Contacts of the helix formed by residues 255 - 266 (chain C) in PDB entry 1Z1G
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 MSE 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C LEU* 5.6 1.1 - - + -
208C VAL* 3.8 34.9 - - + +
209C THR* 5.0 4.5 - - + -
229C LEU* 3.9 20.9 - - + -
242C ILE* 3.5 45.1 - - + +
243C PRO 3.3 19.5 - - - +
244C THR* 3.8 21.3 - - + +
246C LEU* 2.9 29.4 + - - +
254C SER* 1.3 70.2 - - - +
256C LYS* 1.3 53.7 + - - +
258C THR* 3.1 6.6 + - - -
259C LEU* 2.8 51.5 + - + +
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Residues in contact with LYS 256 (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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224C ILE* 6.0 2.0 - - - +
227C GLY* 5.6 3.2 - - - -
244C THR* 3.4 45.1 + - + +
246C LEU 4.6 0.4 + - - -
254C SER* 3.3 5.2 + - - +
255C MSE 1.3 78.3 - - - +
257C GLU* 1.3 61.0 + - - +
259C LEU* 3.3 10.3 + - + +
260C ASP* 3.2 47.1 + - - +
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Residues in contact with GLU 257 (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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254C SER* 3.0 27.2 + - - +
256C LYS* 1.3 76.2 - - - +
258C THR* 1.3 64.5 + - - +
260C ASP* 3.9 2.2 + - - +
261C LYS* 3.5 34.2 + - - +
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Residues in contact with THR 258 (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 LEU* 3.3 14.4 - - + +
204C GLU* 3.4 38.2 + - + +
205C LEU* 3.7 26.2 - - + +
208C VAL* 4.9 1.4 - - - +
253C ILE* 3.2 21.8 - - - +
254C SER 2.6 24.5 + - - -
255C MSE 3.4 10.2 - - - -
257C GLU* 1.3 74.3 - - - +
259C LEU* 1.3 54.0 + - - +
261C LYS* 3.3 8.1 + - - +
262C CYS* 2.5 28.4 + - - -
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Residues in contact with LEU 259 (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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205C LEU* 4.2 13.7 - - + -
221C TRP* 3.2 18.1 - - + -
224C ILE* 3.6 29.6 - - + -
229C LEU* 6.2 2.2 - - + -
244C THR* 5.1 11.4 - - + -
255C MSE 2.8 32.8 + - + +
256C LYS* 3.7 13.0 - - - +
258C THR* 1.3 74.7 - - - +
260C ASP* 1.3 69.4 + - - +
262C CYS* 3.2 24.7 + - - +
263C LYS 3.2 5.7 + - - -
271C ILE* 3.5 33.7 - - + -
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Residues in contact with ASP 260 (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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221C TRP* 4.6 6.6 - - - -
256C LYS* 3.2 37.8 + - - +
257C GLU* 4.9 2.2 - - - +
258C THR 3.4 0.2 - - - -
259C LEU* 1.3 88.4 - - - +
261C LYS* 1.3 63.3 + - - +
262C CYS 3.2 1.1 - - - -
263C LYS* 3.7 15.3 - - + +
264C GLU* 3.2 23.0 + - - +
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Residues in contact with LYS 261 (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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189C TYR* 4.3 6.3 + - - -
200C ARG* 6.1 1.2 - - - +
201C LEU* 3.6 15.7 - - + +
204C GLU* 3.0 38.0 + - - -
257C GLU* 3.5 25.9 + - - +
258C THR 3.3 10.7 + - - +
259C LEU 3.3 0.6 - - - -
260C ASP* 1.3 75.7 - - - +
262C CYS* 1.3 57.7 + - - +
264C GLU* 5.0 2.2 - - - -
265C ILE* 3.0 53.3 + - + +
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Residues in contact with CYS 262 (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 LEU* 3.4 24.0 - - - -
205C LEU* 4.7 4.3 - - - -
221C TRP* 3.6 8.3 + - + -
258C THR* 2.5 38.8 - - - -
259C LEU* 3.2 13.9 - - - +
261C LYS* 1.3 76.8 - - - +
263C LYS* 1.3 57.4 + - - +
266C LEU* 3.1 40.7 + - + +
267C GLY 3.3 3.6 + - - -
271C ILE* 3.6 30.1 - - + +
272C ILE* 5.0 1.8 - - - -
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Residues in contact with LYS 263 (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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221C TRP* 2.9 45.5 - - + -
259C LEU 3.2 2.9 + - - +
260C ASP* 3.7 17.7 - - + +
261C LYS 3.4 0.4 - - - -
262C CYS* 1.3 76.8 - - - +
264C GLU* 1.3 60.2 + - - +
267C GLY* 3.5 19.3 + - - +
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Residues in contact with GLU 264 (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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260C ASP 3.2 14.4 + - - +
261C LYS* 4.3 3.1 - - - +
263C LYS* 1.3 81.1 - - - +
265C ILE* 1.3 75.3 + - + +
266C LEU 3.9 0.2 + - - -
267C GLY* 4.7 1.4 + - - -
277C ARG* 5.3 3.5 + - - -
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Residues in contact with ILE 265 (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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197C CYS* 4.1 24.2 - - + -
201C LEU* 4.9 5.4 - - + -
261C LYS* 3.0 44.5 + - + +
264C GLU* 1.3 88.5 - - + +
266C LEU* 1.3 76.3 + - + +
277C ARG* 4.7 5.9 + - - -
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Residues in contact with LEU 266 (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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197C CYS* 4.9 0.9 - - + -
198C TRP* 4.0 29.2 - - + +
201C LEU* 3.6 17.3 - - + -
262C CYS* 3.1 30.1 + - + +
265C ILE* 1.3 98.1 - - + +
267C GLY* 1.3 68.2 + - - +
270C THR 5.8 0.2 - - - +
271C ILE 3.4 24.7 - - - +
272C ILE* 4.1 14.4 - - + -
273C ALA* 4.3 22.6 - - + +
274C SER 4.5 7.6 - - - +
277C ARG* 3.1 19.3 + - - -
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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