Contacts of the helix formed by residues 124 - 147 (chain B) in PDB entry 4ECB
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 ASP 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER* 3.0 12.5 + - - +
123B LYS* 1.3 103.5 + - - +
125B PHE* 1.3 62.1 + - - +
126B GLU 3.3 2.9 - - - -
127B THR* 3.2 17.0 + - + +
128B LEU* 3.0 34.3 + - + +
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 3.6 47.8 - - + +
122B SER 3.2 14.6 + - - +
123B LYS 3.1 5.3 + - - -
124B ASP* 1.3 77.2 - - - +
126B GLU* 1.3 84.2 + - - +
128B LEU* 3.1 4.0 + - - -
129B LYS* 2.7 53.1 + - + +
175B MET* 4.6 8.5 - - + -
219B THR* 3.8 24.7 - - + -
220B PHE* 3.4 48.9 - + + -
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS 4.8 1.9 + - - +
124B ASP 3.2 0.8 + - - -
125B PHE* 1.3 99.6 - - + +
127B THR* 1.3 60.5 + - - +
129B LYS* 2.8 56.1 + - - +
130B VAL* 3.8 6.2 + - - +
219B THR* 5.0 6.8 - - + +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.2 21.2 + - + +
125B PHE 3.1 0.4 - - - -
126B GLU* 1.3 78.4 - - - +
128B LEU* 1.3 72.4 + - + +
129B LYS 3.2 1.3 - - - -
130B VAL* 3.3 21.9 + - - +
131B ASP* 3.6 11.2 - - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG 5.3 1.1 - - - +
119B ILE* 3.7 34.4 - - + +
122B SER* 3.5 33.7 - - - +
124B ASP* 3.0 24.8 + - + +
125B PHE 3.7 3.4 - - - +
127B THR* 1.3 80.6 - - + +
129B LYS* 1.3 64.6 + - - +
131B ASP* 3.4 17.7 + - - +
132B PHE* 3.2 20.6 + - - +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 3.9 4.9 - - - +
125B PHE* 2.7 36.8 + - + +
126B GLU* 2.8 48.5 + - - +
128B LEU* 1.3 73.6 - - - +
130B VAL* 1.3 80.3 + - - +
132B PHE 3.1 1.0 + - - -
133B LEU* 2.9 39.7 + - + +
175B MET* 3.4 35.0 - - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU 3.9 13.5 - - - +
127B THR* 3.3 11.3 + - - +
128B LEU 3.3 0.4 - - - -
129B LYS* 1.3 88.5 - - - +
131B ASP* 1.3 70.1 + - - +
133B LEU* 3.6 4.6 + - - +
134B SER* 3.1 23.5 + - - -
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR* 3.6 15.6 - - - +
128B LEU* 3.4 18.0 + - - +
129B LYS 3.3 0.6 - - - -
130B VAL* 1.3 82.4 - - - +
132B PHE* 1.3 63.0 + - - +
134B SER* 3.1 11.3 + - - -
135B LYS* 3.0 49.6 + - - +
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP 4.7 0.4 - - - -
112B ILE* 3.6 17.7 - - + -
115B GLY* 3.7 30.3 - - - -
116B VAL* 3.6 28.9 - - + -
119B ILE* 3.9 14.8 - - + -
128B LEU 3.2 12.7 + - - +
129B LYS 3.1 6.9 + - - +
131B ASP* 1.3 75.8 - - - +
133B LEU* 1.3 60.4 + - - +
135B LYS* 3.0 11.2 + - + +
136B LEU* 2.9 50.6 + - + +
139B MET* 4.7 12.8 - - + -
172B VAL* 4.0 12.6 - - + -
175B MET* 3.2 26.0 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LYS* 2.9 31.5 + - + +
130B VAL* 4.2 4.0 - - - +
132B PHE* 1.3 76.9 - - + +
134B SER* 1.3 59.6 + - - +
136B LEU* 3.8 27.9 - - + +
137B PRO* 3.3 19.1 - - - +
172B VAL* 5.1 0.9 - - + +
175B MET* 3.3 36.3 - - + +
176B ASP* 3.8 42.6 - - + +
179B CYS* 4.7 3.1 - - + -
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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 VAL* 3.1 16.5 + - - -
131B ASP* 3.1 12.8 + - - -
132B PHE 3.1 1.0 - - - -
133B LEU* 1.3 78.3 - - - +
135B LYS* 1.3 70.3 + - - +
137B PRO* 3.5 10.7 - - - +
138B GLU* 5.3 1.6 + - - +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP* 3.0 44.1 + - - +
132B PHE* 3.0 11.2 + - + +
134B SER* 1.3 83.3 - - - +
136B LEU* 1.3 60.9 + - - +
137B PRO* 3.5 1.1 - - - -
138B GLU* 3.3 22.8 - - + +
139B MET* 3.5 19.7 - - + +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.0 25.6 - - + -
132B PHE* 2.9 37.7 + - + +
133B LEU* 3.8 29.2 - - + +
135B LYS* 1.3 75.0 - - - +
137B PRO* 1.3 72.5 - - + +
139B MET* 3.0 9.4 + - - +
140B LEU* 3.0 40.4 + - + +
172B VAL* 4.0 23.1 - - + -
179B CYS* 4.1 17.7 - - + -
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Residues in contact with PRO 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 LEU 3.3 17.9 - - - +
134B SER* 3.5 13.0 - - - +
135B LYS 3.5 0.9 - - - -
136B LEU* 1.3 91.6 - - + +
138B GLU* 1.3 54.8 + - - +
140B LEU* 3.4 0.6 + - + -
141B LYS* 3.0 31.9 + - - +
183B PHE* 3.5 29.5 - - + -
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Residues in contact with GLU 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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62A PHE* 5.2 9.9 - - - -
134B SER 5.5 0.9 - - - +
135B LYS* 3.3 15.9 - - - +
137B PRO* 1.3 80.1 - - - +
139B MET* 1.3 64.9 + - + +
