Contacts of the helix formed by residues 256 - 269 (chain C) in PDB entry 1ZVM
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 ASP 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C SER 5.1 2.7 - - - +
215C ILE* 3.9 19.1 + - + +
252C ASP 4.2 1.4 + - - -
253C LEU* 3.1 27.7 + - + +
254C CYS 3.4 0.6 - - - -
255C GLN* 1.3 78.8 - - - +
257C PRO* 1.3 72.9 - - - +
258C THR* 2.9 38.5 + - - +
259C ILE* 2.8 27.0 + - + +
260C LYS* 2.9 10.2 + - - +
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Residues in contact with PRO 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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255C GLN 3.6 3.6 - - - +
256C ASP* 1.3 95.4 - - - +
258C THR* 1.3 58.4 + - + +
260C LYS* 3.4 11.6 + - + +
261C GLU* 2.9 26.7 + - - +
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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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213C SER 4.4 4.9 - - - +
214C LYS* 4.0 22.0 - - + -
215C ILE* 3.6 9.0 - - - +
216C PHE* 3.1 53.5 + - - +
256C ASP* 2.9 20.5 + - - +
257C PRO* 1.3 79.9 - - + +
259C ILE* 1.3 58.0 + - - +
261C GLU* 3.4 13.3 - - - +
262C LEU 3.0 19.4 + - - -
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Residues in contact with ILE 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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208C LEU* 4.1 13.5 - - + -
215C ILE* 3.9 19.1 - - + -
216C PHE* 4.8 2.7 - - + -
240C ALA* 5.3 0.7 - - + -
242C VAL* 3.8 24.5 - - + -
253C LEU 3.3 21.1 - - - +
254C CYS 3.3 21.8 - - - +
256C ASP* 2.8 13.8 + - + +
258C THR* 1.3 76.7 - - - +
260C LYS* 1.3 61.3 + - + +
261C GLU 3.1 1.1 - - - -
262C LEU* 3.6 7.5 - - + +
263C GLU* 2.8 27.0 + - - +
273C PHE* 4.0 16.7 - - + -
275C CYS* 4.0 15.9 - - + -
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Residues in contact with LYS 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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254C CYS 4.4 3.0 + - - +
255C GLN* 2.6 55.1 + - - +
256C ASP 2.9 15.8 + - - +
257C PRO* 3.6 11.0 - - + +
259C ILE* 1.3 77.1 - - + +
261C GLU* 1.3 59.2 + - - +
263C GLU* 3.3 27.7 + - - +
264C SER* 2.9 32.0 + - - -
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Residues in contact with GLU 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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216C PHE* 3.7 26.9 - - + +
218C LYS* 4.1 22.5 + - - +
257C PRO 2.9 17.1 + - - +
258C THR* 3.4 16.7 - - - +
260C LYS* 1.3 75.3 - - - +
262C LEU* 1.3 65.6 + - - +
264C SER* 3.1 15.8 + - - -
265C ILE* 3.2 24.6 + - + +
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Residues in contact with LEU 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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206C VAL* 5.1 0.4 - - + -
208C LEU* 4.2 25.1 - - + -
216C PHE* 3.8 35.7 - - + -
222C PHE* 3.9 14.8 - - + -
227C VAL* 4.0 8.1 - - + -
238C LEU* 4.2 4.5 - - + -
240C ALA* 4.5 3.6 - - + -
258C THR 3.0 15.2 + - - +
259C ILE* 3.3 11.0 + - + +
261C GLU* 1.3 75.1 - - - +
263C GLU* 1.3 64.5 + - - +
265C ILE* 3.2 9.2 + - + +
266C ILE* 2.9 41.9 + - + +
273C PHE* 3.7 30.5 - - + -
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Residues in contact with GLU 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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259C ILE 2.8 14.5 + - - +
260C LYS* 3.3 35.1 + - - +
262C LEU* 1.3 77.7 - - - +
264C SER* 1.3 58.1 + - - +
266C ILE* 3.7 1.4 - - - +
267C SER* 2.7 36.8 + - - +
273C PHE* 3.7 41.2 - - + +
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Residues in contact with SER 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 LYS 2.9 15.6 + - - -
261C GLU* 3.1 9.4 + - - -
263C GLU* 1.3 74.6 - - - +
265C ILE* 1.3 60.9 + - - +
267C SER* 2.6 21.4 + - - -
268C LYS* 2.8 31.6 + - - +
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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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216C PHE* 3.5 39.3 - - + -
218C LYS* 5.3 4.7 - - + -
223C GLY 5.6 1.1 - - - +
227C VAL* 4.8 12.6 - - + -
228C HIS* 3.9 30.5 - - + +
261C GLU* 3.2 21.3 + - + +
262C LEU* 3.4 7.2 - - + +
264C SER* 1.3 78.4 - - - +
266C ILE* 1.3 66.0 + - + +
268C LYS* 3.3 19.3 + - - +
269C ARG* 3.1 26.3 + - + +
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Residues in contact with ILE 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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227C VAL* 4.5 13.7 - - + +
230C LEU* 4.2 16.2 - - + -
238C LEU* 3.3 36.1 - - + -
262C LEU* 2.9 31.3 + - + +
263C GLU 3.8 3.4 - - - +
265C ILE* 1.3 75.7 - - + +
267C SER* 1.3 65.5 + - - +
269C ARG* 3.0 19.3 + - - +
271C ILE* 3.3 45.9 + - + +
272C GLN 4.1 2.2 - - - +
273C PHE* 4.0 19.7 - - + -
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Residues in contact with SER 267 (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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263C GLU* 2.7 24.7 + - - +
264C SER* 2.6 26.2 + - - -
266C ILE* 1.3 73.1 - - - +
268C LYS* 1.3 59.2 + - - +
270C ASN* 2.9 26.0 + - - +
271C ILE 3.9 9.6 - - - -
273C PHE* 6.0 1.6 - - - -
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Residues in contact with LYS 268 (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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276A LYS* 6.0 1.8 - - - +
297A THR* 3.3 26.7 - - - -
264C SER* 2.8 27.9 + - - +
265C ILE* 3.7 15.7 - - - +
266C ILE 3.2 0.4 - - - -
267C SER* 1.3 77.6 - - - +
269C ARG* 1.3 58.7 + - + +
270C ASN* 3.2 2.0 - - - -
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Residues in contact with ARG 269 (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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280A ARG* 5.4 8.9 - - - +
283A LYS* 5.8 3.0 - - - +
297A THR* 3.6 28.6 - - + +
227C VAL 3.2 25.8 + - - -
228C HIS* 3.1 40.0 + - - +
230C LEU* 2.4 33.1 + - - +
231C GLN* 4.3 11.9 - - - +
232C PRO* 3.2 23.7 - - - +
265C ILE* 3.1 22.0 - - + +
266C ILE* 3.0 12.5 + - + +
267C SER 3.0 1.2 - - - -
268C LYS* 1.3 79.7 - - + +
270C ASN* 1.3 70.3 + - - +
271C ILE* 3.4 10.3 + - + +
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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