Contacts of the helix formed by residues 107 - 125 (chain C) in PDB entry 1JPL
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 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 2.8 32.9 + - - +
106C VAL* 1.3 77.5 - - - +
108C GLU* 1.3 64.7 + - - +
109C LYS* 3.8 2.6 + - - -
110C VAL* 3.1 30.7 + - - +
111C LYS* 3.1 23.3 + - - +
203D MSE 4.1 22.9 - - - +
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Residues in contact with GLU 108 (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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106C VAL 3.9 0.4 + - - -
107C SER* 1.3 72.3 - - - +
109C LYS* 1.3 60.7 + - - +
111C LYS* 3.8 26.5 + - - +
112C THR* 2.7 49.8 + - + +
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Residues in contact with LYS 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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59C GLU* 4.4 12.3 + - - +
60C TRP* 5.9 3.2 - - - -
63C LEU* 3.7 34.7 - - + +
107C SER* 3.2 8.1 + - - +
108C GLU* 1.3 79.6 - - - +
110C VAL* 1.3 60.3 + - - +
112C THR* 3.0 19.5 + - - +
113C LYS* 3.2 12.6 + - - +
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 4.4 17.5 - - + +
59C GLU* 4.1 13.2 - - + +
62C ALA* 4.3 9.9 - - + -
63C LEU* 4.0 26.7 - - + -
66C LEU* 3.9 16.3 - - + +
96C VAL* 5.4 4.7 - - + -
106C VAL* 5.0 10.1 - - + -
107C SER* 3.1 27.9 + - - +
108C GLU 3.3 0.2 - - - -
109C LYS* 1.3 73.7 - - - +
111C LYS* 1.3 67.0 + - + +
113C LYS* 3.1 4.7 + - - +
114C VAL* 3.0 27.2 + - + +
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Residues in contact with LYS 111 (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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96C VAL* 3.5 13.9 - - + +
97C VAL* 3.7 29.3 - - + +
103C GLY* 3.0 18.2 + - - +
106C VAL* 2.8 50.7 + - + -
107C SER 3.1 8.3 + - - +
108C GLU* 3.5 33.1 + - - +
110C VAL* 1.3 77.6 - - + +
112C THR* 1.3 62.0 + - + +
114C VAL* 3.2 6.2 + - - +
115C ILE* 3.1 30.2 + - + +
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Residues in contact with THR 112 (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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108C GLU* 2.7 38.2 + - + +
109C LYS* 3.0 14.4 + - - +
111C LYS* 1.3 75.5 - - + +
113C LYS* 1.3 60.4 + - - +
115C ILE* 3.8 9.1 - - - +
116C GLU* 2.8 31.6 + - - +
148C PRO* 5.7 0.9 - - - +
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Residues in contact with LYS 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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63C LEU* 4.7 7.9 - - + +
66C LEU* 3.6 33.4 - - + -
67C THR* 5.5 4.7 - - - -
70C GLU* 3.1 28.7 + - - -
109C LYS 3.2 9.6 + - - +
110C VAL* 3.1 10.4 + - - +
112C THR* 1.3 80.9 + - - +
114C VAL* 1.3 59.0 + - - +
116C GLU* 2.9 34.6 + - - +
117C LEU* 2.8 48.0 + - + +
151C PRO* 5.2 3.8 - - - +
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Residues in contact with VAL 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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54C ILE* 4.4 6.5 - - + -
66C LEU* 4.1 24.2 - - + -
93C LEU* 4.1 33.1 - - + +
96C VAL* 3.7 21.1 - - + -
97C VAL* 3.8 18.2 - - + -
110C VAL* 3.0 20.1 + - + +
111C LYS 3.2 7.6 + - - +
113C LYS* 1.3 77.3 - - - +
115C ILE* 1.3 58.3 + - - +
117C LEU* 3.2 5.2 + - - +
118C LEU* 2.9 36.6 + - + +
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Residues in contact with ILE 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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97C VAL* 4.2 16.2 - - + -
111C LYS* 3.1 19.2 + - + +
112C THR* 3.8 7.0 - - - +
114C VAL* 1.3 78.4 - - + +
116C GLU* 1.3 66.5 + - - +
118C LEU* 3.3 7.8 + - - +
119C TYR* 2.9 23.4 + - - +
135C TYR* 4.3 5.6 - - + -
138C LEU* 5.4 4.7 - - + -
143C ILE* 4.4 19.5 - - + +
144C VAL* 3.7 36.3 - - + -
148C PRO* 4.0 24.0 - - + -
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Residues in contact with GLU 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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112C THR* 2.8 20.8 + - - +
113C LYS* 2.9 39.0 + - - +
115C ILE* 1.3 77.8 - - - +
117C LEU* 1.3 66.0 + - - +
119C TYR* 3.3 2.4 + - - +
120C SER* 2.7 27.1 + - - +
148C PRO* 4.1 13.9 - - + -
149C PRO 4.0 8.9 - - - +
150C ILE* 3.8 18.5 - - + +
151C PRO* 3.4 25.9 - - + +
