Contacts of the helix formed by residues 290 - 306 (chain H) in PDB entry 4ZZ7
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 290 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H PRO* 6.1 0.7 - - - -
288H ALA 3.3 8.7 - - - +
289H VAL* 1.3 80.6 - - - +
291H ASP* 1.3 71.2 + - - +
292H ALA* 3.8 8.1 - - - -
293H ALA 3.9 0.4 - - - -
294H GLY* 3.2 11.4 + - - -
393H VAL 2.7 17.8 + - - -
394H ALA* 3.9 7.1 + - - -
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Residues in contact with ASP 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H GLY* 1.3 77.6 - - - +
292H ALA* 1.3 63.6 + - - +
294H GLY* 3.7 4.3 - - - +
295H ASP* 3.9 14.0 - - - +
392H ARG* 3.2 52.5 + - - +
393H VAL 5.7 0.3 - - - +
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Residues in contact with ALA 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H PRO* 6.1 5.8 - - + -
289H VAL 5.0 0.9 - - - +
290H GLY* 3.8 6.1 - - - -
291H ASP* 1.3 73.8 + - - +
293H ALA* 1.3 68.1 - - + +
294H GLY 3.4 0.5 + - - -
295H ASP* 3.5 13.9 + - - +
296H ALA* 3.5 13.0 + - - +
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Residues in contact with ALA 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H VAL* 4.2 14.8 - - + +
257H PRO* 4.9 12.8 - - + -
261H MET* 3.9 23.4 - - + +
288H ALA* 4.3 5.6 - - + -
289H VAL 3.7 17.7 - - - +
290H GLY 4.4 0.2 - - - +
291H ASP* 3.4 1.4 - - - +
292H ALA* 1.3 79.9 - - + +
294H GLY* 1.3 54.8 + - - +
295H ASP 3.2 0.2 + - - -
296H ALA* 3.2 4.4 + - - +
297H LEU* 2.8 35.5 + - - +
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Residues in contact with GLY 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H ALA* 3.6 20.8 - - - +
290H GLY 3.2 11.3 + - - -
291H ASP* 3.6 3.1 - - - +
292H ALA 3.4 1.0 - - - -
293H ALA* 1.3 76.1 - - - +
295H ASP* 1.3 57.0 + - - +
297H LEU* 3.9 1.5 - - - +
298H VAL* 3.2 21.1 + - - +
390H VAL* 4.9 1.0 - - - +
392H ARG* 2.9 35.2 + - - -
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Residues in contact with ASP 295 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H ASP* 3.9 18.1 - - - +
292H ALA 3.5 7.0 + - - +
293H ALA 3.3 0.8 - - - -
294H GLY* 1.3 70.7 - - - +
296H ALA* 1.3 61.2 + - - +
297H LEU 3.2 1.9 + - - -
298H VAL* 3.3 2.9 + - - +
299H SER* 2.9 34.0 + - - -
371H HIS* 5.7 0.2 + - - -
392H ARG* 3.2 23.5 + - - +
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Residues in contact with ALA 296 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H MET* 4.1 16.4 - - + +
292H ALA 3.5 10.6 + - - +
293H ALA* 3.2 11.8 + - - +
295H ASP* 1.3 77.6 - - - +
297H LEU* 1.3 59.8 - - - +
299H SER* 4.1 4.7 - - - -
300H LYS* 3.2 37.4 + - - +
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Residues in contact with LEU 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H VAL* 4.4 11.2 - - + -
261H MET* 4.1 18.8 - - + -
264H ALA* 5.5 0.7 - - + -
265H VAL* 3.9 21.5 - - + -
268H LEU* 4.1 20.0 - - + -
286H ALA* 3.9 26.0 - - + -
288H ALA* 4.2 14.4 - - + -
293H ALA 2.8 21.3 + - - +
294H GLY 3.9 3.1 - - - +
296H ALA* 1.3 70.2 - - - +
298H VAL* 1.3 57.7 + - + +
300H LYS* 3.2 2.3 + - - +
301H MET* 2.6 45.0 + - + +
388H LEU* 6.3 1.8 - - + -
390H VAL* 4.1 24.7 - - + -
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Residues in contact with VAL 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H GLY 3.2 18.1 + - - +
295H ASP* 3.3 4.3 + - - +
