Contacts of the helix formed by residues 288 - 297 (chain H) in PDB entry 4DVQ
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 288 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160H MET* 4.7 0.6 - - - -
202H LEU 4.5 3.8 - - - -
203H ALA 3.2 15.3 - - - -
204H LEU 3.7 4.3 - - - -
286H TYR* 3.3 33.1 - - - -
287H THR* 1.3 80.7 + - - +
289H ILE* 1.3 64.8 + - - -
290H VAL 3.5 1.8 - - - -
291H ALA* 3.7 3.7 + - - +
292H GLU* 3.5 15.2 + - - +
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Residues in contact with ILE 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H ASP* 3.2 26.5 - - + +
148H VAL* 3.7 28.9 - - + -
157H PHE* 3.9 22.2 - - + -
203H ALA* 2.9 25.6 + - + +
204H LEU* 3.1 26.2 + - + +
286H TYR* 3.5 15.7 - - - +
288H GLY* 1.3 70.1 - - - -
290H VAL* 1.3 68.4 + - + +
292H GLU* 3.2 15.9 + - - +
293H LEU* 3.3 18.4 + - + +
311H LEU* 4.8 1.1 - - + -
455H LEU* 4.3 15.0 - - + -
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Residues in contact with VAL 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H LEU* 3.0 34.8 + - + +
205H PHE* 3.9 23.3 - - + -
271H ILE* 3.5 21.1 - - + -
274H ILE* 4.7 2.2 - - + -
289H ILE* 1.3 76.7 - - + +
291H ALA* 1.3 60.7 + - - +
293H LEU* 3.3 10.6 + - + +
294H LEU* 3.0 36.7 + - + +
304H ILE* 4.4 6.3 - - + -
308H SER* 3.5 27.8 - - - +
311H LEU* 5.1 1.6 - - + -
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Residues in contact with ALA 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H ILE* 3.8 19.9 - - + +
278H LEU* 3.9 21.1 - - + -
287H THR* 3.5 27.1 - - - +
288H GLY 3.7 9.5 + - - +
289H ILE 3.2 0.4 - - - -
290H VAL* 1.3 75.3 - - - +
292H GLU* 1.3 62.1 + - + +
294H LEU* 3.2 0.9 + - - +
295H LEU* 2.8 42.6 + - + +
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Residues in contact with GLU 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H ASP* 3.5 32.5 - - + +
156H ARG* 3.7 23.4 + - - +
285H HIS 5.3 1.0 - - - +
286H TYR* 3.8 26.0 - - + -
287H THR 5.1 1.0 + - - -
288H GLY 3.5 13.2 + - - +
289H ILE* 3.2 9.9 + - - +
291H ALA* 1.3 78.5 - - - +
293H LEU* 1.3 61.8 + - - +
295H LEU* 3.9 16.2 - - - +
296H LYS* 3.1 37.6 + - - +
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Residues in contact with LEU 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H ARG 3.6 24.2 - - - +
144H LEU* 3.9 28.0 - - + +
147H ASP* 4.5 17.9 - - + +
148H VAL* 5.0 3.6 - - + -
289H ILE* 3.3 21.2 + - + +
290H VAL* 3.5 18.4 - - + +
291H ALA 3.2 0.4 - - - -
292H GLU* 1.3 77.9 - - - +
294H LEU* 1.3 63.0 + - - +
296H LYS* 3.3 7.1 + - + +
297H ALA* 3.0 19.6 + - - -
298H GLU 4.5 1.2 + - - -
299H LEU* 5.1 4.9 - - + -
304H ILE* 4.1 30.3 - - + +
307H ASN* 5.4 2.9 - - + -
308H SER* 5.0 2.9 - - - +
311H LEU* 5.0 6.1 - - + -
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Residues in contact with LEU 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271H ILE* 4.6 4.9 - - + -
274H ILE* 3.9 28.5 - - + -
275H TYR* 3.9 24.2 - - + +
278H LEU* 3.8 22.9 - - + -
290H VAL* 3.0 26.3 + - + +
293H LEU* 1.3 75.8 - - - +
295H LEU* 1.3 64.1 + - - +
297H ALA* 3.3 15.9 + - - +
301H LEU* 3.7 30.3 - - + -
304H ILE* 4.1 23.6 - - + -
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Residues in contact with LEU 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H LEU* 4.1 22.2 - - + -
282H ARG* 3.1 62.7 + - + +
283H PRO* 4.6 25.8 - - + +
291H ALA* 2.8 28.7 + - + +
292H GLU* 3.9 18.8 - - - +
294H LEU* 1.3 74.7 - - - +
296H LYS* 1.3 62.5 + - + +
297H ALA* 4.5 2.4 - - - +
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Residues in contact with LYS 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ARG 6.0 0.4 - - - +
146H PRO* 4.3 14.5 - - - +
147H ASP* 2.7 37.6 + - - +
292H GLU* 3.1 26.9 + - - +
293H LEU* 3.7 6.1 - - + +
295H LEU* 1.3 80.4 - - + +
297H ALA* 1.3 67.8 + - - +
298H GLU* 3.0 41.9 + - + +
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Residues in contact with ALA 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293H LEU 3.0 11.9 + - - -
294H LEU 3.3 14.1 + - - +
295H LEU 4.5 2.2 - - - +
296H LYS* 1.3 77.8 - - - +
298H GLU* 1.3 58.7 + - - +
299H LEU 3.2 16.1 + - - +
304H ILE* 4.9 3.8 - - - -
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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
------------------------------------------------------------
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