Contacts of the helix formed by residues 114 - 138 (chain B) in PDB entry 4L5L
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 THR 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLN* 3.8 16.5 + - - +
113B GLU* 1.3 82.4 - - + +
115B PHE* 1.3 65.0 + - - +
116B GLU 3.1 3.4 - - - -
117B GLN* 3.0 35.9 + - - +
118B LEU* 2.9 31.7 + - - +
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 6.0 0.2 - - + -
109B ILE* 3.7 50.0 - - + +
110B ALA* 4.0 4.7 - - - +
112B GLN 3.1 17.8 + - - +
113B GLU 2.9 5.1 + - - +
114B THR* 1.3 75.6 - - - +
116B GLU* 1.3 73.7 + - + +
118B LEU* 3.0 5.6 + - - -
119B LYS* 2.8 53.9 + - + +
165B LEU* 3.5 25.1 - - + -
209B TYR* 4.2 16.4 - - + -
210B PHE* 3.4 38.1 - + + -
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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
----------------------------------------------------------
113B GLU 4.4 2.7 + - - +
114B THR 3.0 1.2 + - - -
115B PHE* 1.3 97.9 - - - +
117B GLN* 1.3 65.1 + - + +
119B LYS* 3.5 33.0 + - - +
120B VAL* 3.8 11.8 - - - +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.0 35.6 + - - +
116B GLU* 1.3 84.8 + - + +
118B LEU* 1.3 65.0 + - + +
119B LYS 3.1 1.3 - - - -
120B VAL* 3.3 10.2 + - - +
121B PRO* 3.2 18.0 - - - +
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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
----------------------------------------------------------
109B ILE* 3.7 40.0 - - + +
112B GLN* 3.3 42.6 - - + +
114B THR* 2.9 22.8 + - - +
115B PHE* 3.6 5.8 - - - +
117B GLN* 1.3 77.5 - - + +
119B LYS* 1.3 62.9 + - - +
120B VAL 3.1 1.6 + - - -
121B PRO* 3.1 17.7 - - + +
122B TYR* 3.3 12.1 + - - +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.1 5.8 - - + +
115B PHE* 2.8 39.3 + - + +
116B GLU* 3.5 31.6 + - - +
117B GLN 3.1 0.2 - - - -
118B LEU* 1.3 77.6 - - - +
120B VAL* 1.3 57.9 + - + +
122B TYR* 3.5 7.7 + - + +
123B LEU* 3.0 57.4 + - + +
165B LEU* 3.3 32.2 + - + +
166B ASP* 5.2 2.2 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU 3.8 16.6 - - - +
117B GLN* 3.7 7.6 - - - +
118B LEU 3.1 0.2 - - - -
119B LYS* 1.3 75.9 - - + +
121B PRO* 1.4 75.6 - - + +
123B LEU* 3.6 3.0 + - - +
124B GLN* 3.1 42.0 + - - +
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Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLN 3.2 12.8 - - - +
118B LEU* 3.1 16.8 - - + +
120B VAL* 1.4 93.8 - - + +
122B TYR* 1.3 65.1 + - - +
124B GLN* 3.0 18.3 + - + +
125B GLN* 3.0 25.0 + - - +
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Residues in contact with TYR 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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102B LEU* 4.5 4.0 + - - +
105B GLY* 3.7 32.3 - - - -
106B VAL* 3.4 24.7 + - + +
109B ILE* 3.9 20.6 - - + -
118B LEU 3.3 13.2 + - - +
119B LYS* 3.5 8.3 - - - +
120B VAL 3.3 0.2 - - - -
121B PRO* 1.3 79.5 - - - +
123B LEU* 1.3 75.6 + - + +
125B GLN* 3.1 7.4 + - + +
126B LEU* 3.0 44.9 + - + +
162B ILE* 3.5 16.6 - - - +
165B LEU* 3.4 25.4 - - + -
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Residues in contact with LEU 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 LYS* 3.0 51.8 + - + +
120B VAL* 4.2 3.4 - - - +
122B TYR* 1.3 85.0 - - + +
124B GLN* 1.3 64.9 + - - +
126B LEU* 3.6 29.5 - - + +
127B PRO* 3.2 19.6 - - - +
165B LEU* 3.9 7.2 - - + -
