 2.8 + - - +
178H THR* 4.8 0.4 - - - +
182H ILE* 3.6 38.0 - - + +
186H ASN* 3.7 18.1 - - + +
187H SER* 3.4 3.8 - - - -
188H GLY 2.8 28.2 + - - -
189H GLY 2.9 10.4 + - - +
190H ALA 3.1 24.7 - - - +
191H LEU* 3.4 24.5 - - - +
201H ILE* 1.4 68.7 - - - +
203H THR* 1.4 57.8 + - - +
217H PHE 3.9 4.0 + - - -
218H ALA* 3.7 8.3 - - - +
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Residues in contact with THR 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ASN* 3.3 22.9 + - - +
82H HIS* 3.3 8.7 + - + -
112H ASP* 3.6 18.4 - - - +
170H GLU* 3.6 14.6 - - - +
175H PHE* 4.1 14.6 - - + -
182H ILE* 5.5 2.6 - - - +
187H SER* 3.1 19.8 + - - -
201H ILE 2.8 16.5 + - - -
202H ASN* 1.4 70.6 - - - +
204H ALA* 1.3 58.0 + - + +
217H PHE 2.9 14.6 + - - -
219H ILE* 3.2 23.9 - - + +
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Residues in contact with ALA 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LEU* 3.8 38.4 - - + -
170H GLU* 5.3 1.3 - - - +
175H PHE* 5.0 1.8 - - + -
182H ILE* 4.7 2.0 - - - +
203H THR* 1.3 86.3 - - + +
205H ILE* 1.3 67.3 + - - +
217H PHE* 2.7 38.1 + - + +
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Residues in contact with ILE 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H LEU* 4.9 6.1 - - - +
182H ILE* 3.4 48.9 - - + +
183H ASN* 4.5 10.8 - - - -
184H ARG* 5.1 4.7 - - + +
204H ALA* 1.3 84.2 - - - +
206H LEU* 1.4 67.2 + - - +
207H ALA* 3.6 27.1 + - + -
210H GLY 4.6 7.4 - - - +
211H GLY 4.2 1.3 - - - -
212H SER* 4.1 14.6 - - - +
215H ILE 3.4 9.6 - - - +
216H GLY* 4.0 6.3 - - - -
217H 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