Contacts of the helix formed by residues 103 - 122 (chain A) in PDB entry 5F0L
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY* 5.9 1.0 - - - -
54A ARG* 3.4 45.5 + - - +
101A ALA* 4.1 2.5 - - - +
102A GLY* 1.3 76.7 - - - +
104A ILE* 1.3 64.7 + - - +
105A ILE 3.4 0.2 + - - -
106A PRO* 3.5 23.7 - - + +
107A ARG* 3.2 22.5 + - - +
501A SO4 4.4 6.0 + - - -
234B GLU* 3.7 4.4 - - - +
401B SO4 3.0 25.7 + - - -
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Residues in contact with ILE 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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102A GLY 3.9 0.8 + - - -
103A ASN* 1.3 70.3 - - - +
105A ILE* 1.3 69.5 + - + +
107A ARG* 3.5 28.9 - - - +
108A LEU* 3.0 46.9 + - + +
136A MET 5.2 1.1 - - - +
139A GLY* 3.6 23.1 - - - -
140A VAL* 4.5 4.3 - - + -
234B GLU* 3.1 29.2 + - + +
235B ILE* 3.4 30.7 - - - +
237B ASP* 3.8 24.7 - - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU 4.3 4.9 - - - +
53A LEU* 4.0 21.1 - - + -
54A ARG* 4.0 11.2 - - + -
63A TYR* 5.4 0.7 - - - +
103A ASN* 4.6 0.4 - - - +
104A ILE* 1.3 76.3 - - + +
106A PRO* 1.4 74.8 - - + +
108A LEU* 4.1 2.0 - - - +
109A TYR* 3.2 52.2 + - + -
140A VAL* 3.7 31.0 - - + -
145A ARG* 4.2 22.7 - - + +
149A LEU* 4.9 2.2 - - + -
234B GLU* 4.6 0.4 + - - -
237B ASP* 3.5 22.2 - - - +
407B EDO 4.1 8.7 - - - +
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Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.8 39.9 - - - +
50A LEU* 3.8 15.9 - - + +
51A GLY* 4.0 15.5 - - - +
54A ARG* 4.1 6.3 - - + -
101A ALA* 4.9 4.3 - - + -
103A ASN* 3.5 28.0 - - + +
105A ILE* 1.4 96.1 - - + +
107A ARG* 1.3 62.8 + - - +
109A TYR 3.4 0.3 + - - -
110A LEU* 3.0 31.9 + - + +
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Residues in contact with ARG 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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98A VAL 3.9 5.7 - - - +
99A GLN* 3.0 46.2 + - + +
101A ALA* 2.6 40.9 + - + +
102A GLY 3.3 18.6 + - - -
103A ASN 3.2 24.1 + - - +
104A ILE* 3.5 27.7 - - - +
105A ILE 3.2 0.2 - - - -
106A PRO* 1.3 80.2 - - - +
108A LEU* 1.3 66.1 - - + +
110A LEU* 3.8 3.3 - - - +
111A LEU* 2.8 29.3 + - + +
233B TYR* 2.9 26.6 + - - -
234B GLU 2.4 27.7 + - - -
235B ILE* 4.3 2.2 - - - +
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Residues in contact with LEU 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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104A ILE* 3.0 41.5 + - + +
105A ILE 4.3 0.9 - - - +
107A ARG* 1.3 81.6 - - + +
109A TYR* 1.3 61.0 + - - +
111A LEU* 3.5 24.8 - - + +
112A ILE* 2.8 40.6 + - + +
136A MET* 3.7 36.6 - - + +
137A CYS* 4.3 5.8 - - - +
140A VAL* 4.0 8.1 - - + +
149A LEU* 3.6 34.5 - - + -
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Residues in contact with TYR 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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50A LEU* 3.5 28.0 - - + -
53A LEU* 3.7 22.7 - - + +
63A TYR* 4.3 5.7 + - - -
67A TYR* 3.7 18.9 - + - -
74A LEU* 4.0 12.1 - - + -
105A ILE* 3.2 44.1 + - + +
106A PRO 4.0 0.7 - - - +
108A LEU* 1.3 75.7 - - - +
110A LEU* 1.3 53.2 - - - +
112A ILE 3.6 0.2 + - - -
113A THR* 2.7 38.1 + - - -
145A ARG 4.4 0.7 + - - -
148A PHE* 3.5 8.8 + - - +
