Contacts of the helix formed by residues 140 - 155 (chain B) in PDB entry 5M2C
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 ALA 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLN* 3.8 17.3 - - + +
134B ALA* 4.7 0.2 - - - -
137B ASP* 3.0 33.2 + - + +
139B ASP* 1.3 73.5 - - - +
141B ASN* 1.3 59.4 + - - +
142B ASN* 3.3 2.9 - - - -
143B ALA* 3.3 14.1 + - + +
144B LYS* 3.1 27.7 + - - +
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Residues in contact with ASN 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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138B ASP 3.7 7.2 - - - +
139B ASP* 2.9 32.2 + - - +
140B ALA* 1.3 69.5 - - - +
142B ASN* 1.3 65.3 + - - +
144B LYS* 3.7 15.1 - - + +
145B ALA* 3.1 23.4 + - - +
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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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199A SER* 3.9 17.0 - - - +
133B GLN* 5.8 1.0 + - - -
140B ALA 3.3 0.6 - - - -
141B ASN* 1.3 76.6 - - - +
143B ALA* 1.3 66.9 + - - +
145B ALA* 3.2 7.2 + - - +
146B VAL* 3.0 33.1 + - - +
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Residues in contact with ALA 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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130B ALA* 3.7 13.9 - - - +
133B GLN* 3.6 39.7 - - + +
134B ALA* 3.9 6.1 - - - +
140B ALA* 3.3 13.7 + - + +
142B ASN* 1.3 84.4 - - - +
144B LYS* 1.3 56.3 + - - +
146B VAL* 3.3 5.5 + - - +
147B VAL* 2.9 34.8 + - - +
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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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134B ALA* 3.3 29.9 + - + +
137B ASP 4.9 0.7 - - - +
138B ASP* 2.8 44.6 + - - +
140B ALA 3.1 14.2 + - - +
141B ASN* 3.7 18.4 - - - +
142B ASN 3.2 0.2 - - - -
143B ALA* 1.3 78.8 - - - +
145B ALA* 1.3 58.7 + - - +
148B LYS* 3.0 30.9 + - - +
171B LYS* 3.2 19.2 - - - +
173B ASN* 4.0 23.6 - - - +
174B LEU* 3.8 15.3 - - + +
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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
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199A SER 4.9 2.0 - - - +
200A GLY* 3.5 22.7 - - - +
141B ASN 3.1 13.2 + - - +
142B ASN* 3.5 10.5 - - - +
144B LYS* 1.3 75.0 - - - +
146B VAL* 1.3 57.3 + - - +
148B LYS* 3.4 5.3 + - - +
149B THR* 2.8 36.4 + - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 4.4 0.9 - - - +
198A PHE 3.6 20.2 - - - +
199A SER 3.9 13.9 - - - +
200A GLY* 3.8 6.3 - - - -
126B PHE* 3.6 30.7 - - + -
127B TYR* 6.0 0.7 - - + -
130B ALA* 3.9 16.2 - - + -
142B ASN* 3.0 33.8 + - - +
143B ALA* 3.7 5.2 - - - +
145B ALA* 1.3 73.0 - - - +
147B VAL* 1.3 66.2 + - - +
149B THR* 3.2 2.9 + - - -
150B PHE* 2.9 40.4 + - + -
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Residues in contact with VAL 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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127B TYR* 4.8 4.9 - - + +
130B ALA* 3.4 36.3 - - + +
131B LEU* 3.4 19.1 - - + +
134B ALA* 3.9 6.3 - - + -
143B ALA 2.9 20.4 + - - +
144B LYS 3.9 3.4 - - - +
146B VAL* 1.3 74.8 - - - +
148B LYS* 1.3 57.6 + - - +
150B PHE* 3.3 5.8 + - - +
151B HIS* 2.9 60.8 + - + +
174B LEU* 4.4 15.5 - - + -
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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
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144B LYS 3.0 19.0 + - - +
145B ALA* 3.8 6.5 - - - +
