Contacts of the helix formed by residues 75 - 86 (chain A) in PDB entry 1OTE
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 PHE 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 4.0 17.0 - + - -
63A PHE* 3.8 22.2 - + - -
70A THR* 3.3 31.4 - - + +
72A SER* 3.2 7.7 + - - +
73A PRO 3.2 0.2 - - - -
74A GLU* 1.3 79.3 - - - +
76A TYR* 1.3 70.4 + - - +
77A GLY 3.1 0.4 - - - -
78A LYS* 2.9 5.8 + - - +
79A PHE* 2.9 19.6 + - - +
92A PHE* 3.6 18.2 - + - -
94A TYR* 3.8 16.8 - + + -
96A PHE* 3.7 16.6 - + - -
107A VAL* 3.9 17.9 - - + -
109A MET* 3.7 24.7 - - - +
120A VAL* 3.9 23.6 - - + -
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP 5.1 8.3 + - - -
63A PHE* 3.3 53.2 - + + -
70A THR 3.0 16.5 + - - +
71A ASP* 3.2 30.5 - - - -
72A SER 3.1 6.6 + - - +
75A PHE* 1.3 79.6 - - - +
77A GLY* 1.3 64.1 + - - +
79A PHE* 3.1 10.1 + + - -
80A LYS* 3.0 30.5 + - + +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER 2.9 13.8 + - - -
73A PRO* 3.4 16.1 + - - -
76A TYR* 1.3 76.9 - - - +
78A LYS* 1.3 57.0 + - - +
80A LYS* 3.0 35.7 - - - +
81A GLU* 3.0 20.5 + - - +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO 3.3 8.7 + - - +
74A GLU* 3.4 23.8 + - - +
75A PHE 2.9 7.9 + - - +
77A GLY* 1.3 75.9 - - - +
79A PHE* 1.4 64.6 + - - +
81A GLU* 3.4 18.8 + - - +
82A GLY 3.0 17.8 + - - -
88A LEU* 3.6 7.3 - - - +
90A THR* 3.9 26.7 + - + +
91A MET 5.0 1.0 + - - -
92A PHE* 4.0 28.8 - - + +
109A MET* 3.9 10.1 - - + -
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 20.6 - - + -
34A ASP 3.4 22.2 - - - -
35A GLY 3.6 20.0 - - - -
36A ASP 4.7 1.1 - - - -
37A GLY 4.1 4.0 - - - -
63A PHE* 3.6 32.3 - + + -
75A PHE 2.9 11.9 + - - +
76A TYR* 3.4 13.5 - + - +
78A LYS* 1.4 77.2 - - - +
80A LYS* 1.3 62.1 + - + +
82A GLY* 3.1 3.1 + - - -
83A VAL* 2.8 44.3 + - + +
88A LEU* 4.1 10.5 - - + +
109A MET* 3.7 27.5 - - - +
118A TYR* 3.5 26.9 - + + -
120A VAL* 4.8 2.2 - - + -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY 5.9 0.7 - - - -
76A TYR* 3.0 20.1 + - + +
77A GLY* 3.0 33.6 - - - +
79A PHE* 1.3 83.8 - - + +
81A GLU* 1.4 74.8 + - + +
83A VAL* 3.2 7.1 + - - +
84A ALA* 2.9 25.1 + - + +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO 5.4 1.2 - - - +
77A GLY* 3.0 25.5 + - - +
78A LYS* 3.6 22.3 - - - +
80A LYS* 1.4 88.4 + - + +
82A GLY* 1.4 58.7 + - - +
84A ALA* 3.3 5.0 + - - +
85A SER* 2.9 31.1 + - - -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS 3.0 10.9 + - - -
79A PHE 3.1 3.1 + - - -
81A GLU* 1.4 76.8 - - - +
83A VAL* 1.4 65.2 + - - +
85A SER* 3.4 8.5 + - - -
86A GLY* 3.0 21.0 + - - -
87A ASN 3.5 5.8 + - - -
88A LEU* 3.8 32.3 + - - +
118A TYR* 4.9 1.0 - - - -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY* 4.1 17.0 - - - +
79A PHE* 2.8 56.5 + - + +
80A LYS* 3.2 6.2 + - - +
82A GLY* 1.4 74.3 - - - +
84A ALA* 1.3 66.2 + - - +
86A GLY* 3.6 6.8 + - - -
88A LEU* 5.3 0.2 - - + -
118A TYR* 3.4 45.2 + - + +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 2.9 18.2 + - + +
81A GLU* 3.8 5.4 - - - +
83A VAL* 1.3 83.1 - - + +
85A SER* 1.3 62.0 + - - +
86A GLY* 3.3 0.7 + - - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU 2.9 22.0 + - - -
82A GLY* 3.4 6.9 + - - -
84A ALA* 1.3 72.6 - - - +
86A GLY* 1.3 60.0 + - - +
87A ASN* 3.0 25.5 + - - +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLY 3.0 9.8 + - - -
83A VAL 3.6 5.8 + - - -
84A ALA 3.2 3.6 - - - -
85A SER* 1.3 80.5 - - - +
87A ASN* 1.3 60.5 + - - +
88A LEU 3.8 2.7 - - - -
111A LYS* 2.9 38.9 + - - +
118A TYR* 6.1 0.4 - - - -
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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