149A LEU* 3.4 39.6 + - + -
152A TYR* 3.5 48.2 - + + -
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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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43A LEU* 4.4 11.7 - - + +
46A ALA* 4.1 18.4 - - + -
47A SER* 4.3 12.8 - - - +
50A LEU* 3.6 22.0 - - + -
74A LEU* 4.7 3.1 - - + -
77A LEU* 4.2 16.4 - - + -
98A VAL* 3.9 29.6 - - + +
101A ALA* 5.1 0.7 - - + -
106A PRO* 3.0 25.7 + - + +
107A ARG 3.8 2.9 - - - +
109A TYR* 1.3 72.3 - - - +
111A LEU* 1.3 57.1 + - - +
113A THR* 3.3 4.2 + - - -
114A VAL* 2.8 40.8 + - + +
502A SO4 4.3 20.4 - - - +
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Residues in contact with LEU 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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95A TYR* 3.5 43.1 - - + +
98A VAL* 3.9 8.7 - - + +
99A GLN* 3.9 29.8 - - + +
107A ARG* 2.8 20.3 + - + +
108A LEU* 3.5 28.3 - - + +
110A LEU* 1.3 76.8 - - - +
112A ILE* 1.3 50.8 + - + +
114A VAL* 3.4 0.9 + - - +
115A GLY* 2.7 32.6 + - - -
132A ASP* 4.8 1.3 - - - +
133A LEU* 3.6 18.2 - - + +
136A MET* 4.4 18.6 - - + -
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Residues in contact with ILE 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 LEU* 2.8 25.8 + - + +
109A TYR 3.9 3.6 - - - +
111A LEU* 1.3 70.4 - - + +
113A THR* 1.3 65.5 + - - +
115A GLY* 3.7 0.5 - - - -
116A VAL* 3.2 25.7 + - + +
133A LEU* 3.8 23.5 - - + +
137A CYS* 3.9 19.3 - - - -
149A LEU* 3.6 27.1 - - + +
152A TYR* 3.6 21.8 - - + -
153A LEU* 4.1 32.3 - - + +
156A CYS* 3.9 17.9 - - + -
157A THR* 5.7 0.2 - - + -
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Residues in contact with THR 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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74A LEU* 4.2 15.1 - - + +
77A LEU* 4.7 14.6 - - + -
78A GLU* 3.8 33.7 - - + +
81A LEU* 5.6 2.5 - - + -
109A TYR 2.7 20.9 + - - -
110A LEU* 3.5 7.2 - - - -
112A ILE* 1.3 76.7 - - - +
114A VAL* 1.3 65.4 + - + +
116A VAL* 3.3 23.0 - - - +
117A VAL* 3.5 10.6 - - + +
152A TYR* 2.7 26.0 + - - +
156A CYS* 4.9 1.8 - - - -
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Residues in contact with VAL 114 (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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43A LEU* 5.6 4.7 - - + -
77A LEU* 6.4 1.3 - - + -
81A LEU* 5.4 7.9 - - + -
94A LEU* 4.0 19.7 - - + -
95A TYR* 3.8 23.3 - - + +
98A VAL* 3.8 25.6 - - + -
110A LEU* 2.8 25.1 + - + +
111A LEU 4.0 2.0 - - - +
113A THR* 1.3 74.8 - - + +
115A GLY* 1.3 64.1 + - - +
117A VAL* 3.5 8.6 + - + +
118A TYR* 3.2 46.5 + - + -
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Residues in contact with GLY 115 (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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95A TYR* 3.9 10.5 - - - -
111A LEU 2.7 21.5 + - - -
112A ILE 3.3 2.2 + - - -
113A THR 3.2 0.8 - - - -
114A VAL* 1.3 72.3 - - - +
116A VAL* 1.3 57.3 + - - +
118A TYR* 3.0 7.7 + - - +
119A VAL* 3.0 28.5 + - - +
129A ILE* 3.8 22.2 - - - +
133A LEU* 4.1 5.6 - - - -
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Residues in contact with VAL 116 (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 GLU* 4.1 24.2 - - + +
