Contacts of the helix formed by residues 199 - 209 (chain C) in PDB entry 1SIW
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 PRO 199 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL 3.5 18.8 - - - +
20C PHE* 4.1 3.6 - - - +
23C GLY* 3.6 27.8 - - - -
24C SER* 3.7 9.2 - - - +
27C ARG* 3.0 31.2 + - - +
195C PHE 3.5 6.1 - - - +
196C LEU 3.4 9.9 - - - +
197C LEU 3.5 0.7 - - - -
198C PHE* 1.3 101.0 - - + +
200C PHE* 1.3 81.8 + - + +
201C SER 3.4 0.4 - - - -
204C ILE* 4.1 7.0 - - + -
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Residues in contact with PHE 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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19C VAL* 3.6 31.6 - - + -
23C GLY* 5.0 9.2 - - - -
27C ARG* 3.7 7.9 - - - +
125C ALA* 4.3 11.6 - - - +
196C LEU* 3.6 15.3 - - + -
197C LEU* 2.9 16.5 + - + +
199C PRO* 1.3 91.5 - - + +
201C SER* 1.3 59.4 + - - +
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Residues in contact with SER 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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27C ARG* 2.8 21.9 + - - -
125C ALA* 4.7 11.9 - - - -
129C ILE* 3.8 24.7 - - - +
197C LEU* 3.6 10.1 + - - -
198C PHE* 3.0 15.5 + - - +
200C PHE* 1.3 81.0 - - - +
202C ARG* 1.3 64.1 + - - +
203C LEU* 3.2 21.3 + - - +
204C ILE* 3.4 6.6 - - - +
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Residues in contact with ARG 202 (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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27C ARG* 5.2 1.8 - - - +
36C ARG* 4.3 6.9 - - - +
37C ALA 2.7 20.1 + - - +
38C ALA* 2.7 37.3 + - + +
112C ARG* 3.3 30.3 - - - +
125C ALA* 5.7 0.8 - - - +
126C ASP* 3.5 32.2 + - - +
129C ILE* 4.2 23.1 - - + -
201C SER* 1.3 73.3 - - - +
203C LEU* 1.3 59.4 + - + +
204C ILE* 2.9 18.0 + - - +
205C HIS* 2.7 33.1 + - - +
806C HEM 3.2 50.1 + - + +
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Residues in contact with LEU 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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129C ILE* 3.3 35.2 - - + -
133C LEU* 4.3 2.0 - - + -
194C LEU* 4.4 19.1 - - + +
198C PHE* 3.1 42.6 - - + -
201C SER* 3.2 15.5 + - - +
202C ARG* 1.3 82.6 - - + +
204C ILE* 1.3 61.6 + - - +
205C HIS* 3.0 8.2 + - + -
206C ILE* 3.0 16.6 + - + +
806C HEM 3.9 46.4 - - + -
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Residues in contact with ILE 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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24C SER* 4.8 2.2 - - - +
27C ARG* 3.7 28.5 - - - +
35C TRP* 3.5 50.7 + - + -
36C ARG 3.7 35.9 - - - +
198C PHE* 4.0 15.0 + - + +
199C PRO* 4.1 22.2 - - + +
201C SER 3.4 14.5 + - - +
202C ARG* 3.9 3.1 - - - +
203C LEU* 1.3 77.0 - - - +
205C HIS* 1.3 79.8 + - - +
206C ILE 3.0 0.4 - - - -
207C TRP* 3.1 21.1 + - + +
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Residues in contact with HIS 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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218B ARG* 6.5 0.4 - - + -
220B TRP* 3.9 11.2 - + + -
35C TRP* 4.8 2.0 - - - +
36C ARG* 4.3 1.6 - - - +
37C ALA* 3.9 28.4 - - + +
202C ARG* 2.7 29.8 + - + +
203C LEU* 3.0 7.1 - - + -
204C ILE* 1.3 83.4 - - - +
206C ILE* 1.3 65.5 + - + +
208C SER* 2.9 32.6 + - - +
209C VAL* 3.7 0.9 + - - -
806C HEM 2.0 101.3 + + + -
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Residues in contact with ILE 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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63C PHE* 6.3 2.7 - - + -
198C PHE* 3.6 20.6 - - + -
203C LEU* 3.0 21.5 + - + +
205C HIS* 1.3 85.4 - - + +
207C TRP* 1.3 62.5 + - - +
208C SER 3.1 1.0 + - - -
209C VAL* 3.3 20.5 + - + +
806C HEM 3.5 74.0 - - + -
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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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1309A 3PH 3.3 92.7 - - + +
20C PHE* 3.6 28.7 - + - -
21C LEU* 4.6 15.5 - - + -
24C SER* 2.9 31.0 + - - -
35C TRP* 3.7 30.5 - + + -
198C PHE* 3.2 28.8 - + - -
204C ILE* 3.1 11.1 + - - +
206C ILE* 1.3 78.6 - - - +
208C SER* 1.3 56.2 + - - +
209C VAL* 3.4 8.8 + - - +
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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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1309A 3PH 2.5 31.8 + - - -
198B SER* 6.0 0.5 - - - -
218B ARG* 3.4 16.0 + - - -
220B TRP* 3.3 14.3 + - - -
35C TRP* 2.8 24.8 + - - -
205C HIS* 2.9 16.4 + - - -
207C TRP* 1.3 77.3 - - - +
209C VAL* 1.3 65.2 + - - -
210C PRO* 2.7 12.2 - - - +
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Residues in contact with VAL 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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220B TRP* 4.8 0.7 - - - -
205C HIS 3.7 2.9 + - - -
206C ILE* 3.3 17.1 + - + +
207C TRP 4.4 5.9 - - - +
208C SER* 1.3 74.0 - - - +
210C PRO* 1.3 60.5 - - + +
211C VAL* 2.8 39.7 + - + +
806C HEM 3.7 35.2 - - + -
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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