Contacts of the helix formed by residues 135 - 158 (chain B) in PDB entry 4U7E
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 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU* 4.4 6.9 + - - +
133B GLU 3.7 2.7 + - - +
134B LEU* 1.3 77.5 - - - +
136B ASP* 1.3 66.1 + - - +
137B GLU* 3.5 7.9 + - - +
138B ASN* 3.0 36.7 + - - +
139B VAL* 3.1 22.5 + - - +
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Residues in contact with ASP 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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134B LEU 5.1 1.0 - - - +
135B THR* 1.3 74.3 - - - +
137B GLU* 1.3 58.5 + - - +
139B VAL* 3.3 8.8 + - - +
140B LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR* 3.2 7.2 + - - +
136B ASP* 1.3 77.1 - - - +
138B ASN* 1.3 60.0 + - - +
140B LYS* 3.3 24.7 + - - +
141B HIS* 2.8 65.6 + - + +
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Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 2.9 30.5 + - - +
125B ILE* 3.5 21.9 - - + +
128B ILE* 3.6 24.2 - - - +
133B GLU 5.0 0.4 + - - -
134B LEU* 3.7 16.7 - - + +
135B THR* 3.0 47.4 + - - +
137B GLU* 1.3 76.9 - - - +
139B VAL* 1.3 62.3 + - - +
141B HIS* 3.4 1.1 + - - -
142B ARG* 3.0 26.3 + - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 4.0 24.0 - - + +
135B THR 3.1 13.8 + - - +
136B ASP* 3.3 10.7 + - - +
138B ASN* 1.3 76.1 - - - +
140B LYS* 1.3 65.0 + - - +
142B ARG* 3.4 20.4 + - - +
143B LYS* 3.1 29.0 + - + +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 2.9 17.1 + - - +
137B GLU* 3.6 27.6 - - - +
139B VAL* 1.3 79.1 - - - +
141B HIS* 1.3 72.3 + - + +
143B LYS* 3.8 6.0 - - - +
144B TYR* 3.0 26.6 + - + +
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.7 31.1 - - + +
98B PHE* 3.8 37.0 - + + +
99B LEU* 6.1 0.4 - - + -
125B ILE* 3.7 18.2 - - + +
137B GLU* 2.8 55.4 + - + +
138B ASN* 4.8 0.6 - - - -
140B LYS* 1.3 76.4 - - + +
142B ARG* 1.3 61.0 + - - +
144B TYR* 4.5 1.6 - - + -
145B ALA* 2.8 33.6 + - - +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B SER* 3.7 27.9 - - - +
125B ILE* 3.4 18.8 - - + +
126B ASP* 2.9 34.6 + - - +
129B THR* 4.7 4.2 - - - +
134B LEU* 3.6 31.7 - - - +
138B ASN 3.0 17.3 + - - +
139B VAL* 3.9 19.8 + - - +
141B HIS* 1.3 76.0 - - - +
143B LYS* 1.3 58.6 + - - +
146B ARG* 2.9 42.6 + - + +
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Residues in contact with LYS 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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139B VAL* 3.1 22.9 + - + +
140B LYS* 3.8 6.7 - - - +
142B ARG* 1.3 78.7 - - - +
144B TYR* 1.3 56.9 + - - +
146B ARG* 4.0 2.9 - - - +
147B TRP* 3.0 32.8 + - + +
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Residues in contact with TYR 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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98B PHE* 3.4 31.6 - + + -
102B ASP* 4.1 15.3 + - - -
105B ASP* 4.3 2.3 + - - -
118B PHE* 4.2 8.1 - + - -
140B LYS* 3.0 21.2 + - + +
141B HIS* 3.8 4.5 - - + +
143B LYS* 1.3 77.0 - - - +
145B ALA* 1.3 56.9 + - - +
147B TRP* 3.3 6.1 + + - +
148B LYS* 2.9 71.9 + - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.8 19.1 - - + -
118B PHE* 3.3 45.0 - - + +
121B ALA* 4.4 1.6 - - + -
122B SER* 4.2 9.0 - - - +
125B ILE* 5.9 0.4 - - + -
141B HIS 2.8 19.1 + - - +
142B ARG 4.0 2.9 - - - +
144B TYR* 1.3 79.4 - - - +
146B ARG* 1.3 57.4 + - - +
148B LYS 3.4 0.7 + - - -
149B ALA* 3.0 24.1 + - - +
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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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118B PHE 5.1 0.2 - - - -
119B TYR* 4.1 20.8 - - + -
122B SER* 3.0 41.4 + - - +
123B LEU* 3.9 8.8 - - - +
126B ASP* 2.9 33.9 + - - -
142B ARG* 2.9 26.9 + - + +
143B LYS* 4.3 2.7 - - - +
145B ALA* 1.3 74.2 - - - +
147B TRP* 1.3 66.1 + - - +
149B ALA* 3.4 5.3 + - - +
150B THR* 3.0 34.6 + - - +
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Residues in contact with TRP 147 (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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143B LYS* 3.0 21.3 + - + +
