Contacts of the helix formed by residues 198 - 207 (chain C) in PDB entry 1ZSV
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 SER 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C VAL* 3.3 2.4 - - - +
197C GLU* 1.3 83.0 - - - +
199C LEU* 1.3 58.2 + - - +
200C GLU* 3.5 11.3 + - - +
201C GLU* 2.7 45.9 + - - +
202C THR* 2.6 32.5 + - - -
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Residues in contact with LEU 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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191C PHE* 3.7 35.7 - - + -
193C TYR* 4.7 4.9 - - + +
196C VAL* 3.9 11.5 + - + +
198C SER* 1.3 71.0 - - - +
200C GLU* 1.3 62.3 + - - +
202C THR* 3.5 4.3 + - - -
203C LEU* 3.0 42.1 + - + +
221C GLU 5.4 0.2 - - - -
222C PHE* 3.6 47.8 - - + +
225C THR* 3.8 25.4 - - + +
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Residues in contact with GLU 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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198C SER* 3.2 9.2 + - - +
199C LEU* 1.3 78.9 - - - +
201C GLU* 1.3 70.9 + - - +
204C LYS* 3.0 12.9 + - - +
225C THR* 3.8 22.4 - - + +
229C GLN* 3.0 32.0 + - - +
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Residues in contact with GLU 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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198C SER* 2.7 37.3 + - - +
200C GLU* 1.3 83.6 - - - +
202C THR* 1.3 67.3 + - - +
204C LYS* 3.2 8.2 + - - +
205C LYS* 3.0 24.3 + - - +
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Residues in contact with THR 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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191C PHE* 3.8 41.5 - - + -
196C VAL* 3.6 22.4 - - + +
198C SER 2.6 21.2 + - - -
199C LEU* 3.6 7.0 - - - -
201C GLU* 1.3 79.0 - - - +
203C LEU* 1.3 62.6 + - - +
205C LYS* 3.4 4.3 + - - +
206C ALA* 3.0 24.6 + - + +
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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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146C MET* 3.6 32.5 - - + -
170C VAL* 5.0 0.2 - - + -
191C PHE* 4.0 21.5 - - + -
199C LEU* 3.0 39.2 + - + +
200C GLU 3.7 2.0 - - - +
202C THR* 1.3 76.3 - - - +
204C LYS* 1.3 56.3 + - - +
206C ALA* 4.3 1.6 - - - -
207C SER 3.3 13.5 + - - +
211C TYR* 2.7 32.9 + - + +
222C PHE* 5.3 0.2 - - + -
225C THR* 4.0 14.8 - - + -
226C VAL* 3.9 29.6 - - + +
229C GLN* 3.5 18.4 - - + +
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Residues in contact with LYS 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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200C GLU* 3.0 17.6 + - + +
201C GLU* 3.5 9.4 - - + +
202C THR 3.1 0.2 - - - -
203C LEU* 1.3 76.3 - - - +
205C LYS* 1.3 59.0 + - - +
207C SER 4.5 1.8 - - - -
208C PRO* 3.1 41.2 - - + +
229C GLN* 3.4 16.4 + - - +
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Residues in contact with LYS 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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201C GLU 3.0 14.7 + - - +
202C THR* 4.2 4.7 - - - +
204C LYS* 1.3 72.7 - - - +
206C ALA* 1.3 63.0 + - - +
207C SER 3.6 0.3 + - - -
208C PRO* 4.1 13.2 - - - +
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Residues in contact with ALA 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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168C LYS* 2.7 34.9 + - - -
170C VAL* 3.9 20.4 - - + +
189C VAL* 4.0 25.2 - - + +
191C PHE* 5.3 2.2 - - + -
202C THR* 3.0 19.6 + - + +
203C LEU* 4.2 1.1 - - - -
204C LYS 3.3 0.2 - - - -
205C LYS* 1.3 78.5 - - - +
207C SER* 1.3 52.8 + - - +
208C PRO* 4.3 0.4 - - - -
211C TYR* 3.7 13.9 - - - +
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Residues in contact with SER 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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144C THR* 3.6 16.5 + - - +
168C LYS* 4.0 5.5 + - - +
203C LEU 3.3 9.1 + - - +
204C LYS* 3.5 5.3 - - - +
206C ALA* 1.3 81.1 - - - +
208C PRO* 1.3 63.7 - - - +
209C ASP* 3.2 6.8 - - - +
210C GLY* 2.7 41.7 + - - -
211C TYR* 3.6 27.2 - - - -
229C GLN* 4.8 1.2 - - - +
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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