Contacts of the helix formed by residues 256 - 268 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D SER 5.2 4.5 - - - +
215D ILE* 3.9 24.5 + - + +
252D ASP 4.4 1.0 + - - -
253D LEU* 2.8 24.1 + - + +
254D CYS 3.4 0.2 - - - -
255D GLN* 1.3 80.1 - - - +
257D PRO* 1.3 79.3 - - - +
258D THR* 2.8 39.8 + - - +
259D ILE* 2.9 17.1 + - + +
260D LYS* 3.2 8.3 + - - +
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Residues in contact with PRO 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D GLN 3.5 3.8 - - - +
256D ASP* 1.3 96.6 - - - +
258D THR* 1.3 59.5 + - + +
260D LYS* 3.2 12.5 + - + +
261D GLU* 3.0 24.4 + - - +
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D SER 4.8 2.9 - - - +
214D LYS* 4.1 22.2 - - + -
215D ILE* 3.6 6.9 - - - +
216D PHE* 3.0 55.0 + - - +
256D ASP* 2.8 23.5 + - - +
257D PRO* 1.3 77.6 - - + +
259D ILE* 1.3 61.8 + - - +
260D LYS 3.2 0.2 - - - -
261D GLU* 3.3 15.4 - - - +
262D LEU 3.0 20.4 + - - -
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Residues in contact with ILE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D LEU* 3.8 29.2 - - + -
215D ILE* 3.9 15.9 - - + -
216D PHE* 4.4 6.1 - - + -
240D ALA* 5.2 0.4 - - + -
242D VAL* 4.0 11.7 - - + -
253D LEU 3.8 17.7 - - - +
254D CYS 3.6 21.5 - - - +
256D ASP* 2.9 12.7 + - + +
258D THR* 1.3 79.2 - - - +
260D LYS* 1.3 60.5 + - + +
262D LEU* 3.3 7.6 + - + +
263D GLU* 2.8 26.9 + - - +
273D PHE* 3.6 26.6 - - + -
275D CYS* 3.9 8.7 - - - -
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Residues in contact with LYS 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D CYS 4.2 3.6 - - - +
255D GLN* 2.6 54.4 + - - +
256D ASP 3.2 12.5 + - - +
257D PRO* 3.2 12.1 + - + +
259D ILE* 1.3 76.9 - - + +
261D GLU* 1.3 59.6 + - - +
263D GLU* 3.6 26.5 + - - +
264D SER* 2.9 29.1 + - - -
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Residues in contact with GLU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D PHE* 3.7 21.8 - - + +
218D LYS* 3.9 27.3 - - - +
257D PRO 3.0 12.4 + - - +
258D THR* 3.3 20.2 - - - +
260D LYS* 1.3 77.1 - - - +
262D LEU* 1.3 56.9 + - - +
264D SER* 3.1 9.0 + - - -
265D ILE* 2.9 45.2 + - + +
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D VAL* 4.9 0.4 - - + -
208D LEU* 4.3 16.6 - - + -
216D PHE* 4.0 27.3 - - + -
222D PHE* 4.2 9.4 - - + -
227D VAL* 3.9 24.5 - - + -
238D LEU* 4.0 7.2 - - + -
240D ALA* 4.6 4.5 - - + -
258D THR 3.0 14.0 + - - +
259D ILE* 3.5 10.3 - - + +
260D LYS 3.3 0.2 - - - -
261D GLU* 1.3 73.4 - - - +
263D GLU* 1.3 59.5 + - - +
265D ILE* 3.1 13.3 + - + +
266D ILE* 2.8 49.6 + - + +
273D PHE* 3.6 28.0 - - + -
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ILE 2.8 18.5 + - - +
260D LYS* 3.6 32.8 + - - +
262D LEU* 1.3 74.3 - - - +
264D SER* 1.3 58.7 + - - +
266D ILE* 3.4 1.4 + - - +
267D SER* 2.8 32.3 + - - -
273D PHE* 3.4 43.4 - - + +
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Residues in contact with SER 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LYS 2.9 15.5 + - - -
261D GLU* 3.1 12.8 - - - -
263D GLU* 1.3 77.3 - - - +
265D ILE* 1.3 64.5 + - - +
267D SER* 2.8 26.2 + - - -
268D LYS* 3.2 18.2 + - - +
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Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D PHE* 3.7 35.2 - - + -
218D LYS* 5.1 5.6 - - + -
227D VAL* 4.4 15.7 - - + -
228D HIS* 3.7 35.7 - - + +
261D GLU* 2.9 30.2 + - + +
262D LEU* 3.1 7.8 + - + +
264D SER* 1.3 76.7 - - - +
266D ILE* 1.3 64.5 + - + +
268D LYS* 3.3 16.4 + - - +
269D ARG* 3.1 23.3 + - - +
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Residues in contact with ILE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D VAL* 4.5 13.2 - - + +
230D LEU* 4.3 16.6 - - + -
238D LEU* 3.6 34.5 - - + -
262D LEU* 2.8 31.6 + - + +
263D GLU 3.7 4.0 - - - +
265D ILE* 1.3 71.5 - - + +
267D SER* 1.3 65.5 + - - +
269D ARG* 3.0 18.7 + - - +
271D ILE* 3.4 47.3 + - + +
272D GLN 3.9 14.6 - - - +
273D PHE* 4.2 10.3 - - + -
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Residues in contact with SER 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D GLU* 2.8 21.3 + - - -
264D SER* 2.8 21.0 + - - -
266D ILE* 1.3 74.3 - - - +
268D LYS* 1.3 62.4 + - - +
269D ARG 3.2 0.2 - - - -
270D ASN* 3.2 20.6 + - - +
271D ILE 3.8 11.2 - - - -
273D PHE* 5.6 0.6 - - - +
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D SER* 3.2 22.3 + - - +
265D ILE* 3.8 11.9 - - - +
266D ILE 3.1 1.2 - - - -
267D SER* 1.3 81.2 + - - +
269D ARG* 1.3 59.1 + - + +
270D ASN* 3.1 13.9 + - - -
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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