144B TYR* 3.6 6.1 - + - +
146B ARG* 1.3 76.9 - - - +
148B LYS* 1.3 84.1 + - + +
150B THR* 3.3 5.2 + - - -
151B TYR* 2.8 82.8 + + + +
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 2.9 38.3 + - - -
118B PHE* 3.7 25.1 - - + -
144B TYR* 2.9 57.7 + - + +
145B ALA 3.8 2.0 - - - +
147B TRP* 1.3 102.3 - - + +
149B ALA* 1.3 57.1 + - - +
151B TYR* 4.5 5.3 - - + -
152B ILE* 2.8 44.3 + - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.6 34.2 - - + +
118B PHE* 3.9 5.7 - - + +
119B TYR* 3.8 27.6 - - + +
145B ALA 3.0 18.3 + - - +
146B ARG 3.8 4.3 - - - +
148B LYS* 1.3 75.8 - - - +
150B THR* 1.3 63.5 + - - +
152B ILE* 4.3 0.8 - - - -
153B HIS* 3.1 27.0 + - - +
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Residues in contact with THR 150 (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* 5.7 2.1 - - - -
146B ARG* 3.0 25.9 + - - +
147B TRP* 3.8 4.3 - - - -
149B ALA* 1.3 78.4 - - - +
151B TYR* 1.3 57.7 + - - +
153B HIS* 3.7 4.2 - - - +
154B ASN* 3.0 52.3 + - - +
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Residues in contact with TYR 151 (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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147B TRP* 2.8 65.0 + + + +
148B LYS* 3.9 5.8 - - + +
150B THR* 1.3 75.0 - - - +
152B ILE* 1.3 68.5 + - + +
154B ASN* 3.3 7.4 + - + +
155B CYS* 2.9 48.7 + - - -
161B THR 4.6 0.7 + - - -
162B PRO* 3.5 38.1 - - + -
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Residues in contact with ILE 152 (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 ASP* 4.2 8.7 - - - +
110B PHE* 4.0 13.0 - - + -
114B MET* 3.7 31.0 - - + -
115B ILE* 3.7 24.0 - - + -
118B PHE* 4.0 16.4 - - + -
148B LYS* 2.8 31.5 + - + +
151B TYR* 1.3 78.8 - - + +
153B HIS* 1.3 63.7 + - - +
155B CYS* 3.3 1.6 + - - +
156B LEU* 3.0 35.0 + - + +
162B PRO* 4.0 29.4 - - + -
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Residues in contact with HIS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 5.3 11.0 - - + +
115B ILE* 4.0 25.7 - - + +
149B ALA 3.1 22.0 + - - +
150B THR* 3.7 4.5 - - + +
152B ILE* 1.3 78.0 - - - +
154B ASN* 1.3 70.7 + - - +
156B LEU* 3.4 2.9 + - - +
157B LYS* 2.9 52.0 + - + +
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Residues in contact with ASN 154 (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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150B THR* 3.0 39.3 + - - +
151B TYR* 3.7 7.0 - - + +
153B HIS* 1.3 88.4 - - - +
155B CYS* 1.3 63.8 + - - +
157B LYS* 3.4 11.7 + - - +
158B ASN* 3.1 32.5 + - - +
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Residues in contact with CYS 155 (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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151B TYR* 2.9 59.2 + - - +
152B ILE 3.7 3.8 - - - +
154B ASN* 1.3 76.3 - - - +
156B LEU* 1.3 57.9 + - - +
158B ASN* 3.0 6.9 + - - +
159B GLY 2.9 22.9 + - - -
160B GLU* 3.0 37.2 + - + +
161B THR 4.6 1.8 - - - -
162B PRO* 3.8 17.9 - - + -
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Residues in contact with LEU 156 (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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110B PHE* 4.0 34.8 - - + +
111B HIS* 4.1 3.1 - - - +
112B LYS* 5.6 6.7 - - + -
115B ILE* 3.9 26.2 - - + -
152B ILE* 3.0 26.2 + - + +
153B HIS* 3.9 3.1 - - - +
155B CYS* 1.3 72.3 - - - +
157B LYS* 1.3 66.8 + - - +
159B GLY* 3.1 15.1 + - - +
160B GLU 4.2 12.6 - - - +
161B THR* 5.5 0.2 - - - -
162B PRO* 4.2 7.6 - - + -
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B HIS* 2.9 44.6 + - + +
154B ASN* 3.6 12.6 - - - +
156B LEU* 1.3 78.4 - - - +
158B ASN* 1.3 64.1 + - - +
159B GLY 3.3 0.6 + - - -
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Residues in contact with ASN 158 (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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154B ASN* 3.1 21.2 + - - +
155B CYS* 3.0 6.5 + - - +
157B LYS* 1.3 81.4 + - - +
159B GLY* 1.3 62.1 + - - +
160B GLU* 3.3 28.9 + - + +
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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