Contacts of the helix formed by residues 137 - 154 (chain B) in PDB entry 5M8L
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 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASP 3.8 1.2 + - - -
136B LEU* 1.3 76.2 - - - +
138B LYS* 1.3 59.3 + - - +
139B GLU* 3.4 15.1 + - - +
140B GLU* 2.7 43.6 + - - +
141B LYS* 2.8 28.2 + - - +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 3.9 0.2 + - - -
137B SER* 1.3 74.1 - - - +
139B GLU* 1.3 77.3 + - + +
141B LYS* 3.6 12.4 + - + +
142B ASN* 3.2 22.5 + - + +
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Residues in contact with GLU 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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137B SER* 3.2 13.8 + - - +
138B LYS* 1.3 94.8 + - + +
140B GLU* 1.3 60.9 + - + +
142B ASN* 3.5 6.1 + - - +
143B HIS* 3.1 27.0 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 3.8 12.1 + - - -
136B LEU* 3.6 29.1 - - + +
137B SER* 2.7 42.4 + - - +
139B GLU* 1.3 74.8 - - + +
141B LYS* 1.3 65.3 + - - +
143B HIS* 3.1 7.6 + - - +
144B PHE* 2.9 24.6 + - - +
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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
----------------------------------------------------------
133B LEU* 3.7 13.5 - - + +
134B LEU* 3.2 23.7 + - - +
136B LEU* 2.8 38.6 + - + +
137B SER 2.8 23.5 + - - +
138B LYS* 3.8 12.5 - - + +
140B GLU* 1.3 72.4 - - - +
142B ASN* 1.3 62.4 + - - +
144B PHE* 3.5 3.6 + - - +
145B VAL* 3.2 29.6 + - - +
264B ASP* 4.1 20.9 - - + +
265B LEU* 3.6 38.8 - - + +
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Residues in contact with ASN 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 LYS 3.2 14.4 + - - +
139B GLU* 3.8 6.7 - - - +
140B GLU 3.2 0.6 - - - -
141B LYS* 1.3 75.6 - - - +
143B HIS* 1.3 66.2 + - - +
145B VAL* 3.5 5.9 + - - +
146B ARG* 3.0 62.6 + - - +
264B ASP 5.3 1.8 - - - -
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Residues in contact with HIS 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 GLU 3.1 17.0 + - - +
140B GLU* 3.1 9.1 + - - +
142B ASN* 1.3 80.0 + - - +
144B PHE* 1.3 57.3 + - - +
146B ARG* 3.9 4.2 - - - +
147B ALA* 2.9 32.3 + - - +
239B LEU* 4.2 22.1 - - + +
241B GLU* 2.5 40.5 + - - -
244B PHE* 4.5 13.0 - + - -
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Residues in contact with PHE 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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133B LEU* 3.9 17.0 - - + -
136B LEU* 4.7 7.2 - - + -
140B GLU 2.9 15.8 + - - +
141B LYS* 4.0 3.1 - - - +
143B HIS* 1.3 78.1 - - - +
145B VAL* 1.3 66.1 + - + +
147B ALA* 3.5 3.8 + - - +
148B LEU* 3.0 64.1 + - + +
244B PHE* 4.1 19.7 - + + -
245B SER 4.9 0.2 - - - -
246B LEU* 4.5 13.5 - - + -
247B PRO* 3.4 39.5 - - + -
266B MET* 4.3 5.8 - - - -
401B VAL* 4.8 6.1 - - + -
402B LEU* 3.9 26.9 - - + -
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Residues in contact with VAL 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 3.2 18.9 + - - +
142B ASN* 3.9 7.6 - - - +
143B HIS 3.3 0.2 - - - -
144B PHE* 1.3 87.5 - - + +
146B ARG* 1.3 65.8 + - + +
148B LEU* 3.3 8.6 + - - +
149B ASP* 3.1 19.9 + - - +
263B ASP 6.1 0.9 - - - +
264B ASP 3.8 12.8 - - - +
265B LEU* 3.7 26.7 - - + +
266B MET* 5.0 1.6 - - - -
282B VAL* 3.7 26.5 - - + -
283B PHE* 4.0 14.0 - - + -
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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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142B ASN* 3.0 42.8 + - - +
143B HIS* 4.2 4.0 - - - +
145B VAL* 1.3 77.5 - - + +
147B ALA* 1.3 60.2 + - - +
149B ASP* 3.3 6.9 + - - +
150B MET* 2.8 29.0 + - - +
153B ARG* 4.9 1.4 + - - -
282B VAL* 6.4 2.2 - - + -
