Contacts of the helix formed by residues 202 - 209 (chain C) in PDB entry 1SL0
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 GLY 202 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A ASN* 5.3 14.3 - - - +
53C GLY 3.7 13.0 - - - -
54C GLY* 4.9 2.5 - - - -
55C LEU* 3.9 1.6 - - - -
201C VAL* 1.3 76.3 - - - +
203C TYR* 1.3 68.0 + - - -
204C THR 3.2 3.1 - - - -
205C THR* 2.8 18.5 + - - -
206C PHE 2.8 10.0 + - - -
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Residues in contact with TYR 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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53C GLY* 3.6 28.8 + - - -
54C GLY 3.7 4.3 - - - +
55C LEU* 3.3 26.7 - - + +
86C GLU* 3.1 67.7 + - + +
87C ASN* 3.5 21.1 - - - -
202C GLY* 1.3 69.6 - - - -
204C THR* 1.3 98.8 + - - +
206C PHE* 3.1 1.0 + - - +
207C TRP* 3.0 33.5 + + - -
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Residues in contact with THR 204 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C GLY 3.1 1.2 + - - -
203C TYR* 1.3 113.4 + - - +
205C THR* 1.3 63.1 + - - +
207C TRP* 4.1 3.7 - - - +
208C SER* 3.0 30.8 + - - +
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Residues in contact with THR 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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489A ALA* 4.1 7.3 + - - +
490A ARG* 4.1 28.4 - - + +
493A ASN* 5.3 5.1 - - - +
196C ILE* 4.7 1.8 - - + -
201C VAL* 3.6 28.5 - - + -
202C GLY* 2.8 16.6 + - - -
204C THR* 1.3 74.5 - - - +
206C PHE* 1.3 66.3 + - - +
207C TRP 3.2 0.4 - - - -
208C SER* 5.0 0.4 - - - -
209C GLU* 2.9 52.9 + - + +
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Residues in contact with PHE 206 (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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1C MET* 3.6 14.8 - - + -
55C LEU* 3.3 36.1 - - + -
89C ILE* 4.0 17.5 - - + -
182C LEU* 5.5 2.0 - - + -
186C LEU* 3.7 23.8 - - + -
192C PHE* 3.9 10.1 - + - -
198C PHE* 3.5 33.0 - - + -
201C VAL* 3.4 9.5 - - + +
202C GLY 2.8 5.3 + - - -
203C TYR* 3.6 3.8 - - - +
205C THR* 1.3 77.4 - - - +
207C TRP* 1.3 88.1 - + + +
209C GLU* 4.0 0.6 - - - -
210C SER* 2.2 36.6 + - - -
214C VAL* 3.9 13.2 - - + -
218C HIS* 5.6 0.9 - + - -
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Residues in contact with TRP 207 (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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55C LEU* 4.4 2.2 - - + +
85C ARG* 3.4 30.8 - - - +
86C GLU* 2.5 30.3 + - + -
88C CYS 3.5 21.3 - - - -
89C ILE* 4.4 7.0 - - + -
203C TYR* 3.0 32.2 + + - +
204C THR* 4.1 4.5 - - - +
206C PHE* 1.3 93.8 - + - +
208C SER* 1.3 65.2 + - - +
210C SER* 2.9 17.0 + - - +
211C LEU 5.0 0.9 - - - +
212C GLU* 5.9 0.5 - - - -
214C VAL* 3.4 35.4 - - + -
215C ASP* 4.2 28.8 + - + +
218C HIS* 3.4 33.0 - + + -
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Residues in contact with SER 208 (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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685A ASN* 6.0 7.0 - - - -
204C THR* 3.0 25.1 + - - +
205C THR* 5.0 0.2 - - - -
207C TRP* 1.3 73.3 - - - +
209C GLU* 1.3 58.7 - - - +
210C SER 2.7 24.1 + - - +
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Residues in contact with GLU 209 (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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486A HIS* 5.5 6.6 + - - -
490A ARG* 2.8 43.0 + - + -
193C PRO* 3.7 13.2 - - - +
196C ILE* 2.9 31.9 - - + +
205C THR* 2.9 39.6 + - + +
206C PHE 4.0 0.2 - - - -
208C SER* 1.3 77.1 - - - +
210C SER* 1.3 58.5 + - - +
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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