Contacts of the helix formed by residues 79 - 99 (chain E) in PDB entry 5OF4
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 ASN 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A VAL* 5.1 22.4 + - + +
71E MET 3.4 22.7 + - - +
72E GLU* 3.7 17.0 - - - +
73E ASP 4.8 3.6 - - - -
74E GLN* 5.4 0.5 + - - -
77E LYS 2.7 11.3 + - - +
78E PRO* 1.3 88.4 - - - +
80E ARG* 1.3 56.4 + - - +
81E LEU* 4.4 5.8 - - + +
82E THR* 2.7 36.5 + - - +
83E CYS 3.7 0.7 + - - -
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Residues in contact with ARG 80 (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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718B LYS* 4.5 13.9 - - - +
722B ARG* 4.7 0.6 - - - +
70E THR* 3.3 34.1 + - - +
71E MET* 3.7 22.0 + - + -
73E ASP* 3.1 29.7 + - - +
74E GLN 3.6 15.0 + - - -
75E ASP* 4.6 3.6 - - - +
76E LEU* 3.6 28.3 - - + +
77E LYS 3.8 1.1 + - - -
79E ASN* 1.3 69.5 - - - +
81E LEU* 1.3 60.6 + - - +
83E CYS* 3.4 3.2 + - - +
84E THR* 2.8 32.9 + - - -
201E LEU* 3.2 49.5 + - + +
202E SER* 3.1 25.5 + - - -
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 4.2 25.8 - - + -
66E ASP 4.7 4.9 - - - +
71E MET* 3.2 24.7 - - + +
79E ASN* 3.1 5.1 + - + -
80E ARG* 1.3 77.8 - - - +
82E THR* 1.3 57.7 + - - +
84E THR* 4.2 2.7 - - - -
85E LEU* 2.8 55.6 + - + +
134E ALA* 3.7 23.3 - - + +
135E VAL 4.4 7.2 - - - +
137E MET* 4.0 15.5 - - + +
139E CYS* 3.7 25.1 - - - -
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Residues in contact with THR 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A VAL* 4.4 20.3 + - + +
653A GLU* 4.1 19.7 - - + +
77E LYS* 4.5 9.4 - - + -
78E PRO* 4.6 7.4 - - + +
79E ASN* 2.7 34.1 + - - +
81E LEU* 1.3 71.5 - - - +
83E CYS* 1.3 57.0 + - - +
85E LEU* 3.7 12.4 - - + +
86E LYS* 2.9 41.1 + - + +
135E VAL* 5.5 2.0 + - + +
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Residues in contact with CYS 83 (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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76E LEU* 3.8 48.2 - - + -
77E LYS* 4.2 16.6 - - + +
79E ASN 3.7 2.2 + - - -
80E ARG 3.4 1.2 + - - -
82E THR* 1.3 74.9 - - - +
84E THR* 1.3 68.6 + - - +
86E LYS* 3.4 6.5 + - - +
87E LEU* 3.0 50.3 + - - +
225E GLU* 4.1 12.1 - - - -
228E TYR* 4.2 12.8 - - - -
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Residues in contact with THR 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 4.1 19.7 - - + -
71E MET* 5.2 3.4 - - - -
76E LEU* 4.5 3.1 - - - +
80E ARG 2.8 19.8 + - - -
81E LEU* 4.0 6.1 - - - -
83E CYS* 1.3 76.8 - - - +
85E LEU* 1.3 57.7 + - - +
87E LEU 3.7 0.9 - - - -
88E LEU* 2.9 38.6 + - + +
170E ILE* 3.6 20.0 - - + -
201E LEU* 4.1 17.5 - - - +
228E TYR* 3.3 32.8 + - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 2.8 36.3 + - + +
82E THR* 3.7 12.6 - - + +
84E THR* 1.3 70.3 - - - +
86E LYS* 1.3 61.9 + - + +
88E LEU* 3.2 9.7 + - - +
89E GLU* 2.9 30.0 + - - +
131E LEU* 3.3 46.7 - - + +
134E ALA* 4.3 15.5 - - + +
135E VAL* 3.6 40.4 - - + +
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Residues in contact with LYS 86 (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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653A GLU* 3.9 21.2 + - - -
77E LYS* 4.1 26.2 - - + +
