Contacts of the helix formed by residues 125 - 146 (chain B) in PDB entry 4U7B
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 ASN 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B HIS* 5.4 0.3 + - - -
123B GLU 3.6 8.3 - - - +
124B LEU* 1.3 80.4 - - - +
126B GLU* 1.3 66.4 + - - +
127B ARG* 3.1 14.3 - - + +
128B GLN* 2.9 29.1 + - - +
129B MET* 3.3 27.8 + - - +
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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
----------------------------------------------------------
125B ASN* 1.3 74.7 - - - +
127B ARG* 1.3 62.2 + - - +
129B MET* 3.8 21.0 - - + +
130B GLU* 3.1 26.2 + - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASN* 3.1 10.2 - - + +
126B GLU* 1.3 79.8 - - - +
128B GLN* 1.3 73.5 + - - +
130B GLU* 3.2 4.0 + - - +
131B ARG* 3.2 44.4 + - - +
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Residues in contact with GLN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B HIS* 4.0 16.6 + - - -
124B LEU* 3.9 19.4 - - + +
125B ASN* 2.9 47.2 + - - +
127B ARG* 1.3 81.6 - - + +
129B MET* 1.3 57.0 + - - +
131B ARG* 3.3 9.8 + - - +
132B ARG* 2.9 36.8 + - - +
275B ALA* 4.3 16.3 + - + +
276B TYR* 3.7 35.9 - - + -
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.2 18.6 - - + +
125B ASN 3.3 23.0 + - - +
126B GLU* 3.8 21.1 - - + +
127B ARG 3.2 0.6 - - - -
128B GLN* 1.3 78.7 - - - +
130B GLU* 1.3 57.3 + - - +
132B ARG* 4.6 0.2 - - - +
133B LYS* 2.9 31.3 + - - +
340B ASP* 3.7 20.4 - - + +
341B GLY* 3.2 29.5 - - - +
342B LYS* 3.9 32.5 - - + +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU 3.1 18.5 + - - +
127B ARG* 3.7 4.5 - - - +
129B MET* 1.3 73.2 - - - +
131B ARG* 1.3 67.2 + - + +
133B LYS* 3.4 16.0 + - + +
134B ASN* 2.9 31.1 + - + +
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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
----------------------------------------------------------
127B ARG* 3.2 39.7 + - - +
128B GLN* 3.6 8.1 - - - +
130B GLU* 1.3 77.0 - - + +
132B ARG* 1.3 60.7 + - - +
134B ASN* 3.1 4.1 + - - +
135B THR* 2.7 38.8 + - - -
250B ASN* 4.6 7.9 - - - +
273B HIS 4.5 3.8 + - - -
274B ALA* 3.8 13.3 - - + +
275B ALA* 3.4 36.6 - - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.8 15.4 - - - +
128B GLN 2.9 21.2 + - - +
129B MET 3.8 3.4 - - - +
131B ARG* 1.3 76.3 - - - +
133B LYS* 1.3 63.6 + - - +
135B THR* 3.3 1.3 + - - -
136B CYS* 2.9 30.1 + - - -
274B ALA* 3.5 17.0 - - + +
275B ALA 4.1 8.3 - - - +
276B TYR 3.5 5.7 + - - -
277B SER* 2.8 47.1 + - - +
279B ASP* 2.8 39.6 + - - -
280B LEU* 3.6 11.2 - - + +
336B CYS* 3.9 11.8 - - - -
341B GLY* 2.9 22.0 + - - +
342B LYS 3.6 18.2 + - - -
343B TYR* 4.0 12.2 - - - -
344B PHE* 4.5 4.8 - - - -
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Residues in contact with LYS 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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129B MET 2.9 20.1 + - - +
130B GLU* 3.6 15.4 + - + +
132B ARG* 1.3 75.6 - - - +
134B ASN* 1.3 59.2 + - - +
136B CYS* 3.5 2.3 + - - +
137B GLU* 2.8 56.8 + - - +
336B CYS* 4.3 9.9 - - - -
337B VAL* 4.1 14.3 - - + +
340B ASP* 3.6 40.4 + - + +
341B GLY* 4.0 8.5 - - - +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 2.9 22.6 + - + +
131B ARG* 3.6 4.7 - - - +
133B LYS* 1.3 73.7 - - + +
135B THR* 1.3 57.1 + - - +
137B GLU* 3.1 19.9 + - - +
138B ILE* 2.7 63.6 + - - +
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Residues in contact with THR 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* 2.7 29.9 + - - -
132B ARG* 3.5 7.0 - - - -
134B ASN* 1.3 76.4 - - - +
136B CYS* 1.3 54.3 + - - +
138B ILE* 3.0 11.7 + - - +
139B LEU* 2.8 48.5 + - + +
272B PRO* 3.7 42.6 - - + +
273B HIS* 4.6 1.1 - - - +
274B ALA* 4.1 15.4 + - + +
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Residues in contact with CYS 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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132B ARG* 2.9 14.6 + - - +
133B LYS 3.8 2.7 - - - +
135B THR* 1.3 78.0 - - - +
137B GLU* 1.3 58.4 + - - +
139B LEU* 3.9 3.7 - - - +
