Contacts of the helix formed by residues 65 - 79 (chain B) in PDB entry 1E78
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 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B GLU* 5.9 2.5 - - - -
64B LYS* 1.3 75.8 - - - +
66B LEU* 1.3 65.7 + - - +
67B HIS* 3.5 11.7 + - - +
68B THR* 2.5 38.6 + - - -
69B LEU* 3.1 16.8 + - - +
95B GLU* 5.5 0.9 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 3.3 31.1 - - + +
7B VAL* 4.2 26.0 - - + +
10B ARG* 4.5 5.6 - - + -
64B LYS 4.0 1.4 + - - -
65B SER* 1.3 71.7 - - - +
67B HIS* 1.3 67.7 + - + +
69B LEU* 4.1 7.9 - - + -
70B PHE* 2.9 63.4 + - + -
251B LEU* 3.8 15.9 - - + -
252B GLU* 3.1 32.5 - - - +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 4.8 5.7 + - - -
65B SER* 3.2 9.6 + - - +
66B LEU* 1.3 82.0 - - + +
68B THR* 1.3 53.5 + - - +
70B PHE* 3.8 3.8 - - - +
71B GLY* 2.7 34.5 + - - -
95B GLU* 3.4 22.4 - - + +
99B ASN* 3.2 41.1 + - + -
247B HIS 5.1 0.4 - - - -
248B GLY 5.2 1.8 - - - -
249B ASP* 3.0 35.3 + - - -
252B GLU* 5.6 3.1 + - - -
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS* 4.6 20.8 - - + +
65B SER* 2.5 35.4 + - - -
67B HIS* 1.3 77.2 - - - +
69B LEU* 1.3 61.9 + - - +
71B GLY* 2.8 12.5 + - - -
72B ASP* 2.6 31.6 + - - +
95B GLU* 4.1 19.9 + - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.9 16.4 - - + -
46B VAL* 6.4 0.4 - - + -
49B PHE* 4.4 20.2 - - + -
61B ASN* 3.5 30.5 - - + +
62B CYS* 6.1 0.2 - - - -
64B LYS* 3.7 26.5 - - + +
65B SER 3.1 20.8 + - - +
66B LEU* 3.9 8.7 - - + +
68B THR* 1.3 80.7 - - - +
70B PHE* 1.3 76.3 + - + +
71B GLY 3.0 0.2 + - - -
72B ASP* 3.2 9.0 + - - +
73B LYS* 3.0 36.1 + - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 5.6 2.2 - - + -
19B PHE* 5.5 1.3 - + - -
23B VAL* 4.2 18.2 - - + -
26B ALA* 5.2 11.4 - - + -
27B PHE* 4.0 31.1 - + + -
30B TYR* 6.0 8.5 - + + -
46B VAL* 4.2 21.3 - - + -
66B LEU* 2.9 54.8 + - + +
67B HIS* 3.8 4.0 - - - +
69B LEU* 1.3 81.1 - - + +
71B GLY* 1.3 62.9 + - - +
73B LYS* 3.5 8.0 - - + +
74B LEU* 3.3 21.1 + - - +
251B LEU* 4.0 17.5 - - + -
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS 2.7 19.0 + - - -
68B THR 2.8 5.8 + - - -
70B PHE* 1.3 75.8 - - - +
72B ASP* 1.3 62.3 + - - -
74B LEU* 3.3 3.2 + - - +
75B CYS* 3.0 28.8 + - - +
95B GLU* 4.2 10.8 - - - -
102B PHE* 4.6 15.2 - - - -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS* 5.8 1.9 + - - +
68B THR* 2.6 35.7 + - - +
69B LEU* 3.6 8.4 + - - +
71B GLY* 1.3 73.1 - - - +
73B LYS* 1.3 68.8 + - + +
75B CYS* 3.0 18.0 + - - +
76B THR* 3.2 15.2 + - + +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.2 12.6 - - + -
42B LEU* 4.1 14.4 - - + +
45B GLU* 3.7 22.3 + - - +
46B VAL* 3.6 46.7 - - + +
49B PHE* 4.6 14.2 - - - +
69B LEU* 3.0 26.9 - - - +
70B PHE* 3.5 10.5 - - + +
71B GLY 3.2 0.2 - - - -
72B ASP* 1.3 77.4 - - + +
74B LEU* 1.3 59.8 + - - +
76B THR* 2.5 34.7 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.6 10.2 - - + -
30B TYR* 6.1 4.3 - - + -
31B LEU* 3.8 23.7 - - + +
42B LEU* 4.2 12.0 - - - +
70B PHE 3.3 9.1 + - - +
71B GLY* 3.8 6.1 - - - +
73B LYS* 1.3 78.2 - - - +
75B CYS* 1.3 54.9 + - - +
76B THR 2.7 11.4 + - - -
77B VAL* 3.1 18.5 + - - +
78B ALA* 3.2 11.7 + - + +
102B PHE* 5.1 12.1 - - + -
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Residues in contact with CYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY 3.0 17.2 + - - +
72B ASP* 3.0 16.7 + - - +
74B LEU* 1.3 75.1 - - - +
76B THR* 1.3 55.2 + - - +
77B VAL 3.1 5.9 + - - -
78B ALA* 3.8 4.7 + - - +
79B THR* 4.0 14.0 + - - -
91B CYS* 2.0 57.8 - - + -
98B ARG* 6.4 0.9 - - - -
102B PHE* 4.1 12.3 - - - -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.3 12.1 - - - +
72B ASP* 3.2 12.6 - - + +
73B LYS* 2.5 27.1 + - - +
74B LEU 2.7 5.5 + - - -
75B CYS* 1.3 74.3 - - - +
77B VAL* 1.3 73.3 + - - +
79B THR* 5.2 1.1 - - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 5.1 2.2 - - + -
34B CYS* 4.7 17.9 - - - -
38B ASP* 5.1 12.3 - - + +
42B LEU* 4.3 19.3 - - + -
74B LEU* 3.2 13.0 - - - +
75B CYS 3.1 0.6 + - - -
76B THR* 1.3 90.6 - - - +
78B ALA* 1.3 68.2 + - - +
79B THR* 3.1 3.6 - - - +
80B LEU* 3.1 26.9 - - + +
84B TYR* 5.7 0.9 - - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.7 20.0 - - + -
74B LEU* 3.2 18.8 + - + +
75B CYS* 3.8 1.5 - - - +
77B VAL* 1.3 75.3 - - - +
79B THR* 1.3 53.0 + - - +
80B LEU 2.8 22.2 + - - +
84B TYR* 3.8 16.7 - - - +
87B MET* 4.9 8.3 - - + +
88B ALA* 3.7 13.6 + - - +
91B CYS* 3.6 23.3 - - - -
102B PHE* 5.4 3.6 - - + -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B CYS 4.0 13.2 + - - -
76B THR 5.8 0.7 - - - -
77B VAL* 3.1 2.4 - - - -
78B ALA* 1.3 77.7 - - - +
80B LEU* 1.3 56.6 + - - +
81B ARG* 2.9 17.0 + - - +
88B ALA* 3.8 15.3 - - - +
91B CYS* 4.5 6.8 - - - -
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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
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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