Contacts of the helix formed by residues 107 - 125 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A MSE 3.4 29.4 - - - -
59B GLU* 2.6 31.3 + - - +
106B VAL* 1.3 80.7 - - - +
108B GLU* 1.3 65.1 + - - +
109B LYS* 3.9 1.8 - - - -
110B VAL* 3.3 23.8 + - - +
111B LYS* 3.1 20.4 + - - -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL 3.8 0.4 + - - -
107B SER* 1.3 73.5 - - - +
109B LYS* 1.3 57.0 + - + +
111B LYS* 3.3 14.4 + - + +
112B THR* 2.9 60.0 + - + +
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 3.1 33.4 - - - +
63B LEU* 4.3 19.9 - - + +
107B SER* 3.1 0.6 - - - -
108B GLU* 1.3 78.6 - - + +
110B VAL* 1.3 62.4 + - - +
112B THR* 3.2 8.4 + - - -
113B LYS* 3.1 24.1 + - - +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.2 16.8 - - + +
59B GLU* 4.1 10.1 - - + -
62B ALA* 4.1 18.4 - - + -
63B LEU* 3.5 25.4 - - + +
66B LEU* 3.8 13.4 - - + +
96B VAL* 4.1 12.3 - - + -
106B VAL* 3.5 25.1 - - + -
107B SER* 3.3 15.1 + - - +
109B LYS* 1.3 78.3 - - - +
111B LYS* 1.3 62.5 + - - +
113B LYS* 3.4 2.6 + - - +
114B VAL* 3.1 24.6 + - + +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 3.6 22.0 - - + +
97B VAL* 3.8 27.1 + - + +
99B PRO* 6.2 1.0 - - - +
103B GLY* 2.9 26.8 + - - +
104B ASP* 5.0 2.8 + - - +
106B VAL* 3.2 35.1 + - + +
107B SER 3.1 11.3 + - - +
108B GLU* 3.8 13.1 - - + +
110B VAL* 1.3 77.7 - - - +
112B THR* 1.3 64.0 + - + +
114B VAL* 3.3 4.1 + - - +
115B ILE* 3.1 28.3 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLU* 2.9 44.9 + - + +
109B LYS* 3.2 12.6 + - - -
111B LYS* 1.3 75.5 - - + +
113B LYS* 1.3 62.5 + - - +
115B ILE* 3.8 8.1 - - - +
116B GLU* 2.9 29.0 + - - +
148B PRO* 5.8 0.9 - - - +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 5.1 4.5 - - + -
66B LEU* 3.3 36.8 - - + -
67B THR* 5.3 5.2 - - - -
70B GLU* 2.4 42.0 + - - -
109B LYS 3.1 17.8 + - - +
110B VAL* 3.6 1.1 - - - +
111B LYS 3.2 0.2 - - - -
112B THR* 1.3 77.8 + - - +
114B VAL* 1.3 59.3 + - - +
116B GLU* 2.8 32.6 + - - +
117B LEU* 3.0 38.5 + - + +
151B PRO* 5.0 3.0 - - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 4.5 5.6 - - + -
66B LEU* 4.3 19.1 - - + -
93B LEU* 4.1 28.5 - - + +
96B VAL* 4.0 20.0 - - + -
97B VAL* 4.0 17.7 - - + -
110B VAL* 3.1 17.9 + - + +
111B LYS 3.3 7.6 + - - +
113B LYS* 1.3 77.4 - - - +
115B ILE* 1.3 58.0 + - - +
117B LEU* 3.3 8.3 + - - +
118B LEU* 3.0 46.5 + - + +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.0 23.3 - - + -
111B LYS* 3.1 17.4 + - + +
112B THR* 3.8 7.2 - - - +
114B VAL* 1.3 73.2 - - - +
116B GLU* 1.3 66.5 + - - +
118B LEU* 3.8 6.4 - - + +
119B TYR* 3.0 24.3 + - - +
135B TYR* 4.4 3.8 - - + -
138B LEU* 4.1 16.8 - - + -
143B ILE* 4.8 4.3 - - + +
144B VAL* 3.6 36.8 - - + -
148B PRO* 3.7 26.2 - - + -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU* 4.0 2.4 - - - +
112B THR 2.9 19.4 + - - +
113B LYS* 2.8 41.8 + - - +
115B ILE* 1.3 76.4 - - - +
117B LEU* 1.3 60.2 + - + +
120B SER* 2.9 31.4 + - - -
148B PRO* 4.3 7.6 - - + +
149B PRO 4.5 5.2 - - - +
150B ILE* 3.7 19.3 - - + +
151B PRO* 3.4 37.2 - - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.8 28.9 - - + +