82E THR* 2.9 23.3 + - + +
83E CYS* 3.8 7.4 - - - +
85E LEU* 1.3 77.1 - - + +
87E LEU* 1.3 73.7 + - + +
89E GLU* 3.2 15.2 + - - +
90E TYR* 3.1 21.8 + - - +
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Residues in contact with LEU 87 (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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83E CYS* 3.0 29.3 + - - +
84E THR 3.7 0.2 - - - -
86E LYS* 1.3 94.9 - - + +
88E LEU* 1.3 58.5 + - - +
90E TYR* 3.5 10.9 - - + +
91E PHE* 2.9 23.7 + - - +
225E GLU* 4.2 8.5 - - + +
228E TYR* 3.5 35.9 - - + -
229E LYS* 3.5 42.8 - - + +
232E LEU* 3.6 12.5 - - + +
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Residues in contact with LEU 88 (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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63E VAL* 3.7 21.8 - - + -
65E VAL* 3.6 31.9 - - + -
84E THR* 2.9 27.8 + - + +
85E LEU* 3.5 8.3 - - - +
87E LEU* 1.3 76.3 - - - +
89E GLU* 1.3 58.5 + - - +
91E PHE* 3.5 26.8 - - + +
92E VAL* 2.9 35.4 + - + +
106E ILE* 6.5 0.4 - - + -
131E LEU* 4.3 15.5 - - + -
168E LEU* 5.3 1.1 - - + -
170E ILE* 3.7 22.0 - - + -
228E TYR* 5.2 1.1 - - - +
232E LEU* 5.0 3.4 - - + -
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Residues in contact with GLU 89 (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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85E LEU* 2.9 16.1 + - - +
86E LYS* 3.3 16.4 - - - +
88E LEU* 1.3 74.1 - - - +
90E TYR* 1.3 62.5 + - - +
92E VAL* 3.5 3.0 + - - +
93E GLU* 3.1 26.9 + - - +
128E ILE* 3.6 36.0 - - + +
131E LEU* 3.6 21.9 - - + +
132E LYS* 5.2 8.6 + - - +
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Residues in contact with TYR 90 (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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86E LYS 3.1 12.2 + - - +
87E LEU* 3.5 16.2 - - + +
89E GLU* 1.3 76.8 - - - +
91E PHE* 1.3 59.1 + + + +
93E GLU* 3.3 8.9 + - + -
94E GLU* 2.5 66.4 + - + +
229E LYS* 3.6 36.3 - - + -
232E LEU* 5.4 5.6 - - + -
233E THR* 4.2 18.7 + - - +
236E VAL* 5.7 2.0 - - + -
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Residues in contact with PHE 91 (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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61E LEU* 4.1 26.0 - - + -
63E VAL* 4.3 15.3 - - + -
87E LEU 2.9 18.3 + - - +
88E LEU* 3.1 28.0 + - + +
90E TYR* 1.3 76.7 - + - +
92E VAL* 1.3 59.8 + - + +
94E GLU* 5.0 0.9 - - - -
95E TYR* 2.8 54.6 + + + +
104E ILE* 5.4 2.7 - - + -
168E LEU* 4.9 8.1 - - + -
232E LEU* 3.4 41.5 - - + -
235E HIS* 4.1 20.0 - - + -
236E VAL* 3.5 24.2 - - + -
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Residues in contact with VAL 92 (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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88E LEU* 2.9 22.2 + - + +
89E GLU 3.8 4.5 - - - +
91E PHE* 1.3 75.2 - - + +
93E GLU* 1.3 67.5 + - - +
95E TYR* 3.3 4.3 + - - +
96E PHE* 3.0 25.5 + - + +
104E ILE* 4.2 27.1 - - + +
106E ILE* 5.8 4.3 - - + -
124E PRO* 4.4 14.4 - - + +
127E HIS* 4.2 19.7 - - + -
128E ILE* 4.1 22.0 - - + -
131E LEU* 4.1 18.4 - - + -
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Residues in contact with GLU 93 (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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89E GLU* 3.1 17.2 + - - +