166B ASP* 3.8 31.2 - - + +
169B SER* 4.3 2.9 + - - +
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Residues in contact with GLN 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 VAL* 3.1 38.3 + - - +
121B PRO* 3.0 20.7 + - + +
123B LEU* 1.3 77.6 - - - +
125B GLN* 1.3 59.8 + - + +
127B PRO* 3.4 11.1 - - - +
128B SER 5.4 0.3 + - - -
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Residues in contact with GLN 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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45A LYS* 6.0 1.6 - - - +
121B PRO 3.0 12.1 + - - +
122B TYR* 3.7 8.3 - - - +
124B GLN* 1.3 76.2 - - + +
126B LEU* 1.3 65.9 + - - +
127B PRO 3.3 1.2 - - - -
128B SER* 3.2 34.8 + - - -
129B THR* 3.5 14.7 + - - +
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Residues in contact with LEU 126 (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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102B LEU* 5.4 1.3 - - + -
122B TYR* 3.0 38.7 + - + +
123B LEU* 3.6 24.9 - - + +
124B GLN 3.4 0.2 - - - -
125B GLN* 1.3 77.8 - - - +
127B PRO* 1.3 70.1 - - + +
129B THR* 3.3 13.1 + - + -
130B LEU* 2.9 43.2 + - + +
162B ILE* 3.7 24.0 - - + -
166B ASP* 5.1 0.2 - - + -
169B SER* 3.4 31.2 - - - +
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Residues in contact with PRO 127 (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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123B LEU 3.2 17.9 - - - +
124B GLN 3.4 11.4 - - - +
125B GLN 3.5 0.7 - - - -
126B LEU* 1.3 90.8 - - + +
128B SER* 1.3 57.1 + - - +
130B LEU* 4.5 7.4 - - + +
131B ARG* 2.7 31.6 + - - +
169B SER* 5.2 9.0 - - - +
173B PHE* 3.7 14.4 - - + -
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Residues in contact with SER 128 (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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125B GLN* 3.2 28.0 + - - -
127B PRO* 1.3 80.0 - - - +
129B THR* 1.3 56.9 + - - +
131B ARG* 3.6 11.6 - - - +
132B MET* 2.9 26.3 + - - +
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Residues in contact with THR 129 (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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102B LEU* 3.8 28.9 - - + -
125B GLN* 3.5 18.9 + - - +
126B LEU* 3.3 15.3 + - + -
128B SER* 1.3 74.8 + - - +
130B LEU* 1.3 65.3 + - - +
132B MET* 3.0 26.5 + - + +
133B TRP* 3.1 24.5 + - + +
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Residues in contact with LEU 130 (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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102B LEU* 4.9 9.0 - - + -
126B LEU* 2.9 49.9 + - + +
127B PRO* 4.7 0.7 - - + -
129B THR* 1.3 74.2 - - - +
131B ARG* 1.3 52.1 + - - +
133B TRP* 3.2 7.0 + - + +
134B SER* 2.7 36.8 + - - -
159B LEU* 3.9 27.8 - - + -
162B ILE* 4.7 9.0 - - + -
169B SER* 3.7 32.1 - - - +
170B VAL* 4.4 10.8 - - + +
173B PHE* 3.6 19.5 - - + -
176B LEU* 4.0 9.3 - - + +
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Residues in contact with ARG 131 (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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127B PRO 2.7 22.7 + - - +
128B SER* 3.6 11.4 - - - +
130B LEU* 1.3 73.6 - - - +
132B MET* 1.3 61.0 + - - +
134B SER* 3.8 1.7 - - - -
135B GLN* 3.0 61.1 + - + +
173B PHE* 3.7 24.0 - - + -