147B VAL* 1.3 76.6 - - - +
149B THR* 1.3 58.4 + - - +
151B HIS* 3.4 1.2 + - - +
152B GLU* 2.8 37.8 + - + +
173B ASN 3.2 21.9 + - - +
174B LEU* 3.9 17.0 - - + +
175B CYS 3.3 24.7 + - - -
177B SER* 4.5 12.9 - - - +
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Residues in contact with THR 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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196A ASP* 4.0 18.4 - - + +
197A LEU* 4.0 14.8 - - + -
200A GLY* 3.3 20.3 + - - -
201A LYS 3.6 16.1 + - - +
145B ALA 2.8 20.8 + - - -
146B VAL 3.2 3.8 + - - -
148B LYS* 1.3 76.4 - - - +
150B PHE* 1.3 59.1 + - - +
152B GLU* 4.1 3.8 - - - +
153B THR* 2.7 46.6 + - - +
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Residues in contact with PHE 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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197A LEU* 3.5 46.9 - - + -
198A PHE* 4.0 24.2 - + - -
123B VAL* 3.9 21.1 - - + -
126B PHE* 4.0 13.2 - + - -
127B TYR* 3.8 37.7 - + + -
146B VAL* 2.9 38.2 + - + +
147B VAL 3.6 7.2 - - - +
149B THR* 1.3 77.6 - - - +
151B HIS* 1.3 57.8 + - - +
153B THR 3.8 0.2 - - - -
154B LEU* 2.9 56.2 + - + +
156B CYS* 4.9 0.2 - - - -
190B CYS* 5.7 0.2 - - - -
194B ILE* 4.3 3.8 - - + -
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Residues in contact with HIS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 2.6 38.3 + + - -
131B LEU* 4.3 6.1 - - + -
147B VAL* 2.9 35.9 + - + +
148B LYS 3.7 1.8 - - - +
150B PHE* 1.3 78.5 - - - +
152B GLU* 1.3 56.6 + - - +
155B ASP* 2.8 31.0 + - - -
156B CYS* 3.1 17.8 + - - +
157B CYS* 3.5 27.9 - - - -
167B THR* 4.7 0.4 - - + -
174B LEU* 2.7 31.1 + - + +
175B CYS 4.6 0.2 - - - -
176B PRO* 3.4 10.2 - - + +
190B CYS* 3.4 16.2 - - - -
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Residues in contact with GLU 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 LYS* 2.8 26.2 + - + +
149B THR* 4.1 4.7 - - + +
151B HIS* 1.3 77.9 - - - +
153B THR* 1.3 65.2 + - - +
155B ASP* 3.8 7.4 + - - +
176B PRO* 3.3 10.5 - - + +
177B SER* 3.1 35.2 + - - +
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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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153A THR* 3.6 44.1 - - + +
154A LEU* 4.2 15.5 - - + -
197A LEU* 4.1 15.9 - - + +
149B THR* 2.7 33.2 + - - +
150B PHE 3.8 2.9 - - - -
152B GLU* 1.3 80.4 - - - +
154B LEU* 1.3 62.0 + - + +
155B ASP* 3.9 0.5 + - - +
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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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153A THR* 4.2 21.5 - - + -
197A LEU* 5.6 3.4 - - + -
150B PHE* 2.9 37.6 + - + +
153B THR* 1.3 81.6 - - + +
155B ASP* 1.3 69.3 + - - +
156B CYS* 3.7 17.7 - - - -
190B CYS* 4.4 4.3 - - + +
193B LYS* 3.2 47.7 + - + +
194B ILE* 3.7 29.4 - - + -
197B LEU* 4.7 15.5 - - + -
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Residues in contact with ASP 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 HIS 2.8 13.3 + - - -
152B GLU 3.8 5.1 + - - +
153B THR 3.5 2.6 - - - +
154B LEU* 1.3 81.8 - - - +
156B CYS* 1.3 55.9 + - - +
176B PRO* 3.7 15.1 - - - +
187B LYS* 3.2 43.9 + - - +
188B GLU 4.5 0.2 - - - +
193B LYS* 3.8 14.9 + - - +
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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
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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