140B LEU* 2.9 34.6 + - - +
280B LEU* 4.2 11.2 - - - -
333B TRP* 3.8 38.7 - - + +
336B CYS* 2.1 52.9 - - + -
337B VAL* 4.5 2.5 - - + +
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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
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133B LYS* 2.8 46.5 + - - +
134B ASN* 3.3 29.0 - - - +
136B CYS* 1.3 76.9 - - - +
138B ILE* 1.3 61.2 + - + +
140B LEU* 3.8 6.2 - - - +
141B SER* 3.3 22.9 + - - -
337B VAL* 3.5 22.8 - - + +
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Residues in contact with ILE 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 ASN* 2.7 47.3 + - - +
135B THR* 3.4 10.1 - - - +
137B GLU* 1.3 71.1 - - + +
139B LEU* 1.3 71.4 + - + +
140B LEU 3.1 1.3 - - - -
141B SER* 2.8 24.1 + - - +
142B ARG* 3.3 12.4 + - + +
272B PRO* 5.6 9.0 - - + -
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Residues in contact with LEU 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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135B THR* 2.8 43.0 + - + +
136B CYS* 3.9 3.4 - - - +
138B ILE* 1.3 75.9 - - + +
140B LEU* 1.3 60.8 + - - +
142B ARG* 3.8 8.0 + - - +
143B TYR* 3.3 20.8 + - - +
148B PHE* 3.7 13.7 - - + -
271B LEU* 3.4 32.3 - - + -
272B PRO* 3.9 25.8 - - + +
333B TRP* 3.7 46.0 - - + +
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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
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136B CYS 2.9 16.7 + - - +
137B GLU* 3.8 6.5 - - - +
139B LEU* 1.3 76.0 - - - +
141B SER* 1.3 67.3 + - - +
143B TYR* 2.8 25.3 + - + +
144B LYS* 2.9 33.8 + - + +
330B PRO* 3.7 26.0 - - + +
333B TRP* 3.7 21.5 - - + -
334B GLU* 3.8 35.4 - - + +
337B VAL* 4.5 10.5 - - + -
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Residues in contact with SER 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 GLU 3.3 12.3 + - - -
138B ILE* 2.8 23.4 + - - +
140B LEU* 1.3 77.9 - - - +
142B ARG* 1.3 60.7 + - - +
144B LYS* 3.2 27.8 - - - +
145B ARG* 3.3 15.9 + - - +
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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
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138B ILE* 3.3 15.0 + - + +
139B LEU* 4.0 6.5 - - - +
140B LEU 3.1 0.2 - - - -
141B SER* 1.3 79.3 + - - +
143B TYR* 1.3 58.8 + - - +
145B ARG* 3.3 24.5 + - - +
146B LYS* 2.8 33.2 + - + +
148B PHE* 3.8 27.3 - - + -
151B ARG* 3.8 23.0 - - - +
245B ILE* 4.1 6.9 - - - +
269B GLU* 2.7 37.7 + - - -
271B LEU* 4.0 18.0 - - - +
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Residues in contact with TYR 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 LEU 3.3 12.0 + - - +
140B LEU* 2.8 21.7 + - + +
142B ARG* 1.3 71.9 - - - +
144B LYS* 1.3 73.6 + - + +
146B LYS 3.3 17.0 - - - +
147B SER* 3.4 27.7 + - - -
148B PHE* 3.6 8.2 - - + -
149B LEU* 3.3 35.8 - - + +
327B HIS* 5.2 3.8 + - - -
330B PRO* 3.6 33.8 - - + +
333B TRP* 4.3 6.7 - + + -
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Residues in contact with LYS 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 40.9 + - + +
141B SER* 3.2 17.3 - - - +
142B ARG 3.2 0.2 - - - -
143B TYR* 1.3 85.8 - - + +
145B ARG* 1.3 65.7 + - + +
334B GLU* 4.4 14.8 + - - +
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Residues in contact with ARG 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 SER* 3.3 11.4 + - - +
142B ARG* 3.3 26.4 + - - +
144B LYS* 1.3 85.2 - - + +
146B LYS* 1.3 67.0 + - + +
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Residues in contact with LYS 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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142B ARG* 2.8 28.6 + - + +
143B TYR* 3.3 10.4 - - - -
145B ARG* 1.3 86.1 - - + +
147B SER* 1.3 70.8 + - - +
148B PHE* 3.3 14.6 + - + -
150B HIS* 4.6 18.6 + - - -
151B ARG* 5.8 2.6 - - - +
243B ARG* 5.0 13.7 - - - +
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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
------------------------------------------------------------
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