Contacts of the helix formed by residues 79 - 92 (chain D) in PDB entry 5E6J
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 SER 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D LEU* 5.5 2.0 - - - -
77D ASP* 2.8 16.8 + - - -
78D GLU* 1.3 78.0 - - - +
80D PHE* 1.3 64.2 + - - +
81D LEU 3.3 0.8 + - - -
82D GLY* 3.3 5.6 + - - +
83D ARG* 2.4 54.5 + - - +
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Residues in contact with PHE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D TYR* 3.8 39.0 - + + -
75D THR* 4.1 16.6 - - + -
77D ASP* 3.0 19.9 + - + +
78D GLU* 3.1 0.6 - - - -
79D SER* 1.3 78.9 + - - +
81D LEU* 1.3 62.5 + - - +
83D ARG* 3.3 27.9 + - - +
84D TYR* 2.8 33.9 + - + +
151D LEU* 4.3 8.1 - - + -
154D ALA* 3.4 29.1 - - + +
155D TYR* 3.4 52.0 - + - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.0 18.6 - - + +
36D TYR* 5.5 2.0 - - + -
57D PHE* 3.8 24.5 - - + -
58D VAL 3.0 39.9 - - - +
59D LEU* 4.0 15.7 - - + -
60D PRO* 4.2 6.3 - - + -
69D ALA* 6.4 0.4 - - + -
73D TYR* 3.8 23.1 - - + +
78D GLU 4.2 3.6 + - - +
79D SER 3.3 0.6 - - - -
80D PHE* 1.3 83.1 - - - +
82D GLY* 1.3 57.6 + - - +
84D TYR* 3.2 10.4 + - + +
85D MET* 2.9 46.5 + - + +
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TYR* 3.8 27.4 + - - -
59D LEU* 4.0 11.2 - - - +
79D SER 3.3 6.5 + - - -
80D PHE 3.3 0.6 - - - -
81D LEU* 1.3 77.9 - - - +
83D ARG* 1.3 58.7 + - - +
85D MET* 4.0 1.2 - - - +
86D SER* 2.8 31.9 + - - -
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASP* 2.7 17.2 + - - -
79D SER* 2.4 48.5 + - - +
80D PHE* 3.3 26.1 + - - +
82D GLY* 1.3 74.2 - - - +
84D TYR* 1.3 53.0 + - - +
86D SER* 3.2 6.1 + - - -
87D ALA* 2.7 37.9 + - - +
154D ALA* 3.0 36.4 + - + +
157D ASN* 3.8 30.2 + - - +
158D LYS 6.6 0.2 - - - -
159D THR* 5.9 8.5 - - + -
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D PHE* 5.1 5.6 - + - -
72D TYR* 6.2 0.9 - + - -
73D TYR* 3.9 26.0 - + - -
80D PHE* 2.8 21.7 + + + +
81D LEU* 3.4 11.0 - - + +
83D ARG* 1.3 77.4 - - - +
85D MET* 1.3 71.8 + - - +
87D ALA* 3.6 3.8 - - - +
88D LEU* 2.8 39.8 + - + +
147D ASN* 3.3 30.0 + - - +
150D ALA* 3.6 26.5 - - + -
151D LEU* 3.3 42.6 - - + +
154D ALA* 4.2 12.5 - - + +
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Residues in contact with MET 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TYR* 3.6 45.3 - - + -
38D ASP* 4.3 5.4 - - - +
39D GLY* 3.3 36.1 - - - +
57D PHE* 3.9 38.1 - - + -
81D LEU* 2.9 30.9 + - + +
82D GLY 4.0 1.3 - - - +
84D TYR* 1.3 87.0 - - - +
86D SER* 1.3 57.9 + - - +
88D LEU* 3.0 14.3 + - + +
89D ASN* 2.8 32.2 + - - +
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Residues in contact with SER 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TYR* 4.8 7.7 - - - -
39D GLY 4.8 2.2 - - - -
82D GLY 2.8 21.0 + - - -
83D ARG* 3.6 7.0 - - - -
85D MET* 1.3 77.2 - - - +
87D ALA* 1.3 58.9 + - - +
89D ASN* 3.9 8.0 - - - +
90D HIS* 3.1 29.6 + - - -
160D VAL* 4.7 1.1 - - - +
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ARG 2.7 20.0 + - - +
84D TYR 3.6 4.0 - - - +
86D SER* 1.3 73.1 - - - +
88D LEU* 1.3 60.5 + - - +
89D ASN 3.2 0.4 - - - -
90D HIS* 3.0 5.2 + - - +
91D THR* 2.9 31.1 + - - +
150D ALA* 3.9 22.7 - - + +
153D LEU* 4.1 20.4 - - + -
154D ALA* 5.5 0.7 - - - +
158D LYS 5.6 0.9 - - - +
159D THR* 6.0 1.1 - - - -
160D VAL* 4.7 12.6 - - + +
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASP* 4.2 22.9 - - + +
39D GLY* 4.7 0.4 - - - -
84D TYR* 2.8 40.8 + - + +
85D MET* 3.0 18.6 + - + +
87D ALA* 1.3 77.5 - - - +
89D ASN* 1.3 58.3 + - - +
91D THR* 3.3 10.5 - - - +
92D LYS* 2.8 51.5 + - + +
146D ALA* 4.7 6.1 - - + +
147D ASN* 3.3 27.8 - - - +
150D ALA* 3.7 5.1 - - + +
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLY* 3.4 30.3 + - - +
40D ALA* 3.6 20.0 + - - +
41D ASP 4.9 2.0 - - - +
85D MET 2.8 9.2 + - - +
86D SER* 3.9 9.6 - - - +
87D ALA 3.2 0.2 - - - -
88D LEU* 1.3 75.4 - - - +
90D HIS* 1.3 68.6 + - - +
92D LYS* 3.7 27.6 + - - +
93D LYS* 4.4 13.9 - - - +
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Residues in contact with HIS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D SER* 3.1 27.7 + - - -
87D ALA 3.0 6.1 + - - +
88D LEU 3.0 0.6 - - - -
89D ASN* 1.3 87.9 - - - +
91D THR* 1.3 60.2 + - - +
92D LYS 3.1 2.0 - - - -
93D LYS* 2.9 29.8 + - - +
94D TRP* 3.7 8.5 - - - -
109D ASP* 4.7 7.9 - - - +
160D VAL* 3.6 41.0 - - + +
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Residues in contact with THR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA 2.9 25.1 + - - +
88D LEU* 3.3 10.0 - - - -
90D HIS* 1.3 73.4 - - + +
92D LYS* 1.3 62.4 + - - +
93D LYS 3.1 0.2 - - - -
94D TRP* 3.1 62.1 + - + +
96D PHE* 3.6 11.8 - - - -
146D ALA* 2.9 26.7 + - - +
149D CYS* 4.5 1.8 - - - -
150D ALA* 3.7 10.3 - - - +
153D LEU* 4.1 16.8 - - + -
160D VAL* 5.2 0.7 - - + -
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Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU 4.8 1.6 + - - -
38D ASP* 2.9 39.8 + - + +
40D ALA* 5.0 3.2 - - - +
88D LEU* 2.8 32.0 + - + +
89D ASN* 3.7 25.4 + - - +
90D HIS 3.1 0.2 + - - -
91D THR* 1.3 78.1 + - - +
93D LYS* 1.3 77.1 + - + +
94D TRP 3.3 5.9 + - - +
96D PHE* 5.4 0.3 - - - -
146D ALA* 4.1 16.7 - - + +
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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