Contacts of the helix formed by residues 92 - 113 (chain N) in PDB entry 2FBW
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 92 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90N LEU 4.2 6.5 - - - +
91N GLY* 1.3 72.0 - - - +
93N GLN* 1.3 60.6 + - - +
94N ASP* 3.3 16.2 - - - +
95N ALA* 3.2 11.4 + - + +
96N ILE* 3.1 27.9 + - - +
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Residues in contact with GLN 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N PHE* 3.6 25.0 - - + -
84N VAL* 3.7 32.2 - - + +
89N TRP* 4.0 15.6 - - - +
91N GLY 3.4 12.2 + - - +
92N ASP* 1.3 70.2 - - - +
94N ASP* 1.3 59.8 + - - +
96N ILE* 3.9 7.0 - - - -
97N HIS* 2.9 29.5 + - - +
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Residues in contact with ASP 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N ASP* 3.4 20.3 - - - +
93N GLN* 1.3 73.3 - - - +
95N ALA* 1.3 73.6 + - - +
97N HIS* 3.4 7.1 - - - +
98N TYR* 3.0 27.0 + - - +
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N ASP* 3.2 13.4 + - + +
94N ASP* 1.3 86.8 + - - +
96N ILE* 1.3 61.2 + - + +
98N TYR* 3.2 8.2 + - - +
99N MET* 2.8 29.7 + - - +
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Residues in contact with ILE 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N PHE* 3.5 24.7 - - + +
83N THR* 3.7 37.0 - - + -
84N VAL* 4.0 26.2 - - + +
87N SER* 4.5 2.2 - - - +
91N GLY* 4.0 25.6 - - - +
92N ASP 3.1 18.8 + - - +
93N GLN* 4.1 3.6 - - - +
94N ASP 3.4 0.2 - - - -
95N ALA* 1.3 73.8 - - + +
97N HIS* 1.3 66.2 + - - +
99N MET* 4.4 7.4 - - + +
100N THR* 3.0 33.2 + - + -
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Residues in contact with HIS 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N TRP* 3.5 23.8 - + - -
80N PHE* 3.6 17.6 - + + -
93N GLN 2.9 19.5 + - - +
94N ASP* 3.4 8.4 - - - +
96N ILE* 1.3 76.9 - - - +
98N TYR* 1.3 65.9 + - - +
100N THR* 3.6 1.0 + - - -
101N GLU* 3.0 45.9 + - - +
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Residues in contact with TYR 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N ASP 3.0 14.3 + - - +
95N ALA* 3.6 10.3 - - - +
97N HIS* 1.3 77.7 - - - +
99N MET* 1.3 66.2 + - - +
101N GLU* 4.1 2.6 - - - +
102N GLN* 2.9 65.0 + - + +
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Residues in contact with MET 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N HIS* 5.2 7.4 - - + +
83N THR* 4.4 19.1 - - + +
95N ALA 2.8 19.8 + - - +
96N ILE* 4.0 7.0 - - + +
97N HIS 3.2 0.2 - - - -
98N TYR* 1.3 79.7 - - + +
100N THR* 1.3 80.5 + - + +
102N GLN* 3.4 4.5 + - - +
103N ALA* 3.2 21.9 + - + +
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Residues in contact with THR 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67N ALA 5.7 0.2 + - - -
76N TRP* 3.5 23.1 - - - +
79N HIS* 3.7 35.0 + - + +
80N PHE* 3.4 40.3 - - - +
83N THR* 3.9 9.4 - - - +
96N ILE* 3.0 21.7 + - + +
97N HIS 3.6 0.9 + - - -
99N MET* 1.3 81.2 - - + +
101N GLU* 1.3 67.3 + - - +
103N ALA* 3.3 16.8 + - - +
104N PRO* 3.7 1.4 - - - +
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Residues in contact with GLU 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N TRP* 3.3 51.2 + - + +
77N ARG* 5.6 0.3 + - - -
97N HIS* 3.0 36.0 + - - +
98N TYR* 4.1 3.1 - - - +
100N THR* 1.3 81.5 + - - +
102N GLN* 1.3 74.4 + - - +
103N ALA 3.4 0.5 + - - -
104N PRO* 3.6 9.5 - - - +
105N ALA* 5.3 1.2 + - - +
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Residues in contact with GLN 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N TYR* 2.9 63.8 + - + +
99N MET* 3.8 4.9 - - - +
100N THR 3.3 0.2 - - - -
101N GLU* 1.3 94.9 + - - +
103N ALA* 1.3 63.7 + - - +
104N PRO* 3.5 0.9 - - - -
105N ALA* 3.3 16.6 + - - +
106N ALA* 3.0 23.6 + - + +
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Residues in contact with ALA 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N ASN 3.6 22.0 - - - +
66N ALA* 3.7 9.2 - - - -
67N ALA 4.8 0.4 - - - +
79N HIS* 4.5 7.0 - - + +
99N MET* 3.2 12.9 + - + +
100N THR* 3.4 13.7 - - - +
101N GLU 3.2 0.4 - - - -
102N GLN* 1.3 77.2 - - - +
