Contacts of the strand formed by residues 198 - 205 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 4.2 11.0 - - + -
70C ILE* 5.2 1.6 - - + -
78C LEU* 4.9 9.2 - - + -
127C ILE* 3.8 17.4 - - + +
128C ALA 2.8 17.0 + - - +
129C ILE* 4.3 16.2 - - + -
130C ALA* 3.0 24.3 + - - +
190C ALA* 3.8 27.6 - - + -
191C LEU 3.6 3.6 - - - +
192C LEU* 4.1 6.0 - - + +
196C GLY 4.1 0.2 + - - -
197C GLU* 1.3 69.6 - - - +
199C ILE* 1.3 60.0 + - - +
200C GLY 3.4 22.4 - - - +
201C ILE* 4.0 25.8 - - + -
221C SER* 3.4 19.0 + - - +
224C ALA* 5.5 0.7 - - + -
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Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ALA* 3.9 17.9 - - + -
131C ASP 5.7 0.4 - - - +
132C SER* 3.8 4.2 - - - -
135C LEU* 3.9 38.8 - - + -
140C PHE 4.8 2.0 - - - +
141C ALA* 4.1 16.8 - - + -
159C VAL* 4.3 9.0 - - + -
176C ILE* 3.2 15.6 - - - +
191C LEU* 2.8 45.2 + - + +
192C LEU 3.9 7.6 - - - +
193C ASN* 3.9 20.9 - - + +
197C GLU 3.4 0.6 + - - +
198C LEU* 1.3 77.3 - - - +
200C GLY* 1.3 58.5 + - - +
221C SER* 3.0 24.9 + - - +
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Residues in contact with GLY 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ILE* 4.4 0.7 - - - -
191C LEU* 3.1 32.9 + - - -
198C LEU* 3.4 14.0 - - - +
199C ILE* 1.3 81.7 - - - +
201C ILE* 1.3 64.0 + - - -
218C ALA* 4.2 5.6 - - - -
219C ILE 3.0 15.3 - - - -
220C PRO* 4.2 0.2 - - - -
221C SER* 3.7 6.3 - - - +
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 3.7 32.5 - - + -
78C LEU* 4.1 18.6 - - + -
79C THR 4.6 9.0 - - - +
80C ASN* 3.8 23.3 - - - +
113C ILE* 5.3 2.0 - - + -
188C GLY* 3.9 20.9 - - - +
189C GLY 3.4 2.5 - - - +
198C LEU* 4.0 18.8 - - + -
200C GLY* 1.3 74.3 - - - +
202C ASN* 1.4 56.1 + - - +
203C THR* 2.7 25.1 + - - +
218C ALA* 3.8 1.8 - - - +
219C ILE* 2.8 33.5 + - + +
224C ALA* 4.0 22.9 - - + -
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 3.2 1.4 - - - +
143C ALA* 3.6 10.4 - - - +
144C VAL 4.1 3.1 + - - +
182C ILE* 3.6 32.5 - - + +
186C ASN* 3.8 17.4 - - - +
187C SER* 3.2 2.8 - - - -
188C GLY* 2.7 31.2 + - - -
189C GLY 2.8 17.9 + - - +
190C ALA 3.0 22.1 + - - +
191C LEU* 3.4 33.3 - - - +
200C GLY 4.1 0.2 - - - -
201C ILE* 1.4 68.4 - - - +
203C THR* 1.3 56.7 + - - +
217C PHE 3.9 4.9 - - - -
218C ALA* 4.0 6.0 - - - +
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Residues in contact with THR 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ASN* 3.1 29.1 + - - +
82C HIS* 3.4 19.0 - - + -
112C ASP* 4.0 8.5 - - - +
170C GLU* 3.7 23.8 - - - +
175C PHE* 4.2 17.7 - - + -
182C ILE* 5.5 2.6 - - - +
187C SER* 3.5 8.9 - - - -
201C ILE 2.7 20.7 + - - -
202C ASN* 1.3 71.7 - - - +
204C ALA* 1.3 60.4 + - + +
217C PHE 2.8 13.7 + - - -
219C ILE* 3.3 14.0 - - + +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LEU* 3.9 37.5 - - + -
170C GLU* 5.3 1.3 - - - +
175C PHE* 5.0 2.0 - - + -
182C ILE* 4.7 2.2 - - - +
203C THR* 1.3 85.5 - - + +
205C ILE* 1.3 66.3 + - - +
217C PHE* 2.7 37.3 + - + +
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LEU* 4.9 5.5 - - - +
182C ILE* 3.4 48.9 - - + +
183C ASN* 4.6 11.7 - - - -
184C ARG* 5.1 3.4 - - + +
204C ALA* 1.3 82.3 - - - +
206C LEU* 1.3 67.4 + - - +
207C ALA* 3.7 26.8 + - + -
210C GLY* 4.7 7.6 - - - +
211C GLY 4.3 1.6 - - - -
212C SER* 4.1 13.5 - - - +
215C ILE 3.4 10.1 - - - +
216C GLY* 4.1 6.7 - - - -
217C 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