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Residues in contact with LEU 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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66C LEU* 4.0 41.1 - - + +
69C LEU* 4.2 14.6 - - + -
70C GLU* 3.9 36.8 - - + +
93C LEU* 6.5 0.4 - - + -
113C LYS* 2.8 35.3 + - - +
114C VAL* 3.6 4.3 - - - +
116C GLU* 1.3 77.4 - - - +
118C LEU* 1.3 62.6 + - - +
120C SER* 3.1 10.4 + - - +
121C TRP* 3.0 49.4 + - + +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.3 10.3 - - + +
93C LEU* 4.0 20.2 - - + -
94C ILE* 5.7 2.9 - - + -
114C VAL* 2.9 27.3 + - + +
115C ILE* 3.6 7.9 - - + +
117C LEU* 1.3 76.1 - - - +
119C TYR* 1.3 62.7 + - - +
121C TRP* 3.3 33.2 + - + +
122C THR* 3.3 24.1 + - - +
131C ILE* 3.9 16.9 - - + +
134C ALA* 5.2 4.3 - - + -
135C TYR* 4.2 22.0 - - + +
138C LEU* 3.8 29.2 - - + -
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Residues in contact with TYR 119 (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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38A LYS* 3.3 28.3 + - + +
115C ILE 2.9 17.2 + - - +
116C GLU 3.8 3.1 - - - +
118C LEU* 1.3 73.6 - - - +
120C SER* 1.3 66.1 + - - +
122C THR* 2.4 34.4 + - - -
123C MSE 3.1 38.4 + - + +
135C TYR* 3.6 34.7 - + + +
147C ASP* 3.6 23.1 - - + -
148C PRO* 3.4 32.8 - - + -
150C ILE* 3.8 17.3 - - + -
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Residues in contact with SER 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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116C GLU* 2.7 23.2 + - - +
117C LEU* 3.3 15.5 - - - +
119C TYR* 1.3 75.9 - - - +
121C TRP* 1.3 59.5 + - - +
123C MSE 3.1 4.0 + - - +
124C ALA* 2.7 38.8 + - - +
150C ILE* 3.4 33.8 - - - +
151C PRO* 4.7 3.3 - - - +
156C LEU* 5.8 0.5 - - - +
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Residues in contact with TRP 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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69C LEU* 3.6 30.1 - - + -
70C GLU* 5.4 1.4 - - - +
73C MSE 3.7 46.5 - - + +
84C VAL* 3.7 23.3 - - + -
90C LEU* 4.6 0.7 - - + -
93C LEU* 4.1 10.8 - - + -
117C LEU* 3.0 36.2 + - + +
118C LEU* 3.6 37.7 - - + +
119C TYR 3.1 0.2 - - - -
120C SER* 1.3 79.1 - - - +
122C THR* 1.3 59.3 + - - +
123C MSE 3.1 1.6 - - - -
124C ALA* 4.8 4.3 - - + -
125C LEU* 2.6 45.2 + - + +
131C ILE* 3.8 29.5 - - + +
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Residues in contact with THR 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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118C LEU 3.3 13.2 + - - +
119C TYR* 2.4 38.5 + - - -
121C TRP* 1.3 77.0 - - - +
123C MSE 1.3 69.6 + - - +
125C LEU 4.9 0.2 - - - -
126C PRO* 3.8 8.1 - - - +
131C ILE* 4.1 7.2 - - + -
132C LYS* 2.9 61.3 - - + +
135C TYR* 4.0 21.5 - - + -
136C HIS* 6.1 0.9 - - + -
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Residues in contact with MSE 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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37A ASN 5.6 2.0 - - - +
38A LYS* 3.6 33.2 - - + +
119C TYR* 3.7 50.7 - - + +
120C SER* 3.1 9.4 + - - +
121C TRP 3.1 0.2 - - - -
122C THR* 1.3 90.9 + - - +
124C ALA* 1.3 60.6 + - + +
126C PRO* 3.5 15.4 - - - +
132C LYS* 6.1 0.7 - - - -
150C ILE* 4.5 11.4 - - + -
156C LEU* 5.2 6.3 - - + +
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Residues in contact with ALA 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 SER* 2.7 21.6 + - - +
121C TRP* 4.8 3.6 - - + -
123C MSE 1.3 71.1 - - - +
125C LEU* 1.3 72.4 + - + +
126C PRO* 3.2 11.9 - - - +
156C LEU* 3.7 34.2 - - + +
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Residues in contact with LEU 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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73C MSE 3.3 34.8 - - + -
81C HIS* 4.0 31.2 - - + +
121C TRP* 2.6 30.9 + - + +
122C THR 4.3 0.2 - - - -
124C ALA* 1.3 91.7 - - + +
126C PRO* 1.3 61.5 - - - +
127C GLU* 2.9 13.7 + - - +
128C GLU* 3.0 39.6 + - + +
131C ILE* 4.5 5.6 - - + +
132C LYS* 4.5 1.6 + - - -
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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
------------------------------------------------------------
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