141B LYS* 3.9 14.8 + - - +
142B MET* 4.1 5.5 + - - +
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Residues in contact with MET 139 (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 ALA 5.1 0.9 - - - +
111B ASP* 3.4 49.6 - - + +
112B ILE* 3.8 21.5 - - + +
132B PHE* 4.7 11.7 - - + -
135B LYS* 3.5 22.9 - - + +
136B LEU* 3.0 17.3 + - - +
138B GLU* 1.3 80.6 - - + +
140B LEU* 1.3 63.3 + - - +
141B LYS 3.5 0.7 + - - -
142B MET* 3.5 13.7 + - - +
143B PHE* 3.5 18.2 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.1 21.1 - - + -
136B LEU* 3.0 44.4 + - + +
137B PRO* 3.9 3.1 - - + +
139B MET* 1.3 73.3 - - - +
141B LYS* 1.3 65.3 + - - +
143B PHE* 3.0 9.9 + - + +
144B GLU 2.9 18.4 + - - -
165B LEU* 5.4 0.7 - - + -
169B LEU* 4.1 25.1 - - + -
172B VAL* 5.3 3.6 - - + -
179B CYS 3.8 12.8 - - - +
180B LEU* 3.8 12.1 - - + -
183B PHE* 3.7 26.7 - - + -
186B LEU* 3.5 20.1 - - + +
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Residues in contact with LYS 141 (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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137B PRO 3.0 17.7 + - - +
138B GLU* 3.9 10.5 - - - +
139B MET 3.3 0.4 - - - -
140B LEU* 1.3 76.1 - - - +
142B MET* 1.3 55.5 + - - +
144B GLU* 3.2 5.9 + - + +
145B ASP* 2.9 59.4 + - - +
183B PHE* 3.8 16.3 - - + -
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Residues in contact with MET 142 (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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104B MET* 6.2 3.8 - - - -
105B LEU* 4.2 12.1 - - + -
108B ALA* 4.5 15.0 - - - -
138B GLU 4.1 5.6 + - - +
139B MET* 3.5 12.2 + - - +
140B LEU 3.2 0.6 - - - -
141B LYS* 1.3 78.5 - - - +
143B PHE* 1.3 77.6 + - + +
145B ASP* 3.6 7.0 + - - +
146B ARG* 3.1 56.9 + - + +
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Residues in contact with PHE 143 (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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105B LEU* 4.4 11.0 - - + -
108B ALA* 3.7 16.4 - - + -
109B VAL* 3.6 42.8 - - + -
112B ILE* 3.8 27.4 - - + -
139B MET* 3.5 17.5 - - + -
140B LEU* 3.0 10.1 + - + +
142B MET* 1.3 88.9 - - + +
144B GLU* 1.3 60.6 + - - +
146B ARG* 3.3 3.5 + - - +
147B LEU* 2.9 37.5 + - - +
153B LEU* 3.7 20.0 - - + -
165B LEU* 3.7 22.2 - - + -
186B LEU* 3.9 18.2 - - + -
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Residues in contact with GLU 144 (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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140B LEU 2.9 12.5 + - - +
141B LYS* 3.4 10.3 - - + +
143B PHE* 1.3 75.9 - - - +
145B ASP* 1.3 66.3 + - - +
147B LEU* 3.3 4.4 + - - +
148B CYS* 3.3 25.0 + - - -
182B ALA 4.9 1.1 - - - +
183B PHE* 3.2 38.2 - - + +
184B PRO* 3.4 11.8 - - - +
185B LYS* 2.9 38.2 + - + +
186B LEU* 3.0 29.7 + - + +
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Residues in contact with ASP 145 (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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141B LYS* 2.9 55.4 + - - +
142B MET* 3.9 6.3 - - - +
144B GLU* 1.3 77.5 - - - +
146B ARG* 1.3 67.0 + - - +
148B CYS* 3.1 26.2 + - - +
149B HIS* 4.3 5.2 + - - -
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Residues in contact with ARG 146 (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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101B GLU* 2.9 40.0 + - - +
105B LEU* 3.8 20.1 - - - +
142B MET* 3.1 38.9 + - + +
143B PHE* 3.3 4.9 + - - +
145B ASP* 1.3 81.0 - - - +
147B LEU* 1.3 58.8 + - - +
148B CYS 3.5 0.5 + - - -
149B HIS* 3.9 1.7 + - - +
150B LYS* 3.6 46.5 + - + +
152B TYR 5.5 0.2 - - - +
153B LEU* 2.7 40.5 + - + +
154B ASN* 3.7 10.7 + - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE 2.9 21.4 + - - +
144B GLU 3.7 6.1 - - - +
145B ASP 3.1 0.6 - - - -
146B ARG* 1.3 76.2 - - - +
148B CYS* 1.3 62.3 + - - +
149B HIS 3.3 0.9 - - - -
150B LYS 3.2 17.0 - - - +
151B THR 3.6 24.5 - - - +
152B TYR 3.8 18.8 - - - +
153B LEU* 4.1 16.6 - - + +
165B LEU* 4.6 0.7 - - + -
185B LYS* 4.0 24.0 - - + +
186B LEU* 3.8 27.6 - - + -
189B PHE* 3.9 29.8 - - + -
192B ARG* 4.9 6.0 + - - +
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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
------------------------------------------------------------
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