Contacts of the helix formed by residues 147 - 163 (chain B) in PDB entry 5M7R
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 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A PHE* 3.9 20.2 - - - -
544A GLU* 3.3 33.1 + - - +
144B THR* 3.3 15.6 + - + +
146B SER* 1.3 79.9 + - - +
148B PRO* 1.4 72.2 - - - +
149B LYS* 2.9 27.7 + - - +
150B GLU* 3.1 20.6 + - + +
151B VAL* 3.1 14.2 + - - +
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Residues in contact with PRO 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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146B SER 3.4 9.1 - - - +
147B ASN* 1.4 88.3 - - - +
149B LYS* 1.3 63.1 + - - +
151B VAL* 3.8 11.9 - - + +
152B SER* 2.9 31.5 + - - -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PHE* 5.3 11.0 - - + -
147B ASN* 2.9 17.9 + - - +
148B PRO* 1.3 80.8 - - - +
150B GLU* 1.3 61.3 + - - +
152B SER* 3.4 7.4 + - - -
153B THR* 2.9 32.0 + - - +
156B ARG* 5.4 0.2 + - - -
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Residues in contact with GLU 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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538A PHE* 3.2 36.2 - - + -
107B TRP* 4.0 7.9 - - - -
108B ARG* 2.9 45.0 + - - +
142B ASP 3.8 0.5 - - - +
143B ILE* 4.1 11.2 - - + -
144B THR* 3.2 36.0 + - - +
147B ASN* 3.1 22.1 + - + +
149B LYS* 1.3 72.7 - - - +
151B VAL* 1.3 65.9 + - - +
153B THR* 3.2 8.6 + - - -
154B LEU* 3.0 22.2 + - - +
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Residues in contact with VAL 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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143B ILE* 5.3 3.8 - - + -
145B PHE* 3.9 19.3 - - - +
146B SER 5.6 0.2 - - - -
147B ASN 3.1 13.9 + - - +
148B PRO* 3.8 12.1 - - + +
150B GLU* 1.3 77.0 - - + +
152B SER* 1.3 56.7 + - - +
154B LEU* 3.4 8.2 + - + +
155B LYS* 3.1 36.7 + - - +
198B ILE* 3.9 20.6 - - + -
201B GLU* 3.5 37.2 - - + +
202B ILE* 4.5 9.9 - - + -
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Residues in contact with SER 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 PRO 2.9 21.4 + - - -
149B LYS* 3.6 9.0 - - - -
150B GLU 3.2 0.2 - - - -
151B VAL* 1.3 75.2 - - - +
153B THR* 1.3 53.9 + - - +
155B LYS* 3.0 17.1 + - - +
156B ARG* 2.8 45.3 + - - +
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Residues in contact with THR 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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538A PHE* 6.0 1.6 - - - +
107B TRP* 4.3 3.1 - - + -
108B ARG* 3.7 51.7 - - + +
149B LYS* 2.9 19.4 + - - +
150B GLU* 3.5 14.4 + - - -
152B SER* 1.3 75.6 - - - +
154B LEU* 1.3 60.9 + - - +
156B ARG* 3.2 32.1 + - - +
157B LYS* 3.0 22.9 + - - +
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Residues in contact with LEU 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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107B TRP* 3.8 28.7 - - + -
137B ILE* 4.0 32.3 - - + -
139B PRO* 4.5 7.0 - - + -
143B ILE* 4.5 8.1 - - + -
150B GLU 3.0 11.9 + - - +
151B VAL* 3.6 11.4 - - - +
152B SER 3.2 0.2 - - - -
153B THR* 1.3 75.3 - - - +
155B LYS* 1.3 62.3 + - - +
157B LYS* 3.5 4.4 + - + +
158B LEU* 3.1 28.7 + - + +
171B LEU* 4.1 16.6 - - + -
198B ILE* 4.3 16.6 - - + -
202B ILE* 3.9 26.9 - - + -
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Residues in contact with LYS 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 VAL* 3.1 25.9 + - - +
152B SER* 3.0 17.2 + - - +
154B LEU* 1.3 73.5 - - - +
156B ARG* 1.3 55.4 + - - +
158B LEU* 3.3 3.6 + - - +
159B ASP* 2.8 38.4 + - - +
201B GLU* 2.7 36.7 + - - +
202B ILE* 3.5 18.4 - - + -
205B TYR* 3.7 59.9 - - + +
