Contacts of the helix formed by residues 137 - 154 (chain A) in PDB entry 5M8Q
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 5.0 0.2 - - - +
135A ASP 3.8 1.6 + - - -
136A LEU* 1.3 76.1 - - - +
138A LYS* 1.3 80.0 + - - +
139A GLU* 3.3 18.9 + - - -
140A GLU* 2.9 45.5 + - - +
141A LYS* 2.9 22.9 + - - +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A SER* 1.3 86.5 - - - +
139A GLU* 1.3 88.2 + - + +
141A LYS* 3.7 7.8 + - - +
142A ASN* 3.2 20.8 + - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A SER* 3.7 10.0 + - - -
138A LYS* 1.3 106.6 + - + +
140A GLU* 1.3 59.8 + - + +
142A ASN* 3.2 7.5 + - - +
143A HIS* 2.8 31.0 + - - +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 4.4 14.9 + - - -
136A LEU* 3.9 23.4 - - + +
137A SER* 2.9 46.5 + - - +
139A GLU* 1.3 73.8 - - + +
141A LYS* 1.3 67.2 + - - +
143A HIS* 3.0 9.2 + - - +
144A PHE* 2.9 23.9 + - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.5 22.4 - - + +
134A LEU* 4.0 19.8 + - - +
136A LEU* 3.2 32.7 - - + +
137A SER 2.9 20.0 + - - +
138A LYS* 3.8 7.9 - - - +
140A GLU* 1.3 76.1 - - - +
142A ASN* 1.3 62.8 + - - +
144A PHE* 3.2 6.3 + - - +
145A VAL* 3.1 27.7 + - - +
264A ASP* 3.9 29.7 + - + +
265A LEU* 3.7 23.0 - - + +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 3.2 10.8 + - - +
139A GLU* 3.2 12.5 + - - +
141A LYS* 1.3 77.8 - - - +
143A HIS* 1.3 59.7 + - - +
145A VAL* 3.5 8.0 + - - +
146A ARG* 2.8 74.0 + - - +
264A ASP 5.2 3.1 - - - -
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU 2.8 18.0 + - - +
140A GLU* 3.0 7.0 + - - +
142A ASN* 1.3 75.8 + - - +
144A PHE* 1.3 57.7 + - - +
146A ARG* 3.6 7.8 - - + +
147A ALA* 2.7 36.1 + - - +
239A LEU* 3.4 33.6 - - + +
241A GLU* 2.7 34.1 + - - -
244A PHE* 4.1 10.6 - + - -
203C VAL* 5.7 2.0 - - + +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.3 11.2 - - + -
136A LEU* 5.0 5.4 - - + -
140A GLU 2.9 13.0 + - - +
141A LYS* 3.6 8.5 - - - +
143A HIS* 1.3 75.8 + - - +
145A VAL* 1.3 63.5 + - + +
147A ALA* 2.8 8.1 + - - +
148A LEU* 2.7 67.3 + - + +
235A MET* 5.1 0.2 - - + -
244A PHE* 3.8 20.4 - + + -
246A LEU* 4.2 15.7 - - + -
247A PRO* 3.3 40.4 - - + -
266A MET* 4.3 7.2 - - - -
401A VAL* 5.0 3.8 - - + -
402A LEU* 3.9 29.6 - - + -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS 3.1 15.5 + - - +
142A ASN* 3.7 8.5 - - - +
144A PHE* 1.3 88.2 - - + +
146A ARG* 1.3 63.2 + - + +
148A LEU* 3.2 3.0 + - - +
149A ASP* 2.9 27.5 + - - +
263A ASP 5.9 2.2 - - - +
264A ASP 3.7 20.6 - - - +
265A LEU* 3.8 19.1 - - + -
266A MET* 4.4 6.1 - - - +
281A SER* 5.6 1.3 - - - +
282A VAL* 3.9 25.8 - - + -
283A PHE* 4.1 15.8 - - + -
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASN* 2.8 56.6 + - - +
143A HIS* 3.9 8.1 - - + +
145A VAL* 1.3 77.8 - - + +
147A ALA* 1.3 56.8 + - - +
149A ASP* 3.9 6.4 - - - +
150A MET* 3.0 34.0 + - + +
