Contacts of the helix formed by residues 87 - 105 (chain E) in PDB entry 1RFU
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 ASP 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E VAL* 4.9 4.7 - - + -
57E LEU 3.5 10.3 - - - +
58E ASN* 3.2 30.3 - - - +
59E SER 4.0 0.7 + - - -
85E THR* 3.1 5.4 - - + +
86E ARG* 1.3 78.7 - - - +
88E LYS* 1.3 59.0 + - - +
89E SER* 2.6 41.1 + - - -
90E PHE* 3.0 23.5 + - + +
91E LEU* 2.8 26.5 + - - +
132E LEU* 3.7 2.5 - - - -
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Residues in contact with LYS 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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86E ARG 3.9 2.8 + - - -
87E ASP* 1.3 73.0 + - - +
89E SER* 1.3 72.5 + - - +
91E LEU* 3.2 2.0 + - - +
92E ALA* 2.8 27.8 + - + +
131E ASP* 3.4 44.1 + - + +
132E LEU* 3.2 19.0 - - + +
135E VAL* 3.7 19.6 - - + +
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Residues in contact with SER 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E SER* 2.9 28.6 + - - -
87E ASP* 2.6 21.2 + - - -
88E LYS* 1.3 83.9 + - - +
90E PHE* 1.3 59.7 + - - -
92E ALA* 3.3 5.7 + - - +
93E MET* 3.0 25.5 + - - +
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Residues in contact with PHE 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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10E ILE* 3.5 32.3 - - + -
38E VAL* 4.4 3.6 - - + -
40E SER* 3.6 24.9 - - - -
57E LEU* 3.9 34.8 - - + -
58E ASN 4.2 2.7 - - - -
59E SER* 4.4 7.0 - - - +
62E LEU* 3.4 40.0 - - + +
85E THR* 3.3 29.8 - - + -
87E ASP* 3.0 25.3 + - + +
89E SER* 1.3 78.4 - - - +
91E LEU* 1.3 63.8 + - - +
93E MET* 3.2 3.5 + - - +
94E VAL* 2.9 32.5 + - + +
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Residues in contact with LEU 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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82E THR* 5.8 4.0 - - - +
83E GLY 5.5 0.4 - - - +
85E THR* 4.8 9.4 - - - +
87E ASP 2.8 15.2 + - - +
88E LYS 3.2 7.4 + - - +
90E PHE* 1.3 75.0 - - - +
92E ALA* 1.3 65.5 + - - +
94E VAL* 2.9 33.1 + - + +
95E VAL* 3.2 6.4 + - - +
110E TYR* 5.6 1.8 - - - +
132E LEU* 3.7 13.7 - - + -
135E VAL* 3.5 24.0 - - + -
136E TYR* 3.3 60.3 - - + +
140E VAL* 3.8 13.0 - - + -
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Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LYS* 2.8 23.8 + - + +
89E SER* 3.6 6.7 - - - +
91E LEU* 1.3 72.2 - - - +
93E MET* 1.3 59.2 + - - +
95E VAL* 2.8 30.5 + - - +
96E ASP* 3.2 9.2 + - - +
135E VAL* 4.0 15.2 - - + +
139E LYS* 4.2 20.5 + - - +
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Residues in contact with MET 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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59E SER* 3.2 35.7 - - - +
62E LEU* 3.9 14.8 - - + -
63E GLN* 2.7 42.6 - - + +
89E SER 3.0 14.6 + - - +
90E PHE* 3.5 5.2 - - - +
92E ALA* 1.3 78.4 - - - +
94E VAL* 1.3 64.9 + - - +
96E ASP* 3.0 18.8 + - + +
97E ILE* 2.8 31.1 + - + +
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Residues in contact with VAL 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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10E ILE* 4.3 15.9 - - + -
62E LEU* 4.0 16.2 - - + -
80E VAL* 5.6 0.2 - - + -
82E THR* 3.8 29.4 - - + -
85E THR* 5.6 0.4 - - - +
90E PHE* 2.9 37.6 + - + +
91E LEU* 2.9 21.4 + - + +
93E MET* 1.3 76.3 - - - +
95E VAL* 1.3 52.7 + - + +
97E ILE* 3.1 11.3 + - - +
98E VAL* 2.7 46.3 + - + +
110E TYR* 4.7 4.5 - - - +
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Residues in contact with VAL 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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91E LEU* 3.7 9.0 - - + +
92E ALA* 2.8 14.6 + - - +
94E VAL* 1.3 75.5 - - + +
96E ASP* 1.3 72.2 + - - +
98E VAL* 2.7 22.3 + - + +
99E GLN* 2.8 29.7 + - - +
110E TYR* 5.9 0.7 - - + +
139E LYS* 3.7 37.5 - - + +
140E VAL* 3.8 29.4 - - + -
143E VAL* 4.3 12.3 - - + -
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Residues in contact with ASP 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 ALA 3.2 6.6 + - - +
93E MET* 3.0 19.8 + - + +
95E VAL* 1.3 75.4 - - - +
97E ILE* 1.3 64.7 + - + +
