Contacts of the helix formed by residues 292 - 306 (chain B) in PDB entry 1Z3E
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 GLY 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B ARG* 6.1 0.8 - - - +
290B ASN 3.2 9.0 + - - -
291B LEU* 1.3 76.0 - - - +
293B ARG* 1.3 61.3 + - - -
294B LYS 3.4 2.2 - - - -
295B SER* 3.4 11.1 + - - -
296B LEU* 2.9 28.7 + - - +
402B SO4 3.7 15.7 - - - -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B GLY* 1.3 71.6 - - - -
294B LYS* 1.3 63.7 + - + +
296B LEU* 3.2 6.8 + - - +
297B GLU* 3.0 32.3 + - + +
402B SO4 2.8 39.9 + - - +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ARG* 6.1 1.8 - - - +
293B ARG* 1.3 74.1 - - + +
295B SER* 1.3 58.8 + - - +
297B GLU* 3.3 17.4 + - - +
298B GLU* 2.9 28.5 + - - +
402B SO4 2.8 32.2 + - - +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B SER* 4.6 1.0 + - - -
261B ARG* 4.0 26.2 + - - +
262B SER* 3.2 23.3 + - - -
291B LEU* 3.5 21.9 - - - -
292B GLY* 3.4 14.2 + - - -
293B ARG 3.2 0.2 - - - -
294B LYS* 1.3 79.4 - - - +
296B LEU* 1.3 56.3 - - - +
298B GLU* 3.2 5.1 + - - +
299B VAL* 2.9 33.7 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU* 4.8 5.2 - - + +
285B MET* 3.5 32.3 - - + +
286B MET* 3.7 51.6 - - + +
291B LEU* 3.9 16.3 - - + +
292B GLY 2.9 17.6 + - - +
293B ARG* 3.7 6.5 - - - +
295B SER* 1.3 76.6 - - - +
297B GLU* 1.3 62.8 + - + +
299B VAL* 3.2 6.6 + - + -
300B LYS* 3.0 48.3 + - + +
310B LEU* 4.8 2.2 - - + -
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 3.0 19.7 + - - +
294B LYS* 3.6 18.5 - - - +
295B SER 3.3 0.2 - - - -
296B LEU* 1.3 77.3 - - + +
298B GLU* 1.3 58.4 + - - +
300B LYS* 3.4 15.4 + - - +
301B ALA* 2.9 29.9 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP 4.1 4.8 - - - +
258B LEU* 3.6 14.9 - - + -
259B SER* 2.9 38.4 + - - -
262B SER* 2.7 28.8 + - - -
294B LYS 2.9 13.8 + - - +
295B SER* 3.2 7.7 + - - +
297B GLU* 1.3 77.4 - - - +
299B VAL* 1.3 57.1 + - - +
301B ALA* 3.2 6.6 + - + +
302B LYS* 2.9 32.9 + - + +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU* 4.1 19.1 - - + -
262B SER* 4.4 9.4 - - - -
266B LEU* 4.4 16.2 - - + -
277B LEU* 3.7 39.4 - - + +
285B MET* 4.5 6.7 - - + -
291B LEU* 4.7 10.1 - - + -
295B SER 2.9 20.3 + - - +
296B LEU* 3.2 13.2 + - + +
298B GLU* 1.3 75.1 - - - +
300B LYS* 1.3 64.3 + - + +
302B LYS* 3.2 2.9 + - - +
303B LEU* 3.0 27.6 + - + +
310B LEU* 5.2 2.9 - - + -
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU* 3.7 24.0 + - + +
286B MET* 6.1 0.4 - - - +
296B LEU* 3.0 35.0 + - + +
297B GLU* 3.8 16.5 - - - +
299B VAL* 1.3 76.8 - - + +
301B ALA* 1.3 59.3 + - - +
303B LEU* 3.3 9.9 + - - +
304B GLU* 3.0 29.8 + - - +
310B LEU* 4.0 28.3 - - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU 2.9 19.0 + - - +
298B GLU* 3.6 7.0 - - - +
300B LYS* 1.3 76.5 - - - +
302B LYS* 1.3 63.7 + - + +
304B GLU* 3.3 11.9 + - - +
305B GLU* 3.1 31.7 + - + +
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 5.1 15.9 - - + -
257B ASP* 3.3 50.7 + - - +
258B LEU* 3.5 29.2 - - + -
277B LEU* 6.4 0.9 - - + -
298B GLU* 2.9 18.8 + - + +
299B VAL 3.2 4.5 + - - +
301B ALA* 1.3 73.2 - - + +
303B LEU* 1.3 66.1 + - + +
305B GLU* 3.1 37.6 + - - +
306B LEU* 3.3 21.3 + - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 6.1 1.1 - - + -
274B VAL* 4.5 10.3 - - + -
277B LEU* 3.9 31.2 - - + -
278B ALA* 4.6 7.9 - - + -
299B VAL* 3.0 20.4 + - + +
300B LYS* 3.6 8.7 - - - +
302B LYS* 1.3 77.4 - - - +
304B GLU* 1.3 60.9 + - - +
306B LEU* 3.0 17.0 + - + +
307B GLY 3.2 0.2 + - - -
308B LEU* 2.9 57.4 + - + +
309B GLY* 4.4 2.7 - - - +
310B LEU* 3.4 45.1 - - + +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LYS 3.0 18.7 + - - +
301B ALA* 3.6 10.4 - - - +
303B LEU* 1.3 77.6 - - - +
305B GLU* 1.3 58.2 + - + +
307B GLY* 2.9 18.9 + - - -
308B LEU 3.4 11.8 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ALA* 3.1 18.8 + - - +
302B LYS* 3.1 42.6 + - - +
303B LEU 3.2 0.2 - - - -
304B GLU* 1.3 76.9 - - + +
306B LEU* 1.3 63.4 + - + +
307B GLY 3.1 1.3 + - - -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B VAL* 4.1 33.9 - - + +
251B MET* 4.1 19.3 - - + -
256B LEU* 3.9 28.5 - - + -
274B VAL* 4.4 13.7 - - + -
302B LYS* 3.5 14.6 - - + +
303B LEU* 3.0 16.0 + - + +
305B GLU* 1.3 79.1 - - + +
307B GLY* 1.3 60.6 + - - +
308B LEU* 3.6 9.0 + - + +
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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