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Residues in contact with ALA 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 HIS* 2.9 20.9 + - + +
144B PHE 3.8 3.6 - - - +
146B ARG* 1.3 74.0 - - - +
148B LEU* 1.3 60.0 + - - +
150B MET* 3.1 6.4 + - - -
151B ALA* 2.8 26.9 + - - +
235B MET* 3.7 17.7 - - + -
238B MET* 3.5 7.8 - - + +
239B LEU* 3.8 32.8 - - + -
244B PHE* 4.0 7.4 - - + -
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Residues in contact with LEU 148 (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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144B PHE* 3.0 53.7 + - + +
145B VAL* 3.3 8.5 + - - +
147B ALA* 1.3 74.5 - - - +
149B ASP* 1.3 58.1 + - - +
151B ALA* 3.2 5.3 + - - +
152B LYS 3.0 21.1 + - - -
185B TYR* 4.2 26.8 - - + +
231B LEU* 5.1 0.7 - - + -
235B MET* 3.7 18.3 - - + +
266B MET* 3.7 12.8 - - + -
283B PHE* 3.7 28.0 - - + -
286B TRP* 3.6 12.7 - - + -
398B PRO* 3.9 8.1 - - + +
401B VAL* 4.7 9.4 - - + -
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Residues in contact with ASP 149 (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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145B VAL 3.1 12.9 + - - +
146B ARG* 3.7 10.5 - - - +
147B ALA 3.2 0.2 - - - -
148B LEU* 1.3 74.2 - - - +
150B MET* 1.3 66.1 + - - +
152B LYS* 3.2 6.9 + - - +
153B ARG* 2.9 54.1 + - - +
282B VAL* 4.0 30.2 - - + +
283B PHE* 4.9 0.2 - - - -
285B GLN* 5.2 3.3 - - - +
286B TRP* 3.0 34.5 + - + +
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Residues in contact with MET 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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146B ARG 2.8 17.2 + - - +
147B ALA* 3.1 5.4 + - - +
149B ASP* 1.3 75.1 - - - +
151B ALA* 1.3 64.4 + - - +
153B ARG* 3.1 26.2 + - - +
154B THR* 2.7 44.7 + - + +
238B MET* 3.6 40.6 - - + +
239B LEU* 4.5 12.3 - - - -
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Residues in contact with ALA 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 ALA 2.8 13.1 + - - +
148B LEU* 3.5 10.5 - - - +
150B MET* 1.3 77.0 - - - +
152B LYS* 1.3 62.8 + - - +
153B ARG 3.4 0.3 + - - -
154B THR 3.9 1.5 + - - +
183B SER* 3.7 0.5 - - - -
184B ILE* 3.2 33.7 + - + +
185B TYR* 2.9 29.9 + - + -
235B MET* 4.2 14.1 - - + -
238B MET* 3.4 16.5 - - + -
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Residues in contact with LYS 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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148B LEU 3.0 4.8 + - - -
149B ASP 3.4 10.8 - - - +
150B MET 3.1 0.4 - - - -
151B ALA* 1.3 78.1 - - - +
153B ARG* 1.3 61.2 + - + +
183B SER* 3.0 18.7 + - - -
185B TYR* 3.8 10.2 - - + +
186B ASN* 3.1 28.6 + - - +
286B TRP* 3.5 69.9 - - + +
287B ARG 2.8 30.2 + - - +
288B VAL* 4.5 0.8 - - - +
307B GLU* 3.1 18.0 + - - +
396B ASN* 4.5 8.9 + - - -
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Residues in contact with ARG 153 (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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146B ARG 4.9 1.2 + - - -
149B ASP* 2.9 48.0 + - - +
150B MET* 3.1 30.8 + - - +
152B LYS* 1.3 84.0 - - + +
154B THR* 1.3 64.6 + - - +
155B THR* 3.7 2.8 + - - -
183B SER* 4.3 2.8 - - - -
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Residues in contact with THR 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 MET* 2.7 42.4 + - + +
151B ALA 3.9 0.4 + - - -
152B LYS 3.7 0.2 - - - -
153B ARG* 1.3 79.2 + - - +
155B THR* 1.3 78.7 + - - +
157B PRO* 6.0 0.2 - - + -
183B SER* 3.1 3.1 - - - -
184B ILE* 3.0 32.5 + - + +
238B MET* 4.4 13.5 - - + -
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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