69B LEU* 4.2 15.0 - - + -
70B GLU* 3.4 37.9 - - + +
93B LEU* 6.2 1.1 - - + -
113B LYS* 3.0 34.5 + - + +
114B VAL* 3.7 5.4 - - - +
116B GLU* 1.3 76.8 - - - +
118B LEU* 1.3 55.2 + - + +
120B SER* 3.1 9.1 + - - -
121B TRP* 2.7 66.6 + - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 4.1 15.3 - - + -
93B LEU* 4.1 21.5 - - + -
94B ILE* 5.8 2.7 - - + -
97B VAL* 6.1 0.2 - - + -
114B VAL* 3.0 34.9 + - + +
115B ILE* 3.8 6.7 - - + +
117B LEU* 1.3 75.0 - - - +
119B TYR* 1.3 64.8 + - - +
121B TRP* 2.9 38.1 + - + +
122B THR* 3.0 16.0 + - - +
131B ILE* 3.9 13.4 - - + +
134B ALA* 5.4 6.7 - - + -
135B TYR* 4.1 15.9 - - + +
138B LEU* 3.8 28.0 - - + -
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE 3.0 17.2 + - - +
116B GLU 4.0 1.3 - - - +
118B LEU* 1.3 76.4 - - - +
120B SER* 1.3 63.1 + - - +
122B THR* 2.6 29.9 + - - -
123B MSE 3.3 41.6 + - + +
135B TYR* 3.6 37.6 - + + +
147B ASP* 3.5 30.6 + - + +
148B PRO* 3.5 33.4 - - + -
150B ILE* 3.8 22.9 - - + -
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLU* 2.9 22.1 + - - -
117B LEU* 3.2 13.0 - - - -
119B TYR* 1.3 77.9 - - - +
121B TRP* 1.3 62.5 + - - +
123B MSE 3.2 6.2 + - - +
124B ALA* 3.0 27.2 + - - +
150B ILE* 3.8 28.7 - - - +
151B PRO* 4.8 5.2 + - - +
156B LEU* 4.5 12.1 - - - +
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Residues in contact with TRP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.6 33.0 - - + -
73B MSE 3.5 44.8 - - + +
84B VAL* 3.6 26.9 - - + -
89B PHE* 4.4 1.3 - + - -
90B LEU* 4.7 0.9 - - + -
93B LEU* 4.0 13.9 - - + -
117B LEU* 2.7 46.7 + - + +
118B LEU* 2.9 35.8 + - + +
120B SER* 1.3 76.1 - - - +
122B THR* 1.3 60.1 + - - +
123B MSE 3.0 1.8 - - - -
124B ALA* 4.3 6.1 - - + +
125B LEU* 2.9 38.4 + - + +
131B ILE* 3.8 22.7 - - + +
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU 3.0 13.6 + - - +
119B TYR* 2.6 31.6 + - - -
121B TRP* 1.3 77.7 - - - +
123B MSE 1.3 73.7 + - - +
125B LEU 4.4 2.6 - - - +
126B PRO* 4.9 1.2 - - - +
131B ILE* 4.1 6.7 - - + +
132B LYS* 3.6 52.6 + - + +
135B TYR* 3.9 32.5 - - + -
136B HIS* 6.0 2.5 - - + -
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Residues in contact with MSE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B TYR* 3.5 53.8 - - + +
120B SER* 3.2 8.9 + - - +
121B TRP 3.0 0.2 - - - -
122B THR* 1.3 97.5 + - - +
124B ALA* 1.3 61.9 + - + +
126B PRO* 4.5 8.7 - - - +
150B ILE* 4.6 11.7 - - + -
156B LEU* 4.9 8.5 - - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B SER* 3.0 15.4 + - - +
121B TRP* 4.7 5.4 - - + -
123B MSE 1.3 78.9 - - - +
125B LEU* 1.3 69.1 + - + +
126B PRO* 2.9 14.8 - - - +
156B LEU* 3.5 32.9 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B MSE 3.4 33.2 - - + -
81B HIS* 3.8 34.3 - - + +
84B VAL* 5.7 0.2 - - + -
121B TRP* 2.9 28.1 + - + +
122B THR 4.6 1.6 - - - -
123B MSE 3.6 0.4 - - - -
124B ALA* 1.3 83.5 - - + +
126B PRO* 1.3 65.2 - - + +
127B GLU* 3.3 2.5 - - + +
128B GLU* 3.4 38.1 + - + +
131B ILE* 4.1 11.7 - - + -
132B LYS* 3.6 10.0 + - - -
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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