104N PRO* 1.3 71.2 - - + +
106N ALA* 3.1 6.7 + - - +
107N VAL* 3.1 28.1 + - - +
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Residues in contact with PRO 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N ALA* 3.8 2.7 - - + -
67N ALA* 4.0 29.4 - - + +
68N LEU* 3.8 24.2 - - + +
76N TRP* 5.0 7.9 - - + -
100N THR 3.7 5.2 - - - +
101N GLU 3.6 13.9 - - - +
102N GLN 3.6 0.4 - - - -
103N ALA* 1.3 95.1 - - + +
105N ALA* 1.3 62.0 + - - +
106N ALA 3.3 0.2 + - - -
107N VAL 3.3 0.2 + - - -
108N ILE* 3.0 33.8 + - + +
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Residues in contact with ALA 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N GLU 5.3 0.8 + - - +
102N GLN* 3.3 18.8 + - - +
104N PRO* 1.3 78.5 - - - +
106N ALA* 1.3 62.2 + - - +
108N ILE* 3.9 9.5 - - - +
109N GLU* 3.0 23.4 + - - +
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Residues in contact with ALA 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N ILE* 5.9 4.3 - - + -
102N GLN* 3.0 18.8 + - + +
103N ALA* 3.1 8.7 + - - +
105N ALA* 1.3 77.9 - - - +
107N VAL* 1.3 63.0 + - + +
109N GLU* 3.4 13.9 + - - +
110N LEU* 3.2 26.4 + - + +
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Residues in contact with VAL 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N ILE* 4.1 31.0 - - + -
65N ASN 4.3 0.9 - - - +
66N ALA* 3.5 29.2 - - + -
68N LEU* 4.3 3.8 - - + -
103N ALA* 3.1 8.0 + - - +
104N PRO 4.1 2.5 - - - +
106N ALA* 1.3 74.6 - - + +
108N ILE* 1.3 66.5 + - - +
110N LEU* 3.0 7.9 + - - +
111N GLU* 2.9 21.8 + - - +
117N PHE* 3.7 27.1 - - + -
125N ILE* 4.2 11.0 - - + -
147N CYS* 4.0 19.1 - - + -
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Residues in contact with ILE 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N LEU* 4.1 21.3 - - + -
104N PRO* 3.0 22.8 + - + +
105N ALA* 3.9 8.1 - - - +
107N VAL* 1.3 76.3 - - - +
109N GLU* 1.3 51.8 + - - +
111N GLU* 3.2 5.9 + - - +
112N ASN* 2.7 54.2 + - - +
125N ILE* 5.3 4.9 - - + -
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Residues in contact with GLU 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ARG* 2.9 39.1 + - - -
105N ALA 3.0 14.7 + - - +
106N ALA* 3.4 14.7 - - - +
108N ILE* 1.3 76.2 - - - +
110N LEU* 1.3 64.4 + - - +
112N ASN* 3.1 8.8 + - - +
113N TYR* 2.9 58.5 + - + +
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Residues in contact with LEU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N ILE* 4.1 17.7 - - + -
106N ALA* 3.2 13.4 + - + +
107N VAL* 3.0 11.1 + - - +
109N GLU* 1.3 80.8 - - + +
111N GLU* 1.3 62.6 + - - +
113N TYR* 3.0 26.7 + - + +
115N MET* 3.2 33.6 + - - +
117N PHE* 4.4 5.2 - - + -
157N LEU* 3.6 35.4 - - + +
160N THR* 4.1 3.3 - - + +
161N LEU* 3.9 34.3 - - + -
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Residues in contact with GLU 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N VAL 2.9 14.5 + - - +
108N ILE* 3.7 3.8 - - - +
110N LEU* 1.3 77.1 - - - +
112N ASN* 1.3 84.5 + - - +
114N GLY* 2.8 21.0 + - - -
115N MET 3.9 5.9 + - - +
117N PHE* 3.8 26.4 - - + -
119N ARG* 2.8 37.2 + - - +
125N ILE* 4.0 17.5 - - + -
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Residues in contact with ASN 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108N ILE* 2.7 40.1 + - - +
109N GLU* 3.7 6.5 - - - +
111N GLU* 1.3 100.7 + - - +
113N TYR* 1.3 63.4 + - + +
114N GLY 3.2 0.6 + - - -
164N ARG* 5.1 2.9 + - - -
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Residues in contact with TYR 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ARG* 3.8 3.9 + - - -
35N PHE* 3.4 38.0 - + - -
39N GLU* 4.9 2.1 + - - -
109N GLU* 2.9 55.8 + - + -
110N LEU* 3.2 20.4 - - + +
111N GLU 3.0 0.6 - - - -
112N ASN* 1.3 80.8 - - + +
114N GLY* 1.3 55.7 + - - +
115N MET 3.6 0.4 - - - -
160N THR* 3.5 18.6 - - + +
161N LEU* 4.0 19.3 - - + -
164N ARG* 3.3 54.1 + - + +
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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
------------------------------------------------------------
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