Contacts of the helix formed by residues 108 - 130 (chain C) in PDB entry 4CNI
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 SER 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ALA* 4.9 5.2 + - - +
39C LEU* 4.1 12.8 - - - +
42C GLU* 2.6 29.9 + - - +
105C PHE* 4.0 8.9 + - - +
106C GLU 3.5 0.8 - - - -
107C SER* 1.3 77.0 + - - +
109C GLU* 1.3 63.4 + - - +
110C GLU* 3.3 3.1 - - - +
111C GLN* 3.2 17.8 + - - +
112C ALA* 3.0 22.5 + - - +
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Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN 5.7 4.7 - - - +
105C PHE 3.5 11.4 + - - +
106C GLU 3.8 15.0 - - - +
107C SER 2.7 12.4 + - - +
108C SER* 1.3 71.1 - - - +
110C GLU* 1.3 62.9 + - - +
112C ALA* 3.3 7.0 + - - +
113C ARG* 3.0 37.0 + - + +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SER 4.5 1.8 + - - +
108C SER 3.3 0.6 - - - -
109C GLU* 1.3 77.7 - - - +
111C GLN* 1.3 57.6 + - - +
113C ARG* 3.5 6.3 + - - +
114C ALA* 3.0 31.8 + - + +
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 5.6 4.2 + - - -
34C ASP 4.7 0.5 - - - +
35C GLY* 3.4 31.9 - - - +
38C ALA* 3.6 20.4 - - + +
39C LEU* 3.6 19.7 - - + -
108C SER* 3.2 20.0 + - - +
110C GLU* 1.3 78.8 - - - +
112C ALA* 1.3 56.5 + - - +
114C ALA* 3.3 14.0 + - - +
115C VAL* 3.1 23.2 + - - +
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.9 13.6 - - + +
101C LEU* 4.6 5.6 - - + +
102C GLN* 3.0 35.3 + - - +
105C PHE* 4.3 25.8 - - + -
108C SER 3.0 15.9 + - - +
109C GLU* 3.7 5.8 - - - +
111C GLN* 1.3 73.5 - - - +
113C ARG* 1.3 65.1 + - - +
115C VAL* 3.4 4.0 + - - +
116C GLN 3.2 12.1 + - - -
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C GLU* 4.2 11.7 + - - -
102C GLN* 3.3 34.1 + - - +
103C ASN* 5.3 5.3 - - - +
109C GLU* 3.0 32.4 + - + +
110C GLU* 3.9 6.7 - - - +
112C ALA* 1.3 73.4 - - - +
114C ALA* 1.3 59.4 + - - +
116C GLN* 2.8 31.1 + - - +
117C MET* 2.8 33.2 + - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 4.2 22.0 - - + +
110C GLU* 3.0 20.6 + - + +
111C GLN* 3.5 19.3 - - - +
112C ALA 3.3 0.2 - - - -
113C ARG* 1.3 76.1 - - - +
115C VAL* 1.3 55.6 + - - +
117C MET* 3.8 11.1 - - + +
118C SER* 2.9 36.5 + - - -
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 4.1 24.3 - - + +
35C GLY* 3.7 35.0 - - - -
36C ILE* 3.8 8.3 - - + +
39C LEU* 3.7 15.9 - - + -
98C LEU* 4.3 12.1 - - + -
101C LEU* 5.6 2.9 - - + -
102C GLN* 6.2 0.2 - - - +
111C GLN* 3.1 19.9 + - - +
112C ALA 3.7 7.0 - - - +
113C ARG 3.3 0.2 - - - -
114C ALA* 1.3 74.2 - - - +
116C GLN* 1.3 61.6 + - - +
118C SER* 4.1 2.8 - - - -
119C THR* 2.8 31.5 + - - -
170C PHE* 4.1 15.0 - - + -
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 5.0 2.6 + - - +
98C LEU* 4.2 18.0 - - + +
99C GLU* 2.9 42.0 + - - +
102C GLN* 3.4 24.3 - - - +
112C ALA 3.2 2.8 + - - -
113C ARG* 2.8 35.9 + - - +
115C VAL* 1.3 77.4 - - - +
117C MET* 1.3 67.8 + - - +
119C THR* 3.5 2.9 + - - -
120C LYS* 3.3 43.3 + - - +
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Residues in contact with MET 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLN* 5.4 0.9 - - - -
31C TYR* 5.0 5.8 - - + +
113C ARG 2.8 22.0 + - - +
114C ALA* 3.8 12.8 - - + +
116C GLN* 1.3 75.7 - - - +
118C SER* 1.3 81.8 + - - +
120C LYS* 3.1 12.4 + - - +
121C VAL* 3.1 35.0 + - + +
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLN* 3.0 27.3 + - - +
31C TYR* 3.2 26.9 - - - -
32C ILE* 3.6 22.1 - - - +
114C ALA 2.9 22.5 + - - -
115C VAL* 4.9 0.2 - - - -
117C MET* 1.3 85.4 - - - +
119C THR* 1.3 56.5 + - - +
121C VAL* 3.4 0.4 + - - -
122C LEU* 2.9 26.2 + - - +
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Residues in contact with THR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 3.8 15.2 - - + +
91C LEU* 4.4 18.8 - - + +
95C GLU* 5.0 2.9 - - + -
98C LEU* 3.5 22.1 - - + +
115C VAL 2.8 22.0 + - - -
116C GLN 3.8 2.7 - - - -
