Contacts of the helix formed by residues 107 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.0 36.2 + - - +
106A VAL* 1.3 82.2 - - - +
108A GLU* 1.3 64.1 + - - +
109A LYS 3.7 1.3 + - - -
110A VAL* 3.2 26.8 + - - +
111A LYS* 3.4 16.8 + - - -
2B ALA* 5.9 0.2 - - - -
203B MSE 3.8 22.9 - - - +
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Residues in contact with GLU 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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107A SER* 1.3 72.5 - - - +
109A LYS* 1.3 66.1 + - - +
111A LYS* 4.0 25.8 + - - +
112A THR* 2.9 57.8 + - + +
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Residues in contact with LYS 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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59A GLU* 3.5 27.1 + - - +
63A LEU* 4.2 22.7 - - + +
107A SER* 3.2 0.4 - - - -
108A GLU* 1.3 78.4 - - - +
110A VAL* 1.3 62.8 + - - +
112A THR* 3.0 19.5 + - - -
113A LYS* 3.0 14.6 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.4 12.3 - - + +
59A GLU* 4.1 12.8 - - + -
62A ALA* 4.1 16.4 - - + -
63A LEU* 3.9 21.7 - - + +
66A LEU* 3.8 14.1 - - + +
96A VAL* 3.9 13.9 - - + -
106A VAL* 3.5 26.7 - - + -
107A SER* 3.2 16.8 + - - +
108A GLU 3.3 0.6 - - - -
109A LYS* 1.3 76.0 - - - +
111A LYS* 1.3 56.9 + - - +
113A LYS* 3.2 3.5 + - - +
114A VAL* 2.9 33.7 + - + +
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Residues in contact with LYS 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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96A VAL* 3.5 25.8 - - + +
97A VAL* 3.9 29.1 + - + +
99A PRO* 6.0 2.2 - - - +
103A GLY 2.9 21.9 + - - +
104A ASP* 5.1 1.0 - - - +
106A VAL* 3.2 32.0 + - + +
107A SER 3.4 6.9 + - - +
108A GLU* 4.0 27.9 + - - +
109A LYS 3.4 0.2 - - - -
110A VAL* 1.3 79.2 - - - +
112A THR* 1.3 58.6 + - - +
114A VAL* 3.4 4.6 + - - +
115A ILE* 3.0 33.9 + - + +
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Residues in contact with THR 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 GLU* 2.9 43.9 + - + +
109A LYS* 3.0 18.9 + - - -
111A LYS* 1.3 73.7 - - - +
113A LYS* 1.3 60.1 + - - +
115A ILE* 3.2 9.8 + - + +
116A GLU* 2.8 30.4 + - - +
148A PRO* 5.6 1.0 - - - +
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Residues in contact with LYS 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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63A LEU* 4.6 7.9 - - + -
66A LEU* 3.9 31.9 - - + -
67A THR* 5.3 7.2 + - - -
70A GLU* 4.3 18.0 + - - -
109A LYS 3.0 18.1 + - - +
110A VAL 3.6 4.5 - - - +
112A THR* 1.3 76.4 + - - +
114A VAL* 1.3 57.1 + - - +
116A GLU* 3.4 36.8 + - - +
117A LEU* 2.9 48.2 + - + +
151A PRO* 5.4 4.0 - - - +
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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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54A ILE* 4.4 5.6 - - + -
66A LEU* 3.8 27.6 - - + -
93A LEU* 4.2 33.4 - - + +
96A VAL* 4.4 10.8 - - + -
97A VAL* 4.0 18.2 - - + -
110A VAL* 2.9 30.1 + - + +
111A LYS 3.6 5.6 - - - +
113A LYS* 1.3 76.6 - - - +
115A ILE* 1.3 56.7 + - - +
117A LEU* 3.3 6.7 + - - +
118A LEU* 3.0 35.6 + - + +
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Residues in contact with ILE 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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97A VAL* 4.0 21.3 - - + -
111A LYS* 3.0 19.1 + - + +
112A THR* 3.2 9.4 + - + +
114A VAL* 1.3 72.3 - - - +
116A GLU* 1.3 66.8 + - - +
118A LEU* 3.3 6.8 + - + +
119A TYR* 2.9 23.9 + - - +
135A TYR* 4.2 5.5 - - + -
138A LEU* 4.0 15.0 - - + -
143A ILE* 4.8 4.5 - - + +
144A VAL* 3.5 37.2 - - + -
148A PRO* 3.9 25.8 - - + -
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Residues in contact with GLU 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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70A GLU* 4.6 2.3 - - - +
112A THR 2.8 16.4 + - - +
113A LYS* 3.4 41.2 + - - +
115A ILE* 1.3 78.1 - - - +
117A LEU* 1.3 64.5 + - - +
119A TYR 3.8 0.2 - - - -
120A SER* 2.8 32.3 + - - -
148A PRO* 4.0 17.4 - - + +
149A PRO 4.3 6.2 - - - +
150A ILE* 3.7 20.5 - - + +
151A PRO* 3.7 25.4 - - + +
