Contacts of the helix formed by residues 107 - 125 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C MSE 3.8 24.1 - - - +
59D GLU* 2.7 30.7 + - - +
106D VAL* 1.3 77.2 - - - +
108D GLU* 1.3 64.6 + - - +
109D LYS* 3.8 2.4 + - - -
110D VAL* 3.4 24.9 + - - +
111D LYS* 2.9 26.7 + - - +
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D VAL 4.1 0.9 - - - +
107D SER* 1.3 73.2 - - - +
109D LYS* 1.3 60.1 + - + +
111D LYS* 2.9 40.6 + - - +
112D THR* 2.7 50.3 + - + +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 4.2 22.4 - - - +
63D LEU* 4.3 21.8 - - + +
107D SER* 3.4 6.5 - - - +
108D GLU* 1.3 78.5 - - + +
110D VAL* 1.3 62.9 + - - +
112D THR* 3.1 7.5 + - - -
113D LYS* 3.0 26.4 + - - +
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.3 12.3 - - + +
59D GLU* 4.1 5.8 - - + +
62D ALA* 4.1 18.8 - - + -
63D LEU* 3.9 25.6 - - + +
66D LEU* 3.7 17.8 - - + +
96D VAL* 4.0 15.3 - - + -
106D VAL* 3.7 26.9 - - + -
107D SER* 3.4 14.2 + - - +
108D GLU 3.3 0.2 - - - -
109D LYS* 1.3 80.0 - - - +
111D LYS* 1.3 57.6 + - - +
113D LYS* 3.4 2.6 + - - +
114D VAL* 3.0 33.0 + - + +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 3.6 21.8 - - + +
97D VAL* 3.9 24.8 - - + +
103D GLY 3.0 29.0 + - - +
104D ASP* 4.3 5.1 - - - +
106D VAL* 3.2 18.1 + - + -
107D SER 2.9 16.7 + - - +
108D GLU* 2.9 35.5 + - - +
110D VAL* 1.3 73.6 - - - +
112D THR* 1.3 65.4 + - + +
114D VAL* 3.4 3.6 + - - +
115D ILE* 3.1 29.5 + - + +
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLU* 2.7 41.5 + - + +
109D LYS* 3.1 12.2 + - - -
111D LYS* 1.3 73.1 - - + +
113D LYS* 1.3 55.9 + - - +
115D ILE* 3.2 8.6 + - - +
116D GLU* 2.7 40.2 + - - +
148D PRO* 5.5 1.7 - - - +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 4.7 10.1 - - + -
66D LEU* 3.7 31.2 - - + -
67D THR* 4.9 10.7 - - - +
70D GLU* 2.8 36.5 + - - -
109D LYS 3.0 15.1 + - - +
110D VAL* 3.5 5.4 - - - +
112D THR* 1.3 80.5 + - - +
114D VAL* 1.3 59.9 + - - +
116D GLU* 3.2 32.4 + - - +
117D LEU* 2.8 47.8 + - + +
151D PRO* 6.0 0.4 - - - +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.5 6.1 - - + -
66D LEU* 4.0 20.0 - - + -
93D LEU* 4.1 23.3 - - + +
96D VAL* 4.2 18.4 - - + -
97D VAL* 4.1 16.6 - - + -
110D VAL* 3.0 24.8 + - + +
111D LYS* 3.6 7.0 - - - +
112D THR 3.3 0.4 - - - -
113D LYS* 1.3 74.8 - - - +
115D ILE* 1.3 60.9 + - + +
117D LEU* 3.1 10.3 + - - +
118D LEU* 2.9 47.0 + - + +
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 4.2 19.3 - - + -
111D LYS* 3.1 17.2 + - + +
112D THR* 3.4 10.3 - - - +
114D VAL* 1.3 77.7 - - + +
116D GLU* 1.3 64.4 + - - +
117D LEU 3.2 0.2 + - - -
118D LEU* 3.3 5.4 + - + +
119D TYR* 2.9 24.3 + - - +
135D TYR* 4.3 5.6 - - + -
138D LEU* 4.1 18.4 - - + -
143D ILE* 4.9 4.0 - - + +
144D VAL* 3.3 39.0 - - + -
148D PRO* 3.9 26.9 - - + -
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 5.2 1.0 - - - +
112D THR* 2.7 23.8 + - - +
113D LYS* 3.2 38.2 + - - +
115D ILE* 1.3 74.2 - - - +
117D LEU* 1.3 61.0 + - + +
119D TYR* 3.8 1.9 - - - +
120D SER* 3.0 29.5 + - - +
148D PRO* 4.3 13.0 - - + -
149D PRO 4.3 8.0 - - - +
150D ILE* 4.2 18.3 - - + +
151D PRO* 3.5 26.8 - - + +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU* 3.8 38.1 - - + +
69D LEU* 4.1 19.1 - - + -
70D GLU* 4.0 35.4 - - + +
93D LEU* 6.1 0.7 - - + -
113D LYS* 2.8 28.5 + - - +
114D VAL* 3.1 7.6 + - - +
