Contacts of the helix formed by residues 285 - 297 (chain H) in PDB entry 3Q2K
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 LYS 285 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H LEU* 4.4 13.7 - - + -
281H PRO* 3.7 10.1 - - + +
282H ASP* 2.8 43.3 + - - +
284H ASP* 1.3 82.4 - - + +
286H ILE* 1.3 58.4 + - - +
287H ARG 3.7 1.1 - - - -
288H GLU* 3.4 21.9 + - + +
289H ALA* 3.1 30.6 + - + +
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Residues in contact with ILE 286 (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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140H LEU* 4.5 8.1 - - + -
271H ILE* 4.4 20.9 - - + +
274H TRP* 3.6 42.0 - - + -
282H ASP 3.8 6.7 - - - +
283H ASP* 2.9 34.5 - - - +
284H ASP 3.4 2.8 - - - -
285H LYS* 1.3 73.6 - - - +
287H ARG* 1.3 70.6 + - + +
288H GLU 3.1 1.6 - - - -
289H ALA* 3.3 4.5 + - - +
290H ASN* 3.0 38.4 + - - +
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Residues in contact with ARG 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ASP 5.3 0.8 + - - -
285H LYS 3.7 0.2 - - - -
286H ILE* 1.3 81.7 - - + +
288H GLU* 1.3 58.4 + - - +
290H ASN* 3.5 11.8 - - + +
291H TYR* 3.2 28.3 + - - +
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Residues in contact with GLU 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ASP 4.6 4.3 - - - +
285H LYS* 3.4 29.1 + - + +
287H ARG* 1.3 77.2 - - + +
289H ALA* 1.3 67.7 + - - +
290H ASN 3.1 0.9 - - - -
291H TYR* 2.7 33.8 - - + +
292H GLU* 2.8 28.1 + - + +
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Residues in contact with ALA 289 (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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136H ALA* 3.7 26.9 - - + +
137H THR* 4.2 4.7 - - + +
140H LEU* 3.9 21.3 - - + -
271H ILE* 5.2 0.7 - - + -
285H LYS* 3.1 21.0 + - + +
286H ILE* 3.8 4.0 - - - +
288H GLU* 1.3 76.1 - - - +
290H ASN* 1.3 69.5 + - - +
291H TYR 3.1 0.5 + - - -
292H GLU* 4.8 2.2 - - - -
293H THR* 2.8 29.9 + - - -
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Residues in contact with ASN 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H THR* 3.5 8.8 - - - +
269H ASN 3.6 8.8 - - - +
270H ARG* 3.9 13.9 - - + +
271H ILE* 2.7 53.0 + - - +
286H ILE* 3.0 26.1 + - - +
287H ARG* 3.5 12.8 - - - +
289H ALA* 1.3 76.1 - - - +
291H TYR* 1.3 58.2 + - - +
294H THR* 2.8 34.9 + - - +
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Residues in contact with TYR 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H ARG* 3.2 18.1 + - - -
288H GLU* 2.7 29.4 + - + +
290H ASN* 1.3 76.0 - - - +
292H GLU* 1.3 59.9 + - + +
294H THR* 3.4 4.7 + - - -
295H SER* 2.8 30.8 + - - -
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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
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136H ALA* 4.2 19.3 - - + +
288H GLU* 2.8 35.5 + - + +
289H ALA* 3.4 1.3 + - - -
291H TYR* 1.3 71.7 - - + +
293H THR* 1.3 60.5 + - - +
295H SER* 3.4 6.5 + - - -
296H VAL* 3.0 33.8 + - + +
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Residues in contact with THR 293 (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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135H ASN* 2.8 50.0 - - + +
136H ALA* 3.1 6.3 + - - +
137H THR* 3.0 30.8 + - - +
268H VAL 3.9 4.7 - - - +
269H ASN* 4.2 8.8 - - + +
289H ALA 2.8 16.8 + - - -
292H GLU* 1.3 75.5 - - - +
294H THR* 1.3 55.6 + - - +
296H VAL* 4.4 4.8 - - + +
297H TYR* 2.7 34.3 + - - +
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Residues in contact with THR 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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269H ASN* 3.3 31.4 + - + +
270H ARG* 5.4 0.9 - - - +
290H ASN* 2.8 23.1 + - - +
291H TYR* 3.9 4.0 - - - -
293H THR* 1.3 78.3 - - - +
295H SER* 1.3 58.0 + - - +
297H TYR* 3.4 18.7 - - + +
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Residues in contact with SER 295 (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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291H TYR* 2.8 21.0 + - - -
292H GLU* 3.4 9.9 + - - -
294H THR* 1.3 76.2 - - - +
296H VAL* 1.3 64.1 + - - +
297H TYR 3.3 1.7 - - - +
299H PHE* 5.7 2.1 - - - +
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Residues in contact with VAL 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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134H ARG 5.9 2.9 - - - +
135H ASN* 5.7 7.6 - - - +
292H GLU* 3.0 19.1 + - + +
293H THR* 4.4 5.4 - - + +
295H SER* 1.3 78.6 - - - +
297H TYR* 1.3 54.6 + - - +
298H GLY 3.0 0.3 + - - -
299H PHE* 2.6 59.1 + - + +
300H GLY* 3.9 10.1 - - - +
303H LEU* 4.0 24.0 - - + -
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Residues in contact with TYR 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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162H TRP* 6.2 0.3 - - - -
247H ASN* 5.0 6.8 + - - -
266H VAL* 4.3 18.2 - - + +
267H ALA* 3.7 34.8 - - + -
269H ASN* 5.2 6.5 - - + -
293H THR* 2.7 20.2 + - - +
294H THR* 3.4 20.2 - - + +
295H SER 3.3 2.2 - - - +
296H VAL* 1.3 76.4 - - - +
298H GLY* 1.3 67.0 + - - +
299H PHE* 3.5 11.2 + + - -
550H HP7 4.2 23.0 + - - -
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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