Contacts of the helix formed by residues 139 - 150 (chain B) in PDB entry 1M6X
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 HIS 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B GLY* 3.1 27.1 - - - +
137B ASN 2.8 0.2 - - - -
138B SER* 1.3 82.2 + - - +
140B SER* 1.3 66.0 + - - +
141B LYS 3.3 0.2 - - - -
142B LYS* 3.2 15.2 + - + +
143B MET* 3.2 38.6 + - + +
298B ILE* 3.6 33.8 - - + +
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Residues in contact with SER 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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136B GLY 3.8 14.3 + - - -
137B ASN* 3.0 15.5 + - - -
139B HIS* 1.3 80.8 - - - +
141B LYS* 1.3 64.7 + - - +
142B LYS 3.1 1.6 + - - -
143B MET 3.2 0.7 + - - -
144B LEU* 3.2 22.5 + - - +
295B ILE* 3.5 8.7 - - - +
298B ILE* 3.6 17.5 - - - +
300B ASN 5.7 0.2 - - - -
301B GLY* 3.8 6.8 - - - -
302B PRO* 3.4 27.9 - - - +
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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
----------------------------------------------------------
137B ASN* 3.2 12.5 + - - +
138B SER* 4.4 7.2 - - - +
140B SER* 1.3 80.3 - - - +
142B LYS* 1.3 61.0 + - - +
144B LEU* 4.0 11.0 - - + +
145B LYS* 3.2 31.4 + - - +
341C THR* 3.3 37.3 + - - +
342C THR* 3.6 34.8 - - - +
345C HIS* 4.7 12.1 + - + +
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Residues in contact with LYS 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 SER 3.5 14.2 + - - +
139B HIS* 3.2 17.4 + - + +
140B SER 3.1 1.0 - - - -
141B LYS* 1.3 76.4 - - - +
143B MET* 1.3 65.5 + - - +
145B LYS* 3.1 14.5 + - + +
146B ALA* 2.9 28.1 + - + +
220C THR* 5.9 4.4 - - - +
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Residues in contact with MET 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 HIS* 3.3 26.9 - - + +
140B SER 3.2 1.2 + - - +
142B LYS* 1.3 79.8 - - - +
144B LEU* 1.3 56.1 + - - +
146B ALA* 3.0 13.6 + - + +
147B LEU* 2.7 36.0 + - - +
294B PRO* 3.4 38.2 - - + +
295B ILE* 3.6 26.1 - - + +
298B ILE* 3.1 27.1 - - + -
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Residues in contact with LEU 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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140B SER* 3.2 22.9 + - - +
141B LYS* 4.0 7.4 - - + +
143B MET* 1.3 78.5 - - - +
145B LYS* 1.3 64.6 + - - +
147B LEU* 3.4 21.1 - - + +
148B LEU* 3.6 12.6 + - - +
295B ILE* 3.5 16.6 - - + -
302B PRO* 4.0 19.1 - - + -
306B ILE* 3.8 29.8 - - + -
309B HIS* 4.6 9.6 - - + +
342C THR 5.3 0.2 - - - +
345C HIS* 3.5 47.4 - - + +
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Residues in contact with LYS 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 23.3 + - - +
142B LYS* 3.1 18.7 + - + +
144B LEU* 1.3 79.7 - - - +
146B ALA* 1.3 61.2 + - - +
148B LEU 3.4 1.2 + - - -
149B SER* 2.6 33.0 + - - +
344C THR* 3.3 22.4 + - - +
345C HIS* 3.2 35.6 - - + +
346C GLN* 4.6 2.6 - - - +
347C ILE* 5.6 2.0 - - - +
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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 LYS* 2.9 14.8 + - + +
143B MET* 3.1 23.6 - - + +
145B LYS* 1.3 76.1 - - - +
147B LEU* 1.3 55.7 + - - +
149B SER* 2.5 30.8 + - - -
150B GLU* 2.9 30.4 + - + +
294B PRO* 6.3 1.3 - - + -
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Residues in contact with LEU 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 MET 2.7 14.6 + - - +
144B LEU* 3.4 17.5 - - + +
146B ALA* 1.3 73.3 - - - +
148B LEU* 1.3 78.2 + - + +
150B GLU* 3.6 16.6 + - - +
152B GLU* 4.8 3.5 - - - +
157B ILE* 3.9 20.4 - - + +
161B ILE* 5.9 1.6 - - + -
293B TYR* 3.4 49.4 - - + -
294B PRO* 5.5 4.9 - - + +
295B ILE* 4.7 10.8 - - + -
296B PHE* 6.1 0.4 - - + -
306B ILE* 4.7 15.3 - - + -
310B LEU* 4.1 17.0 - - + -
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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 LEU* 3.7 10.8 - - + +
145B LYS 3.4 3.5 + - - +
146B ALA 3.2 0.6 - - - -
147B LEU* 1.3 96.8 - - + +
149B SER* 1.3 64.5 + - - +
150B GLU 3.4 7.8 - - - +
152B GLU 4.6 5.3 - - - +
154B ILE* 3.7 22.9 - - + -
157B ILE* 3.9 8.3 - - + -
310B LEU* 4.0 5.8 - - + -
313B SER* 3.2 38.6 - - - +
345C HIS* 4.0 9.6 - - + -
346C GLN* 3.6 46.2 - - + +
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Residues in contact with SER 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 LYS* 2.6 26.1 + - - +
146B ALA* 2.5 23.6 + - - -
148B LEU* 1.3 70.3 - - - +
150B GLU* 1.3 65.9 + - - +
204C LYS* 4.9 10.9 + - - -
345C HIS 5.0 1.9 + - - -
346C GLN* 5.7 3.8 - - - +
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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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146B ALA* 2.9 27.8 + - + +
147B LEU* 3.6 9.4 + - - +
148B LEU 3.4 9.4 - - - +
149B SER* 1.3 85.0 - - - +
151B GLY* 1.3 69.2 + - - +
152B GLU* 3.7 4.2 + - + +
294B PRO* 6.0 2.3 - - - +
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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