Contacts of the helix formed by residues 5027 - 5040 (chain e) in PDB entry 3A0B
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 ILE5027 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5023e HIS* 2.8 26.0 - - + +
5024e SER* 5.0 1.1 - - - -
5026e THR* 1.3 73.7 - - - +
5028e PRO* 1.3 59.4 - - + +
5030e LEU* 2.7 9.9 + - - +
5031e PHE* 2.5 40.2 + - + +
6040e HEM 3.4 43.1 - - + -
5031f ILE* 3.6 27.0 - - + +
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Residues in contact with PRO5028 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5024e SER* 4.2 21.8 - - - +
5025e ILE 4.4 2.2 - - - +
5026e THR 3.9 0.7 - - - -
5027e ILE* 1.3 95.0 - - + +
5029e ALA* 1.3 51.5 + - - +
5030e LEU 2.9 6.2 + - - -
5031e PHE* 3.8 11.0 - - + -
5032e ILE* 2.7 41.4 + - + +
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Residues in contact with ALA5029 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5025e ILE* 2.9 26.0 + - + +
5026e THR* 3.2 8.0 + - - +
5027e ILE 3.1 1.0 - - - -
5028e PRO* 1.3 77.4 - - - +
5030e LEU* 1.3 62.4 + - + +
5032e ILE* 4.3 7.8 - - - +
5033e ALA* 3.1 18.7 - - - +
6040e HEM 5.8 1.1 - - + -
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Residues in contact with LEU5030 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5026e THR 2.9 7.6 + - - +
5027e ILE* 2.7 11.6 + - - +
5029e ALA* 1.3 87.1 - - - +
5031e PHE* 1.3 66.5 + - - +
5032e ILE 3.4 0.9 - - - -
5033e ALA* 3.2 7.1 + - + +
5034e GLY 3.1 15.4 + - - -
6040e HEM 3.3 35.9 - - + +
5028f VAL* 3.0 36.6 - - + +
5031f ILE* 3.1 26.3 - - + +
5032f PHE* 3.3 29.9 - - + +
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Residues in contact with PHE5031 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5027e ILE* 2.5 21.0 + - + +
5028e PRO* 4.0 9.9 - - + -
5030e LEU* 1.3 76.8 - - - +
5032e ILE* 1.3 69.4 + - + +
5034e GLY* 3.3 0.9 + - - -
5035e TRP* 3.1 50.1 + + - -
5031f ILE* 3.5 24.4 + - + +
5032f PHE 4.3 0.2 - - - +
5034f LEU* 4.6 2.9 - - + -
5035f GLY* 3.4 23.2 - - - -
5038f ALA* 3.5 22.4 - - + -
5024j ILE* 4.3 26.0 - - + -
5027j LEU* 5.7 0.4 - - + -
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Residues in contact with ILE5032 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5028e PRO* 2.7 27.8 - - + +
5029e ALA* 4.3 9.2 - - - +
5031e PHE* 1.3 84.4 - - + +
5033e ALA* 1.3 89.9 + - + +
5034e GLY 3.1 1.6 - - - -
5035e TRP* 3.5 18.6 - - + +
5036e LEU* 3.0 42.0 + - + +
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Residues in contact with ALA5033 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5029e ALA 3.1 23.6 - - - +
5030e LEU* 3.2 15.4 + - + +
5032e ILE* 1.3 89.7 - - + +
5034e GLY* 1.3 60.4 + - - +
5036e LEU* 3.4 16.7 + - - +
5037e PHE* 3.7 5.7 + - - +
5032f PHE* 4.6 11.1 - - + -
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Residues in contact with GLY5034 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5030e LEU 3.1 6.7 + - - -
5031e PHE 3.7 0.2 - - - -
5032e ILE 3.1 0.4 - - - -
5033e ALA* 1.3 77.6 - - - +
5035e TRP* 1.3 58.6 + - - +
5036e LEU 3.0 2.5 - - - -
5037e PHE* 2.9 24.3 + - - +
5038e VAL 3.2 3.8 + - - -
5032f PHE* 2.9 39.8 - - - -
5036f ALA* 3.4 14.6 - - - +
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Residues in contact with TRP5035 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5031e PHE* 3.1 39.9 + + - +
5032e ILE* 3.2 27.3 + - + +
5034e GLY* 1.3 75.6 - - - +
5036e LEU* 1.3 55.3 + - + +
5038e VAL* 3.2 3.8 + - - +
5039e SER* 2.4 52.3 + - - -
5035f GLY 3.2 20.3 + - - +
5036f ALA* 3.8 0.2 - - - +
5038f ALA* 4.1 17.3 - - + -
5039f ALA* 3.4 26.6 + - + +
5042f PHE* 4.4 21.1 - + + -
5027j LEU* 5.7 1.3 - - + -
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Residues in contact with LEU5036 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032e ILE* 3.0 33.9 + - + +
5033e ALA* 3.6 8.5 - - - +
5034e GLY 3.0 0.2 - - - -
5035e TRP* 1.3 79.9 - - + +
5037e PHE* 1.3 60.2 + - - +
5038e VAL 2.9 1.6 - - - -
5039e SER* 3.5 18.2 - - - +
5040e THR* 2.9 39.0 + - - +
5042e LEU* 5.0 0.2 - - - +
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Residues in contact with PHE5037 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5054d PHE* 3.9 15.7 - + + -
5033e ALA 3.7 2.7 + - - +
5034e GLY* 2.9 14.1 + - - +
5036e LEU* 1.3 78.8 - - - +
5038e VAL* 1.3 55.2 + - + +
5042e LEU* 3.0 38.6 + - + +
5043e ALA* 2.8 56.8 + - - -
5046e VAL* 3.1 33.0 - - + -
5047e PHE* 3.7 15.3 - + - -
5032f PHE* 3.9 29.4 - + + -
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Residues in contact with VAL5038 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5054d PHE* 4.4 10.3 - - + -
5068d LEU* 5.7 3.6 - - + -
5035e TRP 3.2 6.5 - - - +
5036e LEU 2.9 0.2 - - - -
5037e PHE* 1.3 78.4 - - - +
5039e SER* 1.3 63.8 + - - +
5040e THR 3.3 1.6 - - - -
5041e GLY* 3.3 13.7 + - - -
5043e ALA* 5.0 5.4 - - + -
5044e TYR* 5.7 0.7 - - - -
5036f ALA* 2.8 45.3 - - + +
5039f ALA* 3.1 27.1 - - + +
5040f MET* 3.6 25.8 - - + -
5043f ILE* 4.5 7.9 - - + +
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Residues in contact with SER5039 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5035e TRP* 2.4 53.1 + - - +
5036e LEU* 3.4 18.5 + - - +
5038e VAL* 1.3 71.6 - - - +
5040e THR* 1.3 58.8 + - - +
5041e GLY 3.7 0.2 + - - -
5039f ALA* 5.0 0.9 - - - -
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Residues in contact with THR5040 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5036e LEU* 2.9 27.0 + - - +
5039e SER* 1.3 77.5 - - - +
5041e GLY* 1.3 59.9 + - - +
5042e LEU* 3.5 27.6 - - + +
5045e ASP* 5.7 1.1 - - - +
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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