Contacts of the helix formed by residues 136 - 151 (chain B) in PDB entry 3MB8
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 THR 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B ALA* 1.3 70.4 - - - +
137B PRO* 1.3 76.8 - - + +
138B HIS* 3.5 32.5 - - + +
139B VAL* 3.0 14.0 + - - +
140B TYR* 3.1 11.1 + - - +
197B GLN* 3.7 16.9 + - - +
201B ILE 4.2 0.5 + - - -
202B ALA* 3.3 11.4 - - + -
203B THR* 2.8 34.4 + - - +
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Residues in contact with PRO 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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135B ALA 3.6 8.0 - - - +
136B THR* 1.3 91.0 - - + +
138B HIS* 1.3 57.4 + - - +
140B TYR* 3.3 9.1 + - + +
141B GLN* 2.9 35.0 + - + +
197B GLN* 5.6 0.4 - - - +
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Residues in contact with HIS 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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90B VAL* 5.4 1.0 - - - +
136B THR* 3.3 28.2 - - + +
137B PRO* 1.3 79.3 - - - +
139B VAL* 1.3 67.3 + - + +
141B GLN* 3.8 9.0 - - - +
142B ALA* 3.1 26.2 + - - +
202B ALA* 4.1 12.7 - - + +
246B LEU* 3.9 21.6 - - + +
249B GLN* 4.8 11.5 + - - -
250B TYR* 5.2 7.0 + - - -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 4.4 7.9 - - + -
92B ILE* 3.7 29.2 - - + -
136B THR* 3.0 11.1 + - - +
138B HIS* 1.3 89.0 - - + +
140B TYR* 1.3 64.4 + - - +
142B ALA* 3.2 6.8 + - - +
143B LEU* 3.2 22.2 + - - +
202B ALA* 3.6 31.2 - - + -
203B THR* 3.8 13.5 - - - +
204B CYS* 3.6 20.0 - - + -
246B LEU* 4.3 8.5 - - + -
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Residues in contact with TYR 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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112B VAL* 3.6 28.3 - - + -
114B TYR* 3.7 28.7 - + + -
135B ALA* 4.6 4.7 - - + -
136B THR 3.1 11.3 + - - +
137B PRO* 3.5 11.2 - - + +
139B VAL* 1.3 75.5 - - - +
141B GLN* 1.3 80.8 + - - +
143B LEU* 3.3 4.7 + - - +
144B MET* 3.0 50.2 + - + +
156B SER* 2.6 35.6 + - - -
204B CYS* 3.7 18.6 - - - +
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Residues in contact with GLN 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 PRO* 2.9 24.3 + - + +
138B HIS* 3.8 9.4 - - - +
139B VAL 3.2 0.2 - - - -
140B TYR* 1.3 100.1 - - - +
142B ALA* 1.3 56.6 + - - +
144B MET* 4.0 4.8 - - - +
145B ASP* 2.8 57.5 + - - +
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Residues in contact with ALA 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 HIS 3.1 18.2 + - - +
139B VAL 3.2 5.3 + - - +
141B GLN* 1.3 72.3 - - - +
143B LEU* 1.3 60.1 + - - +
145B ASP* 3.9 5.4 - - - +
146B ALA* 3.0 30.3 + - - +
242B ALA* 3.5 13.5 - - + +
245B ASN* 5.6 6.4 + - + +
246B LEU* 4.1 30.3 - - + -
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Residues in contact with LEU 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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92B ILE* 4.1 27.4 - - + -
112B VAL* 4.3 16.8 - - + -
139B VAL 3.2 8.3 + - - +
140B TYR 3.3 6.0 + - - +
142B ALA* 1.3 75.3 - - - +
144B MET* 1.3 63.4 + - - +
146B ALA 3.3 0.7 + - - -
147B ALA* 3.0 20.6 + - - +
204B CYS* 3.7 37.9 - - + -
205B GLY 4.3 4.5 - - - +
206B ILE* 4.6 6.7 - - + -
238B ILE* 3.4 20.3 - - + +
239B THR* 3.9 24.5 - - - +
242B ALA* 3.7 20.6 - - + -
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.7 31.4 - - + -
140B TYR* 3.0 55.5 + - + +
141B GLN* 4.0 7.9 - - - +
143B LEU* 1.3 76.2 - - - +
145B ASP* 1.3 60.2 + - - +
147B ALA* 3.3 5.8 + - + +
148B LYS* 2.9 29.6 + - - +
154B ALA* 3.8 25.8 - - + +
155B ALA 4.5 3.6 - - - +
156B SER* 4.6 6.3 - - - -
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Residues in contact with ASP 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 GLN* 2.8 43.4 + - - +
142B ALA* 4.0 5.8 - - - +
144B MET* 1.3 77.4 - - - +
146B ALA* 1.3 57.7 + - - +
148B LYS* 3.5 13.0 + - - +
149B GLU* 3.0 29.6 + - - +
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Residues in contact with ALA 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 ALA 3.0 18.6 + - - +
143B LEU 3.6 4.0 - - - +
144B MET 3.2 0.2 - - - -
145B ASP* 1.3 74.7 - - - +
147B ALA* 1.3 65.6 + - - +
149B GLU* 3.3 2.9 + - - +
150B LEU* 3.0 31.2 + - - +
238B ILE* 3.5 26.7 - - + +
241B LYS* 3.8 26.5 - - + -
242B ALA* 3.9 4.0 - - + +
245B ASN* 5.6 2.9 - - - +
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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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112B VAL* 5.9 0.2 - - + -
143B LEU 3.0 13.4 + - - +
144B MET* 3.5 11.4 - - + +
146B ALA* 1.3 75.3 - - - +
148B LYS* 1.3 62.7 + - - +
150B LEU* 3.3 2.1 + - - -
151B GLY 3.0 18.5 + - - -
152B ILE* 3.0 28.3 + - - +
154B ALA* 3.9 16.2 - - + -
238B ILE* 3.8 27.9 - - + +
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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 MET 2.9 17.3 + - - +
145B ASP* 3.8 14.1 - - - +
147B ALA* 1.3 76.1 - - - +
149B GLU* 1.3 63.7 + - - +
151B GLY* 3.1 14.1 + - - -
152B ILE 5.2 0.4 - - - -
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Residues in contact with GLU 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 ASP 3.0 19.4 + - - +
146B ALA* 3.7 6.5 - - - +
148B LYS* 1.3 77.0 - - - +
150B LEU* 1.3 61.2 + - - +
151B GLY* 3.4 0.3 + - - -
241B LYS* 3.3 32.5 + - + +
245B ASN* 5.7 2.0 + - - -
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Residues in contact with LEU 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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59B TYR* 5.9 1.6 - - - +
146B ALA 3.0 20.2 + - - +
147B ALA 3.9 2.5 - - - +
149B GLU* 1.3 75.1 - - - +
151B GLY* 1.3 62.4 + - - +
152B ILE* 3.5 27.0 + - + +
237B LYS* 3.7 39.5 - - + +
238B ILE* 3.9 10.5 - - + +
241B LYS* 3.6 28.5 - - + -
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Residues in contact with GLY 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 3.0 4.6 + - - -
148B LYS* 3.1 12.7 + - - -
149B GLU 3.2 1.4 + - - -
150B LEU* 1.3 79.1 - - - +
152B ILE* 1.3 61.1 + - - +
153B GLU 4.0 1.2 + - - -
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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