99E GLN* 3.1 13.7 + - - +
100E GLU* 2.9 23.3 + - - +
139E LYS* 3.2 26.6 + - - -
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Residues in contact with ILE 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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8E LEU* 4.7 9.2 - - + -
10E ILE* 5.3 6.1 - - + -
62E LEU* 3.9 30.7 - - + -
66E TYR* 3.6 57.7 - - + -
93E MET* 2.8 26.2 + - + +
94E VAL* 3.1 9.4 - - - +
96E ASP* 1.3 76.7 - - + +
98E VAL* 1.3 64.3 + - + +
100E GLU* 3.2 9.1 + - - +
101E LEU* 3.1 33.1 + - + +
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Residues in contact with VAL 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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80E VAL* 4.5 14.1 - - + -
94E VAL* 2.7 43.8 + - + +
95E VAL* 2.7 16.5 + - - +
97E ILE* 1.3 72.1 - - + +
99E GLN* 1.3 57.4 + - - +
101E LEU* 3.1 12.0 + - - +
102E LYS* 2.9 32.4 + - + +
108E LEU* 5.1 3.7 - - + +
110E TYR* 3.5 45.8 - - + -
143E VAL* 4.2 15.9 - - + -
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Residues in contact with GLN 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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95E VAL* 2.8 30.2 + - + +
96E ASP* 3.5 13.7 - - - +
98E VAL* 1.3 73.5 - - - +
100E GLU* 1.3 67.4 + - - +
102E LYS* 2.9 17.4 + - + +
103E GLN* 3.0 29.0 + - - +
139E LYS* 5.8 0.3 + - - -
143E VAL* 4.1 24.0 - - + +
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Residues in contact with GLU 100 (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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66E TYR* 3.3 33.0 + - - +
70E LYS* 4.0 12.7 + - - +
75E ASN* 3.9 5.4 + - - -
96E ASP 2.9 12.6 + - - +
97E ILE* 3.2 9.9 + - - +
99E GLN* 1.3 76.8 - - - +
101E LEU* 1.3 60.0 + - - +
103E GLN* 3.5 9.4 - - - +
104E GLN* 3.0 42.8 + - + +
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Residues in contact with LEU 101 (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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8E LEU* 4.2 5.4 - - + -
66E TYR* 3.4 22.0 - - + +
75E ASN 3.4 23.8 - - - +
76E GLN* 4.9 0.2 - - - -
77E TYR* 3.9 30.5 - - + +
80E VAL* 4.1 21.3 - - + -
97E ILE* 3.1 31.3 + - + +
98E VAL* 3.4 6.7 - - - +
99E GLN 3.0 0.8 - - - -
100E GLU* 1.3 74.2 - - - +
102E LYS* 1.3 53.3 + - - +
103E GLN 3.1 2.0 - - - -
104E GLN* 3.1 11.9 + - - +
105E ASN* 2.7 38.0 + - - +
108E LEU* 3.8 13.7 - - + -
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Residues in contact with LYS 102 (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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98E VAL* 2.9 17.5 + - + +
99E GLN* 2.9 10.3 + - + +
101E LEU* 1.3 76.7 - - - +
103E GLN* 1.3 65.6 + - - +
105E ASN 3.0 26.2 - - - +
106E PRO* 3.1 14.3 + - + +
108E LEU* 3.1 40.9 + - + +
110E TYR* 4.5 4.0 - - - -
143E VAL* 3.6 35.7 - - + -
145E ASP* 2.5 38.4 + - - -
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Residues in contact with GLN 103 (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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99E GLN* 3.0 23.3 + - - +
100E GLU* 3.5 13.2 - - - +
102E LYS* 1.3 86.1 + - - +
104E GLN* 1.3 67.5 + - + +
105E ASN 3.3 0.3 + - - -
106E PRO* 3.9 10.2 - - - +
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Residues in contact with GLN 104 (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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70E LYS* 3.8 8.0 + - - +
75E ASN* 3.2 42.3 + - - +
76E GLN* 4.5 11.5 - - - +
100E GLU* 3.0 33.3 - - + +
101E LEU* 3.1 11.6 + - - +
103E GLN* 1.3 78.7 - - + +
105E ASN* 1.3 60.3 + - + +
106E PRO* 3.5 5.7 - - - +
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Residues in contact with ASN 105 (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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77E TYR 3.2 25.1 - - - +
78E ASP* 4.2 9.5 - - - +
101E LEU 2.7 14.2 + - - +
102E LYS* 3.0 13.2 - - - +
104E GLN* 1.3 75.5 - - + +
106E PRO* 1.3 66.1 - - - +
107E ARG* 2.6 43.8 - - - +
108E LEU* 3.1 29.0 + - + +
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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