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Residues in contact with ARG 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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108B ARG 5.5 1.8 + - - -
110B MET* 3.8 34.3 - - + +
152B SER* 2.8 19.9 + - - +
153B THR* 3.3 45.4 + - - +
155B LYS* 1.3 72.4 - - - +
157B LYS* 1.3 58.0 + - - +
159B ASP* 3.3 5.6 + - - +
160B GLN* 2.9 30.7 + - - +
205B TYR* 5.9 0.2 - - - -
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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
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102B LYS* 2.9 22.9 + - - +
106B PHE 3.8 1.6 + - - -
107B TRP* 2.8 27.3 + - - +
108B ARG 5.1 2.9 - - - +
109B GLU 2.6 32.5 + - - +
110B MET* 4.4 5.1 - - - +
111B TYR* 3.6 31.0 - - + -
135B TYR* 3.6 11.0 - - + +
137B ILE* 3.6 22.2 - - + +
153B THR 3.0 11.7 + - - +
154B LEU* 3.6 11.0 - - - +
156B ARG* 1.3 78.6 - - - +
158B LEU* 1.3 63.3 - - + +
160B GLN* 3.3 15.5 + - - +
161B VAL* 3.3 21.3 + - - +
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Residues in contact with LEU 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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135B TYR* 3.8 22.9 - - + +
137B ILE* 3.9 18.2 - - + -
154B LEU* 3.1 28.1 + - + +
155B LYS* 4.0 3.1 - - - +
157B LYS* 1.3 81.9 - - + +
159B ASP* 1.3 57.3 + - - +
161B VAL* 3.3 6.4 + - - +
162B SER* 3.0 24.9 + - - -
169B PHE* 3.7 31.3 - - + -
170B ALA 5.2 0.2 - - - +
171B LEU* 4.1 13.9 - - + -
202B ILE* 3.6 31.9 - - + -
206B LEU* 4.3 19.0 - - + +
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Residues in contact with ASP 159 (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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155B LYS 2.8 20.6 + - - +
156B ARG* 3.7 5.6 - - - +
158B LEU* 1.3 76.0 - - - +
160B GLN* 1.3 65.6 + - - +
162B SER* 2.9 25.7 + - - -
163B GLN* 3.1 31.2 + - - +
205B TYR* 4.1 26.5 + - + +
206B LEU* 4.7 6.1 - - - +
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Residues in contact with GLN 160 (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 MET* 3.4 35.4 - - + +
111B TYR* 2.8 54.9 + - + +
116B ALA* 5.0 2.4 - - - +
156B ARG 2.9 14.3 + - - +
157B LYS* 3.5 11.8 - - - +
159B ASP* 1.3 75.3 + - - +
161B VAL* 1.3 60.6 + - - +
163B GLN* 3.4 22.2 + - - +
164B PHE* 3.3 41.4 + - + -
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Residues in contact with VAL 161 (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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111B TYR* 3.8 28.9 - - + -
119B LEU* 5.6 0.9 - - + -
123B ILE* 4.7 5.4 - - + -
135B TYR* 3.7 44.0 - - + -
157B LYS 3.3 10.9 + - - +
158B LEU 3.3 9.1 + - - +
159B ASP 3.2 0.8 - - - -
160B GLN* 1.3 73.7 - - - +
162B SER* 1.3 61.5 + - - +
164B PHE* 2.9 37.3 + - + +
166B CYS* 3.6 25.0 - - + +
169B PHE* 4.2 2.2 - - + -
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Residues in contact with SER 162 (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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158B LEU 3.0 7.5 + - - -
159B ASP* 2.9 34.1 + - - -
161B VAL* 1.3 76.1 - - - +
163B GLN* 1.3 58.0 + - - +
165B GLY* 2.9 21.1 + - - -
166B CYS 3.4 22.8 + - - +
169B PHE* 3.8 13.6 - - - -
206B LEU* 5.0 4.7 - - - +
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Residues in contact with GLN 163 (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 MET* 6.1 1.0 - - - +
120B MET* 4.9 7.3 - - - +
159B ASP* 3.1 36.5 + - - +
160B GLN* 3.6 17.6 - - - +
161B VAL 3.1 0.4 - - - -
162B SER* 1.3 78.0 - - - +
164B PHE* 1.3 63.5 + - + +
165B GLY 3.3 0.6 + - - -
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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