Contacts of the helix formed by residues 85 - 107 (chain F) in PDB entry 4IGM
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 LYS 85 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F TYR* 2.9 41.4 + - + +
84F ALA* 1.3 74.1 - - - +
86F PRO* 1.3 77.7 - - + +
87F GLU 4.7 1.3 - - - +
88F ASP* 3.6 18.4 + - - +
89F THR* 3.4 16.3 + - - -
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Residues in contact with PRO 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ALA 3.7 6.5 - - - +
85F LYS* 1.3 89.3 - - + +
87F GLU* 1.3 61.1 + - + +
89F THR* 2.8 21.1 + - - -
90F LEU* 3.0 10.9 + - - +
118F PRO* 4.5 2.6 - - + +
120F GLN* 4.0 18.8 - - + +
121F ALA* 3.9 28.0 - - + -
124F LEU* 4.3 9.1 - - + +
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Residues in contact with GLU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LYS* 3.5 1.8 - - + +
86F PRO* 1.3 80.9 - - + +
88F ASP* 1.3 62.2 + - - +
90F LEU* 3.5 26.1 + - - +
91F ASN* 3.2 23.0 + - - +
124F LEU* 3.6 27.3 - - + +
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Residues in contact with ASP 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F PHE* 3.2 51.0 - - + +
23F TYR* 2.6 42.7 + - - +
26F TRP* 4.2 7.1 - - + -
85F LYS* 3.6 15.6 - - - +
86F PRO 3.1 0.2 - - - -
87F GLU* 1.3 83.1 - - - +
89F THR* 1.3 59.2 + - - +
91F ASN 3.3 0.2 + - - -
92F LEU* 3.1 24.6 + - - +
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Residues in contact with THR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F TRP* 4.5 2.5 - - - -
80F PHE 3.8 13.9 - - - +
81F SER* 2.7 31.6 + - - +
82F TYR* 5.2 0.4 - - + -
84F ALA* 4.1 5.9 - - - +
85F LYS 3.4 6.5 + - - -
86F PRO 2.8 8.8 + - - -
88F ASP* 1.3 75.4 - - - +
90F LEU* 1.3 61.3 + - - +
92F LEU* 3.4 5.8 + - + +
93F CYS* 2.8 41.3 + - - -
117F LEU 4.7 0.4 - - - +
118F PRO* 3.5 27.6 - - + -
120F GLN* 3.1 16.3 + - - +
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F PRO 3.0 10.1 + - - +
87F GLU* 3.5 28.7 - - - +
89F THR* 1.3 78.4 - - - +
91F ASN* 1.3 59.3 + - - +
93F CYS* 3.6 2.3 + - - +
94F GLN* 2.8 53.6 + - - +
118F PRO* 4.0 15.8 - - + +
124F LEU* 3.8 31.4 - - + +
127F LYS* 5.9 3.4 - - + -
128F GLU* 3.8 31.2 - - + -
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Residues in contact with ASN 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ARG* 3.1 45.3 + - - +
21F PHE* 3.5 11.8 - - + -
87F GLU 3.2 13.0 + - - +
88F ASP 3.3 10.1 - - - +
89F THR 3.1 0.4 - - - -
90F LEU* 1.3 73.0 - - - +
92F LEU* 1.3 58.0 + - - +
94F GLN* 2.8 37.3 + - - +
95F LEU* 3.1 12.0 + - - +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F TRP* 5.2 2.9 - - + -
17F LEU* 4.1 29.6 - - + -
21F PHE* 4.3 4.6 - - + -
26F TRP* 3.8 27.4 - - + -
27F VAL* 6.4 0.2 - - + -
79F MET* 3.8 45.5 - - + +
81F SER* 4.1 2.9 - - - +
88F ASP 3.1 12.2 + - - +
89F THR* 3.9 6.5 - - + +
91F ASN* 1.3 78.7 - - - +
