Contacts of the helix formed by residues 190 - 195 (chain B) 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 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TRP* 3.9 0.9 - - - -
187B CYS* 3.4 19.0 - - + +
188B LEU 3.2 9.9 - - - +
189B ASN* 1.3 87.9 - - - +
191B ALA* 1.3 63.4 + - - +
192B CYS* 3.3 10.5 + - - -
193B VAL* 3.5 19.3 + - + -
194B ALA 3.7 2.1 + - - -
203B LYS* 5.1 6.7 - - + -
210B VAL* 4.6 7.0 - - + -
349B THR* 4.6 0.2 - - - -
804B SF4 3.7 29.4 - - - -
219C GLN* 2.8 41.3 + - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY* 4.0 18.4 - - - +
66B TRP* 3.7 24.9 - - + +
76B PRO* 5.9 0.9 - - + -
189B ASN 3.4 2.2 + - - -
190B PRO* 1.3 72.2 - - - +
192B CYS* 1.3 63.3 + - - +
194B ALA 3.2 1.6 + - - -
195B THR* 2.9 35.2 + - + +
226B GLY* 3.3 24.2 - - - +
228B PRO* 4.2 7.9 - - + -
349B THR* 4.2 2.5 - - + +
804B SF4 3.6 4.6 - - - -
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Residues in contact with CYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PRO* 3.9 10.5 - - - -
191B ALA* 1.3 79.4 - - - +
193B VAL* 1.3 72.2 + - - +
195B THR* 3.3 19.2 + - - -
196B CYS* 3.3 8.1 + - - +
201B ILE* 3.5 31.4 - - + +
210B VAL* 4.1 2.7 - - - -
223B CYS* 4.2 7.0 - - - +
226B GLY 4.6 1.0 - - - -
227B CYS* 4.7 1.6 - - + +
232B ILE* 3.3 29.6 - - + -
243B LYS* 5.0 0.4 - - - -
804B SF4 2.3 42.7 - - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PRO* 3.5 25.1 + - + +
191B ALA 3.3 0.4 - - - -
192B CYS* 1.3 78.7 - - - +
194B ALA* 1.3 59.4 + - - +
195B THR 3.6 0.3 + - - -
196B CYS* 3.8 6.9 + - - +
199B GLY* 5.5 0.3 - - - -
201B ILE* 3.5 47.4 - - + +
202B TYR* 4.2 5.6 - - - +
203B LYS 4.9 0.9 - - - +
210B VAL* 4.1 7.2 - - + -
216C ARG* 2.8 21.8 + - - -
218C TYR 3.7 4.3 - - - +
219C GLN* 3.4 22.2 - - - +
220C LEU* 3.6 26.2 - - + +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TRP* 3.4 38.8 - - + -
76B PRO* 4.4 4.4 - - + +
190B PRO 3.7 2.8 + - - +
191B ALA 3.2 5.7 + - - +
192B CYS 3.2 0.4 - - - -
193B VAL* 1.3 79.7 - - - +
195B THR* 1.3 54.7 + - - +
196B CYS 3.5 0.4 - - - -
213C TYR* 2.6 34.5 + - - -
216C ARG* 3.7 1.8 - - - +
218C TYR* 3.6 31.8 - - + +
219C GLN* 4.2 0.9 - - - +
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Residues in contact with THR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY 5.9 0.2 - - - +
76B PRO* 3.7 31.4 - - + -
78B MET* 3.8 21.3 - - - -
84B LEU* 3.6 20.0 - - + +
191B ALA* 2.9 19.5 + - + +
192B CYS* 3.3 12.4 + - - -
194B ALA* 1.3 79.0 - - - +
196B CYS* 1.3 58.1 + - - +
197B PRO* 3.3 11.8 - - - +
222B MET* 3.4 15.2 - - - +
223B CYS* 3.6 7.7 + - - -
226B GLY* 3.6 15.7 - - - -
213C TYR* 4.2 0.7 - - - -
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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