117C MET 3.2 0.2 - - - -
118C SER* 1.3 75.1 - - - +
120C LYS* 1.3 59.7 + - - +
122C LEU* 3.2 3.7 + - + +
123C ILE* 2.8 42.8 + - + +
170C PHE* 3.5 28.2 - - + -
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 2.7 38.1 + - - +
116C GLN* 3.3 34.9 + - + +
117C MET* 3.1 11.3 + - - +
119C THR* 1.3 76.3 - - - +
121C VAL* 1.3 64.4 + - + +
123C ILE* 3.3 10.8 + - - +
124C GLN* 3.1 27.6 + - - +
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLN* 3.5 24.0 - - - +
117C MET* 3.1 30.2 + - + +
118C SER 3.6 0.7 - - - +
119C THR 3.3 0.2 - - - -
120C LYS* 1.3 77.0 - - + +
122C LEU* 1.3 56.6 + - - +
124C GLN* 3.2 9.1 + - - +
125C PHE* 2.9 53.8 + - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 4.0 26.7 - - + +
28C GLN* 3.8 11.6 - - + +
29C ILE* 3.7 33.4 - - + -
32C ILE* 3.9 17.0 - - + -
91C LEU* 3.8 20.2 - - + -
118C SER 2.9 14.7 + - - +
119C THR* 3.5 8.5 - - + +
121C VAL* 1.3 72.4 - - - +
123C ILE* 1.3 68.3 + - - +
125C PHE* 3.1 10.0 + - + +
126C LEU* 2.9 40.8 + - + +
174C LEU* 4.2 10.1 - - + -
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 4.7 6.6 - - + +
91C LEU* 3.8 32.3 - - + +
92C LEU* 3.9 25.8 - - + +
95C GLU* 3.5 41.1 - - + +
119C THR* 2.8 23.8 + - + +
120C LYS* 3.5 9.4 - - - +
122C LEU* 1.3 75.9 - - - +
124C GLN* 1.3 65.8 + - - +
126C LEU* 3.2 5.4 + - - +
127C GLN* 2.9 47.0 + - - +
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Residues in contact with GLN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LYS 3.1 13.8 + - - +
121C VAL* 3.2 8.9 + - + +
123C ILE* 1.3 81.2 - - - +
125C PHE* 1.3 68.0 + - + +
127C GLN* 3.3 22.7 + - - +
128C LYS* 3.1 23.0 + - - +
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 3.5 38.6 - - + -
25C ILE* 3.6 34.3 - - + +
28C GLN* 3.8 28.0 - - + -
121C VAL* 2.9 38.3 + - + -
122C LEU* 3.1 14.1 + - + +
124C GLN* 1.3 78.7 - - + +
126C LEU* 1.3 57.7 + - - +
128C LYS* 3.3 8.3 + - - +
129C LYS* 3.1 23.6 + - - +
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.8 26.7 - - + -
84C LEU* 4.0 10.2 - - + +
87C ILE* 3.8 16.6 - - + -
88C ILE* 3.5 21.5 - - + +
91C LEU* 3.6 31.6 - - + -
122C LEU* 2.9 29.2 + - + +
123C ILE* 3.8 3.4 - - - +
125C PHE* 1.3 74.0 - - - +
127C GLN* 1.3 62.3 + - - +
129C LYS* 3.3 7.0 + - + +
130C ALA* 2.8 28.6 + - - +
181C LEU* 3.9 27.8 - - + -
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 3.9 31.6 - - + +
92C LEU* 4.2 13.4 - - - +
123C ILE* 2.9 29.0 + - - +
124C GLN* 3.3 22.8 + - - +
126C LEU* 1.3 73.6 - - - +
128C LYS* 1.3 64.4 + - - +
130C ALA* 3.4 6.2 + - + +
131C LYS* 3.2 18.4 + - - +
136C ILE* 4.6 13.6 - - + +
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLN 3.1 12.9 + - - +
125C PHE* 3.4 11.7 - - - +
126C LEU 3.3 0.2 - - - -
127C GLN* 1.3 76.1 - - - +
129C LYS* 1.3 62.9 + - - +
131C LYS* 3.0 43.1 + - + +
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Residues in contact with LYS 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER* 6.4 3.5 - - - -
22C SER* 4.1 12.2 + - - +
25C ILE* 4.1 21.5 - - + -
80C GLU* 4.6 6.5 + - - -
84C LEU* 4.1 22.3 - - + +
125C PHE 3.1 13.3 + - - +
126C LEU* 3.3 11.4 + - + +
128C LYS* 1.3 76.9 - - - +
130C ALA* 1.3 55.7 + - - +
131C LYS* 3.2 4.9 + - - +
132C ASN* 5.0 2.4 + - - -
181C LEU* 4.2 8.5 - - + -
184C MET* 2.9 55.3 + - - +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 3.8 14.6 - - + -
88C ILE* 3.7 19.7 - - + -
126C LEU 2.8 15.3 + - - +
127C GLN* 3.4 8.7 + - + +
128C LYS 3.2 0.8 - - - -
129C LYS* 1.3 74.3 - - - +
131C LYS* 1.3 65.5 + - - +
132C ASN 3.2 2.5 - - - -
133C LEU* 2.8 36.7 + - + +
134C ASP 5.4 0.2 - - - +
136C ILE* 4.8 7.9 - - + -
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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
------------------------------------------------------------
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