Contacts of the helix formed by residues 92 - 113 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY* 1.3 69.7 - - - -
93A GLN* 1.3 60.0 + - - +
94A ASP* 3.3 15.7 - - - +
95A ALA* 3.1 5.0 + - + +
96A ILE* 3.1 26.4 + - - +
245A GLN* 4.7 0.2 + - - -
372A THR 5.0 0.5 - - - +
401A ALA 3.4 7.1 - - - +
402A SER* 2.8 37.3 + - - +
582A HIS* 2.9 29.8 + - - -
599A ARG* 4.3 10.3 + - - -
600A PRO 4.8 0.2 - - - +
601A VAL* 3.7 1.4 - - - +
602A ILE* 3.2 36.2 + - + +
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.6 17.2 - - + -
84A VAL* 3.7 25.9 - - + +
89A TRP* 4.0 7.9 - - - +
91A GLY 3.8 10.4 + - - +
92A ASP* 1.3 69.4 - - - +
94A ASP* 1.3 58.8 + - - +
96A ILE* 3.9 7.4 - - + -
97A HIS* 3.0 28.6 + - - +
602A ILE 2.8 14.8 + - - +
603A ASP* 3.5 31.8 + - - +
604A ARG 3.5 5.4 - - - +
605A THR* 4.0 3.1 - - + -
613A SER* 3.4 12.1 + - - -
614A VAL* 3.0 45.2 + - - +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 3.4 20.4 - - - +
93A GLN* 1.3 73.1 - - - +
95A ALA* 1.3 65.6 + - - +
97A HIS* 3.4 3.6 + - - +
98A TYR* 3.0 22.5 + - - +
373A ASN* 6.0 0.2 - - - +
374A TYR* 3.7 24.7 + - + +
401A ALA 5.3 0.3 - - - +
602A ILE* 3.7 27.4 - - + +
604A ARG* 3.1 20.9 + - + +
605A THR* 4.1 9.0 - - - +
606A LEU* 3.5 30.7 - - + +
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Residues in contact with ALA 95 (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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92A ASP* 3.1 7.5 + - + +
94A ASP* 1.3 83.3 + - - +
96A ILE* 1.3 59.2 + - - +
98A TYR* 3.2 5.0 + - - +
99A MET* 2.9 30.0 + - - +
374A TYR* 3.7 21.8 - - + -
401A ALA* 4.0 26.9 - - + +
402A SER 4.6 0.9 - - - +
403A VAL* 3.7 17.2 - - + +
420A PHE* 3.8 4.5 - - + -
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Residues in contact with ILE 96 (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 PHE* 3.6 24.9 - - + +
83A THR* 3.7 26.2 - - + +
84A VAL* 4.0 25.6 - - + +
87A SER* 4.5 0.2 - - - +
91A GLY* 4.0 22.0 - - - +
92A ASP 3.1 18.3 + - - +
93A GLN* 4.1 4.5 - - + +
95A ALA* 1.3 72.8 - - - +
97A HIS* 1.3 66.6 + - - +
99A MET* 4.4 2.2 - - + +
100A THR* 2.9 33.4 + - + +
403A VAL* 3.5 36.8 - - + +
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TRP* 3.5 19.4 - + - -
80A PHE* 3.6 16.3 - - + -
93A GLN 3.0 20.2 + - - +
94A ASP 3.5 5.8 - - - +
96A ILE* 1.3 75.6 - - - +
98A TYR* 1.3 64.1 + - - +
100A THR* 3.6 1.3 + - - -
101A GLU* 3.0 45.9 + - - +
605A THR* 3.4 7.7 - - - -
606A LEU* 3.0 31.7 + - + +
607A ASN* 3.5 28.0 - - + -
610A ASP* 4.7 3.4 + - - -
611A CYS* 3.8 18.5 - - + +
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Residues in contact with TYR 98 (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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94A ASP 3.0 13.8 + - - +
95A ALA* 3.2 9.6 + - - +
97A HIS* 1.3 77.3 - - - +
99A MET* 1.3 60.9 + - - +
101A GLU* 4.1 2.4 - - - -
102A GLN* 2.9 59.9 + - + +
374A TYR* 4.5 18.4 - + + -
419A VAL* 3.5 29.7 + - + -
420A PHE* 4.1 12.8 - + + -
422A ARG* 4.6 4.5 + - - +
423A ALA* 4.0 22.8 - - + +
426A LEU* 4.1 21.1 - - - +
606A LEU* 3.8 19.5 - - + +
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Residues in contact with MET 99 (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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83A THR* 4.4 6.1 - - + -
95A ALA 2.9 17.2 + - - +
96A ILE* 3.2 3.1 + - - +
98A TYR* 1.3 77.3 - - - +
100A THR* 1.3 76.3 + - + +
102A GLN* 3.4 2.8 + - - +
103A ALA* 3.2 21.7 + - - +
403A VAL* 4.0 26.5 - - + -
404A HIS* 4.9 0.2 - - + -
412A ASN* 3.9 33.2 - - + +
415A LEU* 3.8 20.3 - - + +
416A ASP* 3.8 31.9 - - - -
419A VAL* 4.1 17.3 - - + +