297H LEU* 1.3 75.6 - - + +
299H SER* 1.3 60.3 + - - +
301H MET* 3.9 5.8 - - - +
302H THR* 2.6 39.7 + - - +
347H VAL* 3.9 24.0 - - + -
368H LEU* 4.1 6.2 - - + +
370H ASP* 3.0 37.2 - - + +
390H VAL* 4.2 20.9 - - + -
392H ARG* 3.7 1.8 - - - +
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Residues in contact with SER 299 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H ASP 2.9 18.2 + - - -
296H ALA* 4.1 5.6 - - - -
298H VAL* 1.3 79.7 - - - +
300H LYS* 1.3 64.8 + - - +
302H THR* 3.4 4.9 + - - -
303H GLN* 3.2 28.8 + - - +
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Residues in contact with LYS 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H MET* 4.1 24.7 - - + +
262H ASP* 2.6 37.7 + - - +
265H VAL* 3.7 20.8 - - + +
296H ALA* 3.2 23.3 + - - +
297H LEU 3.2 3.4 + - - +
299H SER* 1.3 79.5 - - - +
301H MET* 1.3 64.7 + - - +
303H GLN* 3.5 8.8 + - - +
304H ALA* 3.2 19.4 + - - +
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Residues in contact with MET 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H VAL* 3.8 27.2 - - + +
268H LEU* 4.5 11.0 - - - -
269H LEU* 3.3 42.0 - - + -
273H PHE* 4.3 3.8 - - + -
297H LEU* 2.6 29.1 + - + +
298H VAL* 4.3 0.2 - - - -
300H LYS* 1.3 72.3 - - - +
302H THR* 1.3 56.7 + - - +
304H ALA* 3.3 2.5 + - + -
305H MET* 2.9 56.6 + - + +
368H LEU* 3.8 14.8 - - + -
388H LEU* 4.1 23.8 - - + -
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Residues in contact with THR 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298H VAL* 2.6 24.6 + - - +
299H SER* 3.6 5.4 - - - -
301H MET* 1.3 74.8 - - - +
303H GLN* 1.3 61.5 + - + +
305H MET* 3.5 2.3 + - - +
306H GLN* 2.8 42.8 + - - +
347H VAL* 3.2 27.1 - - + +
348H VAL* 3.8 22.7 - - + -
368H LEU* 3.8 4.7 - - - +
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Residues in contact with GLN 303 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H SER* 3.2 20.9 + - - +
300H LYS* 3.6 11.2 - - - +
301H MET 3.3 0.4 - - - -
302H THR* 1.3 79.3 - - + +
304H ALA* 1.3 61.7 + - - +
305H MET 3.4 0.3 + - - -
306H GLN* 3.4 17.7 + - - +
307H LYS* 4.2 9.5 - - - +
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Residues in contact with ALA 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H VAL* 4.3 12.8 - - + -
266H ASN* 6.1 0.2 - - - -
269H LEU* 3.9 32.6 - - + +
300H LYS 3.2 13.7 + - - +
301H MET 4.0 2.2 - - - +
303H GLN* 1.3 76.0 - - - +
305H MET* 1.3 63.7 + - - +
307H LYS* 3.3 27.9 + - + +
308H LEU* 4.2 2.9 + - - +
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Residues in contact with MET 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H LEU* 4.3 2.2 - - - +
273H PHE* 3.7 29.2 - - + -
301H MET* 2.9 43.7 + - + +
302H THR* 3.8 7.4 - - - +
303H GLN 3.3 0.4 - - - -
304H ALA* 1.3 76.2 - - - +
306H GLN* 1.3 63.8 + - - +
307H LYS 3.2 0.2 - - - -
308H LEU* 3.2 45.1 - - + +
348H VAL* 4.0 32.0 - - + +
366H GLY 4.2 9.9 - - - +
368H LEU* 3.6 26.5 - - + -
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Residues in contact with GLN 306 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302H THR* 2.8 34.4 + - - +
303H GLN* 3.4 13.3 + - - +
304H ALA 3.3 1.2 - - - -
305H MET* 1.3 77.6 - - - +
307H LYS* 1.3 60.4 + - + +
308H LEU 3.2 6.2 + - - +
348H VAL* 4.0 29.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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