93F CYS* 1.3 59.8 + - - +
95F LEU* 3.3 19.7 + - + +
96F LEU* 2.9 46.9 + - + +
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Residues in contact with CYS 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F MET 6.1 0.7 - - - -
80F PHE 5.2 2.9 - - - -
89F THR* 2.8 41.2 + - - +
90F LEU* 3.7 7.4 - - - +
92F LEU* 1.3 75.1 - - - +
94F GLN* 1.3 58.5 + - - +
96F LEU* 4.8 1.6 - - - -
97F ASN* 2.9 35.7 + - - -
116F THR* 4.0 31.0 - - + +
117F LEU 3.8 27.6 - - - -
118F PRO* 3.8 1.8 - - + -
128F GLU* 3.6 13.7 - - + +
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Residues in contact with GLN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LEU* 2.8 42.8 + - - +
91F ASN* 2.8 30.5 + - - +
93F CYS* 1.3 69.6 - - - +
95F LEU* 1.3 54.2 + - - +
97F ASN* 3.3 1.2 + - - +
98F ASN* 2.8 48.8 + - - +
128F GLU* 3.3 20.2 + - - +
131F ARG* 3.5 18.4 - - - +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F PRO* 4.2 11.0 - - + -
13F GLU 5.3 0.9 - - - +
14F TRP* 3.9 20.9 - - + -
15F PRO* 3.6 32.1 - - + -
17F LEU* 5.5 1.3 - - + -
20F ARG* 4.5 14.8 - - - +
91F ASN 3.1 9.1 + - - +
92F LEU* 3.5 20.9 - - + +
94F GLN* 1.3 76.5 - - - +
96F LEU* 1.3 78.9 + - + +
98F ASN* 3.4 5.7 + - - +
99F ASP* 3.1 25.6 + - + +
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F PRO* 3.9 30.3 - - + -
14F TRP* 5.3 2.2 - - + -
75F THR* 4.4 15.5 - - + +
79F MET* 4.0 42.6 - - + +
92F LEU* 2.9 44.0 + - + +
93F CYS* 4.3 2.5 - - - +
95F LEU* 1.3 83.9 - - + +
97F ASN* 1.3 59.5 + - - +
99F ASP* 3.8 4.6 - - - +
100F LEU* 3.0 34.4 + - + +
116F THR* 4.3 20.2 - - + -
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Residues in contact with ASN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F CYS 2.9 26.2 + - - +
94F GLN 3.7 2.0 - - - +
96F LEU* 1.3 78.5 - - - +
98F ASN* 1.3 57.8 + - - +
100F LEU* 3.7 7.5 - - - +
101F ALA* 3.0 21.8 + - - +
115F GLY* 3.6 5.7 - - - -
116F THR* 3.0 48.7 + - - +
128F GLU* 3.1 18.8 + - - +
131F ARG* 4.2 1.1 - - - +
132F CYS* 3.2 20.2 - - - -
136F LEU* 3.7 15.3 - - + +
138F PHE* 3.3 12.0 - - + -
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Residues in contact with ASN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLN* 2.8 31.4 + - - +
95F LEU* 4.0 4.8 - - - +
96F LEU 3.3 0.2 - - - -
97F ASN* 1.3 71.8 - - - +
99F ASP* 1.3 61.1 + - - +
101F ALA* 3.3 5.9 + - - +
102F SER* 2.9 29.0 + - - -
131F ARG* 2.2 37.1 + - - +
136F LEU* 4.1 7.3 - - - +
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Residues in contact with ASP 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 5.8 2.1 - - - +
10F LEU 4.2 2.9 - - - +
11F PRO* 3.5 44.9 - - + +
12F LYS 4.9 1.0 + - - -
95F LEU* 3.1 18.7 + - + +
96F LEU 3.8 4.1 - - - +
98F ASN* 1.3 74.0 - - - +
100F LEU* 1.3 71.5 + - - +
102F SER* 3.1 9.7 + - - -
103F THR* 2.8 33.2 + - - -
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 3.3 36.3 - - + +