420A PHE* 3.9 15.0 - - + -
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Residues in contact with THR 100 (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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67A ALA 5.7 0.2 + - - -
76A TRP* 3.6 22.2 - - - +
79A HIS* 3.6 38.0 + - + +
80A PHE* 3.4 40.0 - - - +
83A THR* 3.8 9.0 - - - +
96A ILE* 2.9 24.1 + - + +
97A HIS 3.6 1.0 + - - -
99A MET* 1.3 84.1 - - + +
101A GLU* 1.3 65.8 + - - +
103A ALA* 3.3 15.8 + - - +
104A PRO* 3.7 1.4 - - - +
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Residues in contact with GLU 101 (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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76A TRP* 3.3 50.4 + - + +
77A ARG* 5.5 0.2 + - - -
97A HIS* 3.0 36.9 + - - +
98A TYR* 4.1 2.7 - - - +
100A THR* 1.3 80.5 + - - +
102A GLN* 1.3 74.5 + - - +
103A ALA 3.5 0.5 + - - -
104A PRO* 3.6 9.5 - - - +
105A ALA* 5.3 0.7 + - - +
606A LEU* 5.5 1.9 - - - +
610A ASP* 3.7 8.5 - - - +
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Residues in contact with GLN 102 (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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98A TYR* 2.9 61.3 + - + +
99A MET 4.1 3.1 - - - +
101A GLU* 1.3 93.5 + - - +
103A ALA* 1.3 64.2 + - - +
104A PRO* 3.5 1.1 - - - -
105A ALA* 3.3 15.9 + - - +
106A ALA* 3.0 21.4 + - + +
419A VAL* 4.3 15.0 - - + -
422A ARG* 4.8 10.2 + - - -
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Residues in contact with ALA 103 (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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65A ASN 3.6 22.2 - - - +
66A ALA* 3.7 8.5 - - - -
67A ALA 4.8 0.2 - - - +
79A HIS* 4.5 2.7 - - - +
99A MET 3.2 7.8 + - - +
100A THR* 3.3 11.4 + - - +
102A GLN* 1.3 77.6 - - - +
104A PRO* 1.3 72.2 - - + +
106A ALA* 3.1 2.3 + - - +
107A VAL* 3.1 27.0 + - - +
415A LEU* 3.6 25.8 - - + -
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Residues in contact with PRO 104 (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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66A ALA* 3.8 2.9 - - + -
67A ALA* 4.1 28.5 - - + +
68A LEU* 3.8 23.2 - - + +
76A TRP* 5.0 7.9 - - + -
100A THR 3.7 5.8 - - - +
101A GLU 3.6 13.7 - - - +
102A GLN 3.6 0.4 - - - -
103A ALA* 1.3 95.6 - - + +
105A ALA* 1.3 63.2 + - - +
107A VAL* 3.2 1.9 + - - +
108A ILE* 3.0 32.6 + - + +
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Residues in contact with ALA 105 (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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101A GLU 5.3 0.6 + - - +
102A GLN* 3.3 19.1 + - - +
104A PRO* 1.3 78.9 - - - +
106A ALA* 1.3 63.5 + - - +
108A ILE* 3.5 9.6 + - - +
109A GLU* 3.0 22.9 + - - +
138B GLY* 4.6 9.5 - - - +
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Residues in contact with ALA 106 (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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102A GLN* 3.0 17.6 + - + +
103A ALA* 3.1 6.3 + - - +
105A ALA* 1.3 77.9 - - - +
107A VAL* 1.3 62.8 + - + +
109A GLU* 3.3 13.5 - - - +
110A LEU* 3.2 25.6 + - - +
415A LEU* 4.5 2.7 - - + -
418A VAL* 4.0 18.8 - - + +
419A VAL* 4.0 23.3 - - + +
422A ARG* 6.6 0.7 - - - +
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Residues in contact with VAL 107 (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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64A ILE* 4.2 29.6 - - + -
65A ASN 4.3 1.1 - - - +
66A ALA* 3.5 19.7 - - + -
68A LEU* 4.3 3.6 - - + -
103A ALA 3.1 15.4 + - - +
104A PRO 4.0 2.5 - - - +
106A ALA* 1.3 74.6 - - + +
108A ILE* 1.3 67.7 + - - +