153A ARG* 5.1 1.2 + - - -
282A VAL* 6.4 2.0 - - + -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 2.7 22.1 + - - +
144A PHE 2.8 6.4 + - - +
146A ARG* 1.3 71.2 - - - +
148A LEU* 1.3 66.2 + - - +
150A MET* 3.0 8.4 + - - +
151A ALA* 2.8 22.7 + - - +
235A MET* 3.5 20.0 - - + +
238A MET* 3.9 2.4 - - - +
239A LEU* 3.8 31.6 - - + -
244A PHE* 4.1 6.5 - - + -
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 2.7 49.9 + - + +
145A VAL 3.6 7.2 - - - +
147A ALA* 1.3 70.9 - - - +
149A ASP* 1.3 63.9 + - - +
151A ALA* 3.0 6.6 + - - +
152A LYS 3.0 18.2 + - - -
185A TYR* 3.7 32.9 - - + +
231A LEU* 5.2 0.7 - - + -
235A MET* 3.6 20.2 - - + +
266A MET* 3.9 3.8 - - + -
283A PHE* 3.9 18.8 - - + -
286A TRP* 3.6 9.8 - - + -
398A PRO* 3.7 27.1 - - + +
401A VAL* 4.5 9.4 - - + -
402A LEU* 5.5 0.2 - - + -
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL 2.9 16.3 + - - +
146A ARG* 3.9 7.6 - - - +
148A LEU* 1.3 75.8 - - - +
150A MET* 1.3 63.1 + - - +
152A LYS* 3.1 11.8 + - - +
153A ARG* 3.2 47.2 + - - +
282A VAL* 3.9 35.4 - - + +
285A GLN* 5.3 4.5 - - - +
286A TRP* 2.9 32.6 + - + +
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 3.0 22.1 + - + +
147A ALA* 3.0 4.9 + - - +
149A ASP* 1.3 76.2 - - - +
151A ALA* 1.3 61.7 + - - +
153A ARG* 3.2 31.0 + - - +
154A THR* 2.8 40.4 + - - +
238A MET* 3.9 26.5 - - + +
239A LEU* 4.0 24.7 - - + -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ALA 2.8 12.7 + - - +
148A LEU* 3.0 11.2 + - - +
150A MET* 1.3 76.9 - - - +
152A LYS* 1.3 62.0 + - - +
153A ARG 3.4 0.2 + - - -
154A THR 3.7 2.6 + - - -
184A ILE* 3.3 23.2 + - + +
185A TYR* 3.1 28.1 + - + -
231A LEU* 5.2 0.2 - - + -
235A MET* 4.2 22.0 - - + -
238A MET* 3.5 19.4 - - - -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU 3.0 5.5 + - - -
149A ASP 3.1 10.5 + - - +
151A ALA* 1.3 77.5 - - - +
153A ARG* 1.3 61.2 + - + +
183A SER* 2.9 21.8 + - - -
185A TYR* 3.7 13.1 - - + +
186A ASN* 2.4 37.2 + - - +
286A TRP* 3.7 54.2 - - + +
287A ARG 3.1 33.2 + - - +
288A VAL* 4.7 0.4 - - - +
289A VAL 5.0 0.2 - - - +
307A GLU* 3.3 23.4 - - - +
396A ASN* 4.2 11.5 + - - +
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG 5.1 1.0 + - - -
149A ASP* 3.2 42.7 + - - +
150A MET* 3.2 36.5 + - - +
152A LYS* 1.3 82.2 - - + +
154A THR* 1.3 61.2 + - - +
155A THR* 3.8 1.7 + - - -
183A SER* 4.5 1.6 - - - -
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Residues in contact with THR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A MET* 2.8 34.0 + - - +
151A ALA 4.5 0.2 - - - -
152A LYS 3.5 0.8 - - - -
153A ARG* 1.3 79.6 + - - +
155A THR* 1.3 73.1 + - - +
157A PRO* 6.0 0.2 - - + -
183A SER* 3.3 2.5 - - - -
184A ILE* 2.9 47.1 + - + +
238A MET* 4.3 10.2 - - + +
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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