90E TYR* 3.8 9.7 - - + +
91E PHE 3.3 0.2 - - - -
92E VAL* 1.3 84.1 - - - +
94E GLU* 1.3 56.2 + - - +
96E PHE* 3.8 4.0 - - - +
97E ASP* 2.9 28.1 + - + +
124E PRO* 6.5 0.4 - - - -
128E ILE* 5.0 12.8 - - + +
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Residues in contact with GLU 94 (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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90E TYR* 2.5 60.4 + - + +
91E PHE 4.3 1.6 - - - +
93E GLU* 1.3 77.2 - - - +
95E TYR* 1.3 57.8 + - - +
97E ASP* 3.7 12.9 - - + +
98E GLN* 2.9 41.7 + - + +
233E THR* 4.3 10.5 + - - +
236E VAL* 4.0 26.9 - - + +
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Residues in contact with TYR 95 (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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59E ARG* 3.4 20.3 + - - +
61E LEU* 3.2 40.8 - - + +
91E PHE* 2.8 38.3 + + + +
92E VAL* 3.3 4.0 + - - +
94E GLU* 1.3 78.1 - - - +
96E PHE* 1.3 59.1 + + - +
98E GLN* 4.5 0.9 - - - +
99E ASN* 2.8 59.6 + - + +
102E SER* 3.3 29.5 - - - -
103E GLN 4.2 2.5 + - - -
104E ILE* 3.4 45.5 - - + -
236E VAL* 4.5 8.0 - - - +
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Residues in contact with PHE 96 (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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92E VAL* 3.0 17.4 + - + +
93E GLU* 4.2 3.6 - - - +
95E TYR* 1.3 77.9 - + - +
97E ASP* 1.3 64.0 + - - +
98E GLN 3.1 1.7 + - - -
99E ASN 3.4 19.5 - - - -
100E PRO* 3.9 22.5 - - + +
102E SER 4.0 15.9 - - - -
104E ILE* 3.6 31.6 - - + -
121E SER 4.1 1.3 - - - -
122E GLY* 3.6 25.8 - - - -
123E ASN 4.1 0.9 - - - -
124E PRO* 3.5 52.9 - - + -
127E HIS* 4.6 1.1 - + - -
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Residues in contact with ASP 97 (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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93E GLU* 2.9 22.8 + - - +
94E GLU* 3.1 20.7 + - + +
96E PHE* 1.3 77.5 - - - +
98E GLN* 1.3 62.9 + - + +
100E PRO* 5.2 2.0 - - - +
186F LYS* 3.3 48.0 + - - +
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Residues in contact with GLN 98 (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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94E GLU* 2.9 25.9 + - + +
97E ASP* 1.3 89.8 - - + +
99E ASN* 1.3 72.0 + - - +
100E PRO* 3.4 11.2 - - - +
101E ILE* 5.9 0.2 - - - +
236E VAL* 3.7 26.9 - - + +
237E SER* 5.9 3.2 - - - +
186F LYS* 4.7 6.1 + - - +
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Residues in contact with ASN 99 (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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57E MET 5.2 1.7 - - - +
59E ARG* 4.0 5.9 - - - +
95E TYR* 2.8 48.7 + - + +
96E PHE* 3.4 15.0 - - - -
98E GLN* 1.3 88.6 - - - +
100E PRO* 1.3 64.1 - - - +
101E ILE* 3.6 9.8 + - + +
102E SER* 3.6 28.3 + - - +
236E VAL 3.2 22.0 + - - -
238E PRO* 3.6 20.4 - - - +
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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
------------------------------------------------------------
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