110A LEU* 3.1 8.4 + - - +
111A GLU* 2.9 21.5 + - - +
117A PHE* 3.7 27.1 - - + -
125A ILE* 4.2 10.5 - - + -
147A CYS* 3.9 19.7 - - + -
415A LEU* 5.2 0.9 - - + -
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Residues in contact with ILE 108 (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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68A LEU* 4.1 20.4 - - + -
104A PRO* 3.0 23.3 + - + +
105A ALA* 3.8 6.5 - - - +
107A VAL* 1.3 76.0 - - - +
109A GLU* 1.3 56.9 + - - +
111A GLU* 3.2 6.3 + - - -
112A ASN* 2.8 31.1 + - - +
125A ILE* 5.3 1.6 - - + -
138B GLY* 3.5 25.1 - - - +
139B LYS 4.1 13.9 - - - +
140B GLU* 3.6 32.5 - - - +
141B GLN* 3.9 16.8 - - + +
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Residues in contact with GLU 109 (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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32A ARG* 2.8 39.9 + - - -
105A ALA 3.0 15.0 + - - +
106A ALA* 3.3 16.4 - - - +
108A ILE* 1.3 76.7 - - - +
110A LEU* 1.3 64.5 + - - +
112A ASN* 3.2 3.1 + - - +
113A TYR* 2.9 58.8 + - + +
418A VAL* 5.4 4.5 - - - +
422A ARG* 3.9 14.5 + - - -
137B GLN* 5.9 2.9 - - - +
138B GLY* 4.5 16.1 - - - -
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Residues in contact with LEU 110 (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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32A ARG* 6.3 0.2 - - - -
64A ILE* 4.1 17.9 - - + -
106A ALA 3.2 13.4 + - - +
107A VAL* 3.1 11.5 + - - +
109A GLU* 1.3 80.5 - - + +
111A GLU* 1.3 63.1 + - - +
113A TYR* 3.1 21.8 + - + +
115A MET* 3.2 37.7 + - + +
117A PHE* 4.4 4.9 - - + -
157A LEU* 3.7 32.1 - - + +
160A THR* 4.1 3.8 - - + +
161A LEU* 3.9 33.7 - - + -
418A VAL* 4.4 16.4 - - + -
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Residues in contact with GLU 111 (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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107A VAL 2.9 14.4 + - - +
108A ILE* 3.8 3.4 - - - +
110A LEU* 1.3 76.5 - - - +
112A ASN* 1.3 85.4 + - - +
114A GLY* 2.7 21.7 + - - -
115A MET 4.2 2.9 - - - -
117A PHE* 3.7 27.1 - - + -
119A ARG* 2.9 32.8 + - - +
125A ILE* 4.0 17.3 - - + -
129B LEU* 4.3 2.3 - - - +
141B GLN* 3.7 3.0 - - - -
142B TYR* 3.0 23.8 + - - +
195B ARG* 3.0 23.5 + - - +
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Residues in contact with ASN 112 (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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108A ILE* 2.8 23.8 + - - +
109A GLU* 3.6 4.3 - - - +
111A GLU* 1.3 92.7 + - - +
113A TYR* 1.3 62.1 + - + +
114A GLY 3.2 0.4 - - - -
164A ARG* 5.1 3.1 + - - -
129B LEU* 3.3 16.2 - - - +
136B LYS 4.0 1.0 - - - +
137B GLN* 3.5 12.9 - - + +
138B GLY* 2.8 30.5 + - - +
139B LYS 4.0 1.4 + - - -
140B GLU 3.1 25.5 + - - +
141B GLN* 4.2 0.2 - - - +
142B TYR* 3.5 34.1 + - + +
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Residues in contact with TYR 113 (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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32A ARG* 3.8 2.9 + - - -
35A PHE* 3.4 36.2 - + - -
39A GLU* 4.8 2.9 + - - -
109A GLU* 2.9 56.4 + - + -
110A LEU* 3.2 20.0 - - + +
111A GLU 3.1 0.4 - - - -
112A ASN* 1.3 77.8 - - + +
114A GLY* 1.3 58.1 + - - +
160A THR* 3.4 20.2 - - + +
161A LEU* 3.9 20.0 - - + -
164A ARG* 3.4 53.2 + - + +
128B TYR* 5.0 2.6 - - - +
129B LEU* 3.4 21.1 + - - +
137B GLN* 4.8 8.0 + - + -
190B TRP* 4.2 2.9 - - - -
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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
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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