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Residues in contact with LEU 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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66A LEU* 3.8 44.6 - - + +
69A LEU* 4.2 6.7 - - + -
70A GLU* 3.9 32.5 - - + +
93A LEU* 6.2 0.9 - - + -
113A LYS* 2.9 25.0 + - + +
114A VAL* 3.6 5.2 - - - +
115A ILE 3.2 0.2 - - - -
116A GLU* 1.3 83.8 - - - +
118A LEU* 1.3 67.3 + - - +
120A SER* 3.2 5.9 + - - -
121A TRP* 2.8 62.3 + - + +
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Residues in contact with LEU 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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90A LEU* 4.0 20.0 - - + -
93A LEU* 4.1 17.9 - - + -
94A ILE* 5.6 3.4 - - + +
97A VAL* 6.2 0.2 - - + -
114A VAL* 3.0 29.5 + - + +
115A ILE* 3.7 5.4 - - + +
117A LEU* 1.3 75.1 - - - +
119A TYR* 1.3 63.8 + - - +
121A TRP* 3.1 36.7 + - + +
122A THR* 3.1 18.5 + - - +
131A ILE* 3.9 14.6 - - + +
134A ALA* 5.2 5.4 - - + +
135A TYR* 4.1 17.0 - - + +
138A LEU* 3.7 31.2 - - + -
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Residues in contact with TYR 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 ILE 2.9 16.6 + - - +
116A GLU 3.8 1.8 - - - +
118A LEU* 1.3 74.6 - - - +
120A SER* 1.3 68.0 + - - +
122A THR* 2.5 34.9 + - - -
123A MSE 3.3 26.3 + - + +
135A TYR* 3.6 36.5 - + + +
147A ASP* 3.5 30.5 + - + +
148A PRO* 3.5 33.4 - - + -
150A ILE* 3.7 25.8 - - + -
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Residues in contact with SER 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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116A GLU* 2.8 25.1 + - - -
117A LEU* 3.5 10.5 - - - -
119A TYR* 1.3 74.0 - - - +
121A TRP* 1.3 63.7 + - - +
123A MSE 3.3 4.5 + - - +
124A ALA* 3.0 27.8 + - - +
150A ILE* 3.6 31.3 - - - +
151A PRO* 4.6 6.5 + - - +
156A LEU* 4.3 10.6 - - - +
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Residues in contact with TRP 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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69A LEU* 3.7 30.3 - - + -
70A GLU* 5.7 1.4 - - - +
73A MSE 3.6 44.5 - - + +
84A VAL* 3.6 22.4 - - + -
89A PHE* 4.5 0.2 - + - -
90A LEU* 4.8 0.9 - - + -
93A LEU* 4.0 13.5 - - + -
117A LEU* 2.8 44.5 + - + +
118A LEU* 3.4 34.3 - - + +
119A TYR 3.0 0.2 - - - -
120A SER* 1.3 80.9 - - - +
122A THR* 1.3 59.9 + - - +
124A ALA* 4.4 4.3 - - + +
125A LEU* 2.6 42.5 + - + +
131A ILE* 4.0 27.8 - - + +
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Residues in contact with THR 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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118A LEU 3.1 12.9 + - - +
119A TYR* 2.5 35.2 + - - -
121A TRP* 1.3 78.3 - - - +
123A MSE 1.3 64.0 + - - +
125A LEU 4.7 1.1 - - - -
126A PRO* 4.1 6.2 - - - +
131A ILE* 4.0 8.3 - - + -
132A LYS* 3.3 59.7 + - + +
135A TYR* 4.0 20.1 - - + -
136A HIS* 5.8 1.6 - - - +
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Residues in contact with MSE 123 (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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119A TYR* 3.9 40.8 - - + +
120A SER* 3.3 7.8 + - - +
121A TRP 3.1 0.2 - - - -
122A THR* 1.3 89.2 + - - +
124A ALA* 1.3 60.2 + - - +
126A PRO* 4.1 8.5 - - - +
150A ILE* 4.6 10.5 - - + -
156A LEU* 5.1 5.8 - - + -
157A ILE* 3.4 44.7 - - - +
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Residues in contact with ALA 124 (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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120A SER* 3.0 16.0 + - - +
121A TRP* 4.4 3.8 - - + +
123A MSE 1.3 79.1 - - - +
125A LEU* 1.3 72.3 + - + +
126A PRO* 3.1 9.8 - - - +
127A GLU* 4.6 0.5 - - - +
156A LEU* 3.3 30.3 - - + -
157A ILE* 4.8 10.2 - - - +
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Residues in contact with LEU 125 (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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73A MSE 3.4 32.5 - - + -
81A HIS* 3.9 36.6 - - + +
121A TRP* 2.6 29.7 + - + +
122A THR* 4.2 1.8 - - - -
124A ALA* 1.3 90.0 - - + +
126A PRO* 1.3 63.4 - - - +
127A GLU* 3.3 20.4 - - - +
128A GLU* 3.2 27.9 + - + +
131A ILE* 4.3 11.5 - - + +
132A LYS* 4.1 3.1 + - - -
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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