Contacts of the helix formed by residues 267 - 281 (chain H) in PDB entry 1P8J
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 ALA 267 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530E ASP* 5.9 0.2 - - - +
233H ASP* 3.3 31.1 + - + +
236H GLU* 4.9 0.6 + - - -
265H GLY 3.5 2.1 + - - +
266H PRO* 1.3 74.8 - - - +
268H ARG* 1.3 67.8 + - + +
269H LEU 3.5 1.3 - - - -
270H ALA* 3.4 1.0 + - - +
271H GLU* 2.9 29.2 + - - +
308H TYR* 4.6 1.4 + - - -
4045H SO4 6.0 0.2 - - - +
802R ARG* 5.6 0.4 - - - +
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Residues in contact with ARG 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490E ARG* 4.1 15.7 - - - +
529E ASN* 3.4 33.5 + - - -
530E ASP* 3.6 41.6 + - - +
233H ASP* 3.5 0.6 + - - -
267H ALA* 1.3 82.9 - - - +
269H LEU* 1.3 62.2 + - - +
271H GLU* 3.4 5.6 + - - +
272H GLU* 3.1 28.1 + - - +
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Residues in contact with LEU 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E LYS* 4.4 8.7 + - - +
451E ILE* 4.1 29.6 - - + -
488E GLN* 5.2 0.7 - - - +
490E ARG* 3.6 33.7 - - - +
530E ASP* 5.3 0.4 - - - +
565E LYS* 6.4 0.2 - - - +
567E THR* 4.2 16.4 - - + +
569E VAL* 4.3 9.9 - - + -
233H ASP* 2.7 26.2 + - + +
234H ALA* 4.2 13.7 - - + +
237H ALA* 3.6 13.5 - - + +
268H ARG* 1.3 71.3 - - - +
270H ALA* 1.3 58.8 + - - +
272H GLU* 3.3 22.8 + - - +
273H ALA* 2.9 27.0 + - - +
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Residues in contact with ALA 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233H ASP* 2.9 18.8 + - - +
236H GLU* 3.8 26.5 - - + +
237H ALA* 4.0 4.9 - - - +
240H LEU* 4.2 8.0 - - + +
266H PRO* 3.6 23.1 - - + -
267H ALA 3.9 1.1 - - - +
268H ARG 3.3 0.2 - - - -
269H LEU* 1.3 73.0 - - - +
271H GLU* 1.3 65.9 + - - +
273H ALA* 3.1 9.6 + - - +
274H PHE* 2.9 26.3 + - - -
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Residues in contact with GLU 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E ARG* 6.4 3.8 - - + -
272E GLU* 4.4 14.4 - - + +
266H PRO* 3.2 31.3 - - - +
267H ALA 2.9 20.0 + - - +
268H ARG* 3.7 5.4 - - - +
270H ALA* 1.3 77.6 - - - +
272H GLU* 1.3 61.8 + - + +
274H PHE* 3.3 7.6 + - - +
275H PHE* 3.2 21.8 + - + +
311H SER* 5.2 1.8 + - - -
313H TYR* 3.8 21.5 + - + -
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Residues in contact with GLU 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU* 4.4 15.0 - - + +
275E PHE* 4.2 16.6 - - + -
313E TYR* 4.3 12.4 + - - -
449E LYS* 2.6 35.1 + - - +
488E GLN* 5.2 4.0 + - - +
490E ARG* 4.0 17.5 + - - -
571E TYR* 3.9 8.7 + - - -
268H ARG* 3.1 17.4 + - - +
269H LEU* 3.5 20.1 - - - +
271H GLU* 1.3 78.0 - - + +
273H ALA* 1.3 52.3 + - - +
275H PHE* 3.2 5.4 + - - +
276H ARG* 2.7 38.1 + - - +
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Residues in contact with ALA 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E LYS* 5.0 1.7 - - - +
237H ALA* 3.7 31.2 - - + +
240H LEU* 4.0 16.6 - - + +
241H GLY* 4.6 5.7 - - - +
269H LEU 2.9 13.8 + - - +
270H ALA 3.1 9.2 + - - +
272H GLU* 1.3 77.2 - - - +
274H PHE* 1.3 53.9 + - - +
276H ARG* 3.7 9.0 - - - +
277H GLY* 2.8 32.7 + - - -
289H PHE* 4.6 2.8 - - - -
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Residues in contact with PHE 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H LEU* 3.8 24.0 - - + -
266H PRO* 4.2 21.3 - - + -
270H ALA 2.9 18.5 + - - -
271H GLU* 3.5 9.4 - - - +