116D GLU* 1.3 76.7 - - + +
118D LEU* 1.3 68.6 + - + +
120D SER* 3.1 7.7 + - - +
121D TRP* 3.0 50.7 + - + +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 3.8 20.9 - - + -
93D LEU* 3.6 28.9 - - + -
114D VAL* 2.9 37.5 + - + +
115D ILE* 3.7 8.3 - - - +
117D LEU* 1.3 71.0 - - + +
119D TYR* 1.3 66.2 + - - +
121D TRP* 2.9 22.0 + - + +
122D THR* 3.1 17.6 + - - +
131D ILE* 3.7 31.6 - - + +
134D ALA* 5.0 5.2 - - + -
135D TYR* 3.9 18.4 - - + -
138D LEU* 4.9 14.6 - - + -
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Residues in contact with TYR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ILE 2.9 18.0 + - - +
116D GLU 3.8 3.1 - - - +
118D LEU* 1.3 76.4 - - - +
120D SER* 1.3 61.8 + - - +
121D TRP 3.1 0.3 + - - -
122D THR* 2.8 30.0 + - - -
123D MSE 3.6 28.2 + - + +
135D TYR* 3.3 37.8 - + - +
147D ASP* 3.4 33.2 + - + +
148D PRO* 3.6 26.5 - - + -
150D ILE* 3.7 26.2 - - + -
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Residues in contact with SER 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU* 3.0 14.7 + - - +
117D LEU* 3.1 14.2 + - - +
119D TYR* 1.3 78.3 - - - +
121D TRP* 1.3 63.9 + - - +
123D MSE 3.4 14.4 + - - +
124D ALA* 2.9 27.9 + - - +
150D ILE* 3.9 21.4 - - - +
151D PRO* 5.6 1.2 - - - +
156D LEU* 4.2 18.0 - - - +
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Residues in contact with TRP 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 3.5 32.5 - - + -
70D GLU* 6.1 0.4 - - - +
73D MSE 3.4 46.8 - - + +
84D VAL* 3.8 27.1 - - + -
89D PHE* 4.4 0.7 - + - -
90D LEU* 4.7 1.6 - - + -
93D LEU* 3.9 22.9 - - + -
117D LEU* 3.2 40.3 + - + +
118D LEU* 2.9 28.3 + - + +
120D SER* 1.3 80.9 - - - +
122D THR* 1.3 60.4 + - - +
123D MSE 2.9 2.2 - - - -
124D ALA* 4.2 7.0 - - + +
125D LEU* 2.7 38.1 + - + +
131D ILE* 3.7 20.8 - - + +
156D LEU* 6.2 0.7 - - + -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU 3.1 14.3 + - - +
119D TYR* 2.8 25.4 + - - +
121D TRP* 1.3 76.9 - - - +
123D MSE 1.3 64.6 + - - +
125D LEU 4.8 0.9 - - - -
126D PRO* 3.9 4.2 - - - +
131D ILE* 4.1 14.8 - - + +
132D LYS* 2.8 47.0 + - - +
135D TYR* 3.7 35.2 - - + -
136D HIS* 5.7 3.6 - - + -
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Residues in contact with MSE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D TYR* 4.0 35.4 - - + +
120D SER* 3.4 7.6 + - - +
121D TRP 2.9 0.4 - - - -
122D THR* 1.3 85.7 + - - +
124D ALA* 1.3 60.2 + - - +
126D PRO* 3.1 23.1 - - - +
150D ILE* 4.0 30.1 - - + -
156D LEU* 4.2 32.2 - - + +
157D ILE* 4.6 5.5 - - - +
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER 2.9 17.7 + - - +
121D TRP* 4.4 7.2 - - + +
123D MSE 1.3 77.1 - - - +
125D LEU* 1.3 73.1 + - + +
126D PRO* 3.1 7.9 - - - +
127D GLU* 3.9 0.9 - - - +
155D THR 5.4 1.6 - - - +
156D LEU* 3.6 35.9 - - + +
157D ILE* 3.3 17.5 - - + +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D MSE 3.6 29.8 - - + -
78D ARG* 3.0 31.2 - - - +
81D HIS* 3.8 30.7 - - + +
121D TRP* 2.7 25.2 + - + +
122D THR* 4.2 0.7 - - - -
124D ALA* 1.3 85.6 - - + +
126D PRO* 1.3 59.9 - - - +
127D GLU* 2.8 17.0 - - - +
128D GLU* 3.1 30.5 + - + +
131D ILE* 4.1 16.3 - - + +
132D LYS* 4.1 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
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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