Contacts of the helix formed by residues 72 - 81 (chain B) in PDB entry 5E0T
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 LEU 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.7 19.3 - - + +
19B LEU* 4.2 17.0 - - + -
20B LYS* 4.4 9.8 - - - +
23B ILE* 3.2 51.4 - - + +
24B ASN 2.7 18.6 + - - +
25B GLU* 4.4 0.9 - - - +
26B ALA* 4.1 10.5 - - + +
28B TRP* 3.7 30.3 - - + +
37B LEU* 4.9 0.2 - - + -
70B VAL* 4.0 13.5 - - + +
71B ASN* 1.3 70.7 - - - +
73B THR* 1.3 61.3 + - - +
75B MET* 4.3 2.0 - - - +
76B SER* 2.8 31.7 + - - -
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Residues in contact with THR 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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20B LYS* 4.9 11.9 + - + +
24B ASN* 4.1 18.0 + - - +
71B ASN* 2.9 10.5 + - - -
72B LEU* 1.3 76.2 - - - +
74B SER* 1.3 65.0 + - - +
76B SER* 3.6 7.4 - - - -
77B LYS* 3.1 44.8 + - + +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 2.9 35.7 + - - +
73B THR* 1.3 76.8 - - - +
75B MET* 1.3 63.4 + - - +
77B LYS* 3.0 16.1 + - - +
78B ILE* 3.1 15.7 + - - +
116B MET* 4.3 14.4 - - - -
117B LYS 5.8 1.1 - - - -
175C LEU* 3.9 34.1 - - - +
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Residues in contact with MET 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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12B LEU* 5.0 6.7 - - + -
16B LEU* 3.5 30.3 - - + -
28B TRP* 3.8 36.3 - - + -
70B VAL* 3.9 16.2 - - + -
71B ASN 3.0 12.7 + - - +
74B SER* 1.3 73.7 - - - +
76B SER* 1.3 60.7 + - - +
78B ILE* 3.4 4.3 + - + +
79B LEU* 2.8 41.8 + - + +
90B LEU* 5.0 7.0 - - + -
99B LEU* 4.2 19.1 - - + -
101B LEU* 4.4 12.3 - - + -
116B MET* 3.5 26.9 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.6 17.3 - - - +
17B GLU* 3.2 23.4 + - - -
20B LYS* 3.3 28.7 + - - +
72B LEU 2.8 18.6 + - - -
73B THR* 3.6 6.5 - - - -
75B MET* 1.3 77.4 - - - +
77B LYS* 1.3 56.0 + - - +
79B LEU* 3.2 3.1 + - - +
80B LYS* 2.9 38.4 + - - +
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Residues in contact with LYS 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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73B THR* 3.1 31.7 + - + +
74B SER* 3.0 9.7 + - - +
76B SER* 1.3 74.2 - - - +
78B ILE* 1.3 66.9 + - - +
80B LYS* 3.3 24.4 + - - +
81B CYS* 3.5 15.0 + - - -
153C HIS* 4.1 31.4 + - + +
154C ILE* 5.3 1.1 - - + -
175C LEU* 3.6 29.2 - - + +
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Residues in contact with ILE 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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74B SER 3.1 8.6 + - - +
75B MET* 3.7 6.7 - - - +
77B LYS* 1.3 74.9 - - - +
79B LEU* 1.3 57.7 + - - +
81B CYS* 2.8 33.0 + - - +
101B LEU* 4.1 15.9 - - + -
103B PHE* 3.4 16.5 - - + -
114B TYR* 3.7 35.4 - - + -
115B GLU 4.8 1.1 - - - -
116B MET* 3.5 42.2 - - + +
154C ILE* 4.1 11.9 - - + -
175C LEU* 4.0 23.3 - - + -
177C ASN 5.7 0.9 - - - +
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Residues in contact with LEU 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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12B LEU* 4.2 20.4 - - + +
13B LYS* 3.1 38.5 + - + +
16B LEU* 3.4 37.0 - - + -
75B MET* 2.8 40.6 + - + +
76B SER* 3.2 6.5 + - - +
78B ILE* 1.3 73.8 - - - +
80B LYS* 1.3 59.7 + - - +
81B CYS 3.0 0.9 - - - -
82B ALA* 3.1 8.2 + - - +
88B ILE* 3.9 27.4 - - + -
101B LEU* 4.3 12.1 - - + -
103B PHE* 4.2 13.5 - - + -
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Residues in contact with LYS 80 (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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13B LYS* 3.9 9.3 + - - +
17B GLU* 3.9 24.0 - - - +
20B LYS* 4.8 11.9 - - - +
76B SER* 2.9 28.9 + - - +
77B LYS* 3.7 18.0 - - - +
78B ILE 3.1 0.8 + - - -
79B LEU* 1.3 77.4 - - - +
81B CYS* 1.3 57.9 + - - +
82B ALA 3.2 2.1 + - - +
146C ARG* 3.0 22.3 + - - -
149C ARG* 5.6 0.3 + - - -
150C ASP* 4.0 3.5 - - - +
153C HIS* 4.8 20.5 + - + +
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Residues in contact with CYS 81 (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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77B LYS 3.5 16.8 - - - -
78B ILE* 2.8 13.2 + - - +
80B LYS* 1.3 78.6 - - - +
82B ALA* 1.3 58.9 + - - +
83B GLY 4.0 1.0 + - - -
86B ASP* 4.8 0.7 - - - +
103B PHE* 3.6 8.5 - - - -
110B LYS* 5.5 4.0 + - - -
112B SER* 5.0 3.6 + - - -
114B TYR* 3.3 36.1 + - + +
146C ARG* 3.9 3.7 + - - -
150C ASP* 3.6 54.8 - - - +
153C HIS* 4.5 4.9 - - - -
154C ILE* 4.9 1.8 - - - -
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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