273H ALA* 1.3 76.7 - - - +
275H PHE* 1.3 62.1 + - - +
277H GLY 3.5 0.2 + - - -
278H VAL* 3.1 27.5 + - - +
289H PHE* 3.8 28.1 - + - -
291H TRP* 3.5 32.1 - + - -
308H TYR* 3.9 21.8 - + + -
311H SER* 4.6 8.1 - - - -
313H TYR* 3.5 25.1 - + + -
314H THR* 3.6 23.6 - - + -
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Residues in contact with PHE 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E GLU* 4.1 33.4 - - + -
275E PHE* 4.1 25.1 - + + -
276E ARG* 4.2 33.7 - - + -
279E SER* 5.8 1.3 - - - -
280E GLN* 4.3 15.3 - - - -
271H GLU* 3.2 9.5 + - + +
272H GLU* 3.2 8.1 + - - +
274H PHE* 1.3 76.2 - - - +
276H ARG* 1.3 64.1 + - - +
278H VAL* 3.3 6.6 + - + +
279H SER* 2.8 45.7 + - - -
313H TYR* 3.6 36.8 - + + +
390H TRP* 6.2 0.7 - + - -
447H GLN* 5.9 0.9 - - - -
449H LYS* 6.1 1.1 - - - -
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Residues in contact with ARG 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E PHE* 4.2 23.6 - - + -
447E GLN* 3.0 51.5 + - - -
448E ARG* 3.9 0.4 - - - +
449E LYS* 3.5 52.4 - - - +
479E ASN* 4.7 3.8 + - - -
571E TYR* 4.4 4.0 - - - -
241H GLY* 6.6 0.2 - - - -
244H PRO* 6.3 1.9 - - - +
272H GLU 2.7 22.0 + - - +
273H ALA* 3.7 7.2 - - - +
275H PHE* 1.3 73.8 - - - +
277H GLY* 1.3 58.2 + - - +
279H SER* 3.2 2.5 + - - -
280H GLN* 2.8 57.5 + - + +
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Residues in contact with GLY 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H LEU 5.7 1.6 - - - -
241H GLY* 6.3 2.0 - - - -
244H PRO* 5.5 5.6 - - - -
273H ALA 2.8 21.8 + - - -
274H PHE 4.0 0.7 - - - -
276H ARG* 1.3 72.7 - - - +
278H VAL* 1.3 53.0 + - - +
281H GLY* 2.9 19.9 + - - -
287H SER* 2.7 42.2 + - - -
289H PHE* 4.4 4.7 - - - -
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Residues in contact with VAL 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H PHE 3.1 18.6 + - - +
275H PHE* 3.8 10.8 - - + +
276H ARG 3.3 0.2 - - - -
277H GLY* 1.3 76.7 - - - +
279H SER* 1.3 64.2 + - - +
284H GLY 4.8 1.0 - - - +
285H LEU 4.4 0.5 - - - -
286H GLY* 3.1 19.8 + - - -
287H SER 4.0 11.0 - - - +
289H PHE* 4.4 3.6 - - + -
313H TYR* 3.9 30.1 - - + +
390H TRP* 3.2 66.2 + - + +
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Residues in contact with SER 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E PHE* 5.7 1.8 - - - -
279E SER* 4.6 19.4 + - - -
280E GLN* 4.9 4.6 + - - -
275H PHE* 2.8 41.7 + - - -
276H ARG* 3.8 3.6 - - - -
278H VAL* 1.3 81.5 - - - +
280H GLN* 1.3 68.4 + - - +
281H GLY 3.8 0.2 - - - -
284H GLY* 3.5 22.8 - - - +
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Residues in contact with GLN 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E PHE* 4.3 17.8 - - - -
279E SER* 4.8 5.8 + - - -
447E GLN* 4.6 9.5 + - - +
244H PRO* 5.1 3.2 - - + +
245H ASN* 3.8 5.9 + - - +
276H ARG* 2.8 61.6 + - + +
279H SER* 1.3 79.8 - - - +
281H GLY* 1.3 68.0 + - - +
283H GLY* 3.6 5.2 + - - -
284H GLY* 3.1 11.8 + - - +
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Residues in contact with GLY 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H PRO* 3.7 19.7 - - - +
276H ARG 3.8 0.4 + - - -
277H GLY* 2.9 23.6 + - - -
280H GLN* 1.3 75.4 - - - +
282H ARG* 1.3 71.3 + - - -
284H GLY 2.8 10.7 + - - -
286H GLY* 2.9 16.6 + - - -
287H SER* 3.8 8.3 - - - -
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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