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Residues in contact with MET 132 (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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51A GLU 4.2 3.5 - - - +
52A LEU* 3.8 22.2 - - + -
53A PRO* 3.7 39.7 - - + +
98B GLY* 6.3 0.4 - - - -
128B SER 2.9 15.6 + - - +
129B THR* 3.0 17.7 + - + +
131B ARG* 1.3 74.8 - - - +
133B TRP* 1.3 99.8 + - + +
135B GLN* 3.5 8.8 + - - +
136B PHE* 3.1 22.1 + - - +
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Residues in contact with TRP 133 (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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52A LEU* 3.8 29.4 - - + -
95B ILE* 3.7 23.3 - - + -
98B GLY* 3.4 29.7 + - - -
99B LEU* 3.4 29.8 - - + -
102B LEU* 4.0 31.9 - - + +
129B THR* 3.1 25.7 + - + +
130B LEU* 3.7 9.4 - - + +
132B MET* 1.3 94.1 - - + +
134B SER* 1.3 66.8 + - - +
136B PHE* 3.1 13.1 + + - +
137B LEU* 3.0 24.8 + - - +
143B LEU* 4.3 11.2 - - + -
155B PHE* 3.8 31.0 - + + -
176B LEU* 4.4 4.4 - - + +
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Residues in contact with SER 134 (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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130B LEU 2.7 21.5 + - - -
131B ARG* 3.3 4.9 + - - -
133B TRP* 1.3 73.1 - - - +
135B GLN* 1.3 58.9 + - - +
137B LEU 3.5 0.2 + - - -
138B GLY* 2.9 22.9 + - - -
173B PHE* 3.8 27.4 - - - +
175B ASN* 2.6 40.0 + - - +
176B LEU* 4.0 9.1 - - - +
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Residues in contact with GLN 135 (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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131B ARG* 3.0 58.1 + - + +
132B MET* 3.9 7.5 + - - +
134B SER* 1.3 77.1 - - - +
136B PHE* 1.3 63.0 + - - +
138B GLY* 3.1 15.5 + - - +
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Residues in contact with PHE 136 (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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51A GLU* 3.7 48.5 - - + +
52A LEU* 4.2 17.0 - - + -
91B LYS* 6.2 0.7 - - + -
94B MET* 5.0 2.7 - - + -
95B ILE* 3.5 37.7 - - + -
132B MET 3.1 17.1 + - - +
133B TRP* 3.1 15.7 + + - +
135B GLN* 1.3 73.7 - - - +
137B LEU* 1.3 66.9 + - - +
138B GLY* 3.4 0.5 + - - -
140B ASN* 4.4 5.9 - - - +
143B LEU* 3.6 42.9 - - + +
144B HIS* 6.3 0.2 - - - -
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Residues in contact with LEU 137 (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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133B TRP 3.0 15.2 + - - +
134B SER* 4.0 4.0 - - - +
136B PHE* 1.3 79.5 - - - +
138B GLY* 1.3 66.9 + - - +
140B ASN* 2.9 52.1 + - - +
142B TYR* 3.8 30.3 - - - +
143B LEU* 4.0 18.2 - - + +
155B PHE* 4.7 3.8 - - + -
175B ASN* 3.6 34.8 - - + +
176B LEU* 4.3 8.7 - - + -
179B PHE* 3.9 26.2 - - + -
182B ARG* 5.1 1.6 - - - +
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Residues in contact with GLY 138 (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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134B SER 2.9 14.7 + - - -
135B GLN* 3.1 15.6 + - - -
136B PHE 4.5 0.4 - - - -
137B LEU* 1.3 78.1 - - - +
139B ASN* 1.3 63.9 + - - +
140B ASN 3.5 0.7 + - - +
175B ASN* 2.8 26.4 + - - +
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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