Contacts of the helix formed by residues 263 - 275 (chain A) in PDB entry 2ZHB
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 GLU 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ILE* 1.3 84.0 - - - +
264A PRO* 1.3 75.7 - - + +
265A GLU* 3.0 11.7 + - + +
266A ARG* 3.0 51.8 + - - +
267A LEU 3.4 6.4 + - - -
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Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE 3.5 6.3 - - - +
263A GLU* 1.3 84.7 - - + +
265A GLU* 1.3 65.1 + - + +
267A LEU* 3.0 20.3 + - + +
268A ARG* 3.0 12.8 + - - +
421A PHE* 4.1 33.0 - - + +
422A LYS* 5.9 4.0 - - + -
426A THR* 4.7 8.1 - - + -
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLU* 3.0 12.0 + - + -
264A PRO* 1.3 81.9 - - + +
266A ARG* 1.3 63.8 + - - +
268A ARG* 2.7 54.8 + - - +
269A LYS* 3.1 29.3 + - - +
418A GLU* 4.8 1.9 - - - +
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 6.1 3.0 - - - +
262A ILE* 3.4 31.8 - - - +
263A GLU* 3.0 35.8 + - - +
265A GLU* 1.3 80.1 - - - +
267A LEU* 1.3 61.8 + - - +
269A LYS* 3.4 13.5 + - + +
270A ILE* 3.1 33.8 + - + +
435A VAL* 4.4 12.1 - - - +
436A LYS 3.2 24.4 + - - -
437A ASP* 3.2 30.7 + - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE* 4.1 8.7 - - + +
263A GLU 3.4 5.1 + - - +
264A PRO* 3.0 14.4 + - + +
266A ARG* 1.3 80.2 - - - +
268A ARG* 1.3 66.0 + - - +
270A ILE* 3.3 8.1 + - + +
271A VAL* 3.1 25.3 + - - +
421A PHE* 3.3 30.1 - - + -
426A THR* 3.6 27.1 - - + +
429A LEU* 3.8 18.4 - - + -
430A CYS* 3.4 30.3 - - - -
433A MET* 3.7 23.1 - - + -
435A VAL* 4.7 3.8 - - + -
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PRO 3.0 10.2 + - - +
265A GLU* 2.7 42.8 + - - +
267A LEU* 1.3 77.2 - - - +
269A LYS* 1.3 88.4 + - - +
271A VAL* 3.2 4.2 + - - +
272A GLU* 2.9 53.9 + - - +
418A GLU* 2.7 39.9 + - - +
421A PHE* 3.9 23.9 - - + -
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 3.1 38.7 + - - +
266A ARG* 3.6 14.4 - - + +
268A ARG* 1.3 97.9 - - - +
270A ILE* 1.3 57.5 + - + +
272A GLU* 3.0 12.1 + - - +
273A GLU* 2.8 42.5 + - + +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE* 4.7 2.7 - - + -
266A ARG* 3.1 37.3 + - + +
267A LEU* 3.6 9.0 - - + +
268A ARG 3.2 0.2 - - - -
269A LYS* 1.3 76.1 - - - +
271A VAL* 1.3 57.3 + - - +
273A GLU* 2.8 27.0 + - + +
274A ARG* 2.8 45.0 + - + +
433A MET* 4.8 4.3 - - + -
435A VAL* 3.5 44.4 - - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU 3.1 16.5 + - - +
268A ARG 3.2 4.9 + - - +
270A ILE* 1.3 76.3 - - - +
272A GLU* 1.3 52.2 + - - +
274A ARG* 3.4 9.5 + - - +
275A GLY* 2.7 30.0 + - - -
276A THR* 3.6 15.3 + - - +
278A VAL* 3.5 31.2 - - + -
336A LYS* 5.3 1.1 + - - +
421A PHE* 3.9 26.2 - - + -
433A MET* 4.1 21.8 - - + -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ARG* 2.9 39.7 + - - +
269A LYS* 3.0 15.0 + - - +
270A ILE 2.9 0.4 - - - -
271A VAL* 1.3 76.3 - - - +
273A GLU* 1.3 58.9 + - + +
274A ARG 3.0 1.6 - - - -
275A GLY* 2.9 20.1 + - - -
336A LYS* 5.9 2.5 - - - +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 2.8 24.2 + - + +
270A ILE* 3.1 37.7 + - + +
272A GLU* 1.3 76.9 - - + +
274A ARG* 1.3 58.7 + - + +
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 2.8 23.7 + - + +
271A VAL* 3.6 9.0 - - - +
273A GLU* 1.3 81.2 - - + +
275A GLY* 1.3 63.3 + - - +
276A THR* 3.3 20.6 + - + +
316A LEU* 4.1 9.7 - - - +
332A GLU* 2.5 52.0 + - - -
433A MET* 2.4 57.7 + - - +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A VAL 2.7 13.3 + - - -
272A GLU* 2.9 11.7 + - - -
274A ARG* 1.3 78.8 - - - +
276A THR* 1.3 55.6 + - - +
334A GLN 4.7 6.8 - - - +
336A LYS* 3.3 30.5 - - - +
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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