73F LEU* 3.7 26.2 - - + +
74F SER* 4.2 9.4 - - - +
75F THR* 4.4 7.9 - - + +
96F LEU* 3.0 19.5 + - + +
97F ASN* 3.7 15.0 - - - +
99F ASP* 1.3 83.8 + - - +
101F ALA* 1.3 62.7 + - - +
103F THR* 3.1 6.7 + - - +
104F VAL* 3.1 22.7 + - + +
113F GLY* 4.8 3.4 - - - -
114F LEU 3.7 25.8 - - - +
115F GLY 5.4 0.4 - - - -
116F THR* 5.5 0.9 - - + +
138F PHE* 3.8 11.7 - - + -
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Residues in contact with ALA 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ASN 3.0 19.2 + - - +
98F ASN* 3.7 5.2 - - - +
99F ASP 3.2 0.6 - - - -
100F LEU* 1.3 73.9 - - - +
102F SER* 1.3 57.1 + - - +
104F VAL* 3.0 7.5 + - - +
105F VAL* 3.0 33.7 + - + +
136F LEU* 3.8 31.6 - - + +
138F PHE* 3.7 17.5 - - + -
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Residues in contact with SER 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ASN 2.9 14.5 + - - -
99F ASP* 3.3 14.1 - - - -
101F ALA* 1.3 77.7 - - - +
103F THR* 1.3 62.0 + - - +
105F VAL* 3.3 16.7 + - - +
106F SER* 3.3 18.0 + - - -
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Residues in contact with THR 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 4.3 10.8 - - + +
56F PRO* 4.0 35.4 - - + +
73F LEU* 3.7 27.1 - - + -
99F ASP* 2.8 25.6 + - - -
100F LEU* 3.5 10.4 - - - +
102F SER* 1.3 74.4 - - - +
104F VAL* 1.3 62.1 + - - +
106F SER* 3.4 16.1 + - - -
107F TYR* 3.6 10.6 + - - -
111F PHE* 4.0 9.0 - - + -
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Residues in contact with VAL 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 5.0 3.4 - - + -
100F LEU 3.1 12.6 + - - +
101F ALA* 3.0 12.4 + - - +
103F THR* 1.3 73.6 - - - +
105F VAL* 1.3 62.1 + - + +
107F TYR 3.1 1.7 + - - -
108F PRO* 2.9 39.9 - - + +
111F PHE* 3.6 28.5 - - + +
112F VAL* 3.8 33.2 - - + +
113F GLY* 3.9 7.0 - - - +
138F PHE* 4.9 2.7 - - + -
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ALA* 3.0 20.1 + - + +
102F SER* 3.3 12.1 + - - +
104F VAL* 1.3 76.3 - - + +
106F SER* 1.3 63.2 + - - +
108F PRO* 3.3 16.6 - - - +
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Residues in contact with SER 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F PRO* 6.1 0.9 - - - -
102F SER* 3.3 14.0 + - - -
103F THR* 3.8 5.9 + - - -
104F VAL 3.2 1.4 - - - -
105F VAL* 1.3 79.3 - - - +
107F TYR* 1.3 89.9 + - - +
108F PRO* 3.6 3.1 - - - +
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Residues in contact with TYR 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F PRO* 4.0 17.3 - - + -
57F GLU* 3.1 34.8 - - + +
60F ILE* 3.4 37.0 - - + -
103F THR 3.6 4.6 + - - -
104F VAL 3.1 6.3 + - - +
106F SER* 1.3 100.0 - - - +
108F PRO* 1.3 60.5 - - - +
109F ARG* 2.8 12.3 + - - -
110F ARG* 2.9 25.9 + - + -
111F PHE* 3.2 31.5 + + + +
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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