112A ILE* 3.2 13.1 + - + +
113A THR* 3.3 18.2 - - - +
115A GLY* 1.3 71.7 - - - +
117A VAL* 1.3 63.6 + - - +
119A VAL* 3.8 1.7 - - + +
120A LYS* 3.2 34.8 + - - +
133A LEU* 5.1 3.1 - - + -
156A CYS* 3.6 37.0 - - + +
157A THR* 4.2 9.4 - - + +
160A ILE* 3.4 30.4 - - + +
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Residues in contact with VAL 117 (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 GLU* 3.9 20.4 - - + +
81A LEU* 3.8 31.4 - - + -
82A THR* 3.9 11.4 - - + +
85A PHE* 3.9 38.8 - - + -
94A LEU* 6.1 0.7 - - + -
113A THR 3.5 15.9 - - - +
114A VAL* 3.5 12.1 + - + +
115A GLY 3.2 0.6 - - - -
116A VAL* 1.3 76.6 - - - +
118A TYR* 1.3 58.7 + - + +
120A LYS* 3.5 9.5 + - - +
121A SER* 2.9 28.1 + - - -
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Residues in contact with TYR 118 (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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85A PHE* 4.0 26.9 - + - -
91A VAL 3.7 7.5 + - - -
92A ALA* 5.1 0.2 - - - -
93A ASP* 3.9 5.0 + - - -
94A LEU* 3.0 29.6 + - + +
95A TYR* 3.2 20.0 + + + +
114A VAL* 3.2 41.0 + - + +
115A GLY* 3.0 10.8 + - - +
117A VAL* 1.3 78.7 - - + +
119A VAL* 1.3 57.0 + - - +
121A SER* 4.6 0.7 - - - -
122A PHE* 2.7 54.7 + + - +
125A SER* 3.9 0.2 + - - -
129A ILE* 3.6 18.2 - - + -
5C VAL* 3.6 41.3 + - + -
6C ALA* 4.5 1.3 - - + -
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Residues in contact with VAL 119 (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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115A GLY 3.0 17.9 + - - +
116A VAL 3.9 1.1 - - - +
117A VAL 3.3 0.4 - - - -
118A TYR* 1.3 74.5 - - - +
120A LYS* 1.3 67.0 + - - +
122A PHE 3.5 16.8 - - - +
123A PRO* 3.6 7.6 - - - +
126A ARG* 3.4 45.3 - - + +
129A ILE* 3.8 26.9 - - + -
130A LEU* 4.6 6.1 - - + -
133A LEU* 5.8 0.2 - - + -
160A ILE* 3.8 37.5 - - + -
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Residues in contact with LYS 120 (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 GLU* 2.9 27.5 + - - +
82A THR* 3.7 27.8 + - + +
116A VAL* 3.2 22.1 + - - +
117A VAL* 3.7 4.7 - - - +
119A VAL* 1.3 82.0 - - - +
121A SER* 1.3 60.9 + - - +
122A PHE 3.6 0.2 + - - -
123A PRO* 3.9 8.8 - - - +
156A CYS 6.1 0.2 - - - -
160A ILE* 4.1 20.9 - - + -
505A GOL 3.3 39.1 + - - -
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Residues in contact with SER 121 (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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85A PHE* 3.5 33.4 + - - +
86A ALA* 4.9 1.0 + - - -
90A LYS* 3.5 30.7 + - - +
117A VAL 2.9 19.1 + - - -
120A LYS* 1.3 79.5 - - - +
122A PHE* 1.3 68.0 + - - +
123A PRO* 3.5 7.1 - - - +
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Residues in contact with PHE 122 (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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85A PHE* 3.9 26.7 - + - -
90A LYS* 3.6 38.1 - - + -
118A TYR* 2.7 49.7 + + - +
119A VAL* 3.5 4.0 - - - +
121A SER* 1.3 79.0 - - - +
123A PRO* 1.3 65.4 - - - +
124A GLN* 3.2 27.8 - - - +
125A SER* 3.0 25.3 + - - +
126A ARG 4.0 1.9 + - - -
5C VAL* 3.8 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
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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