Contacts of the helix formed by residues 269 - 282 (chain B) in PDB entry 1ML3
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 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B THR* 1.3 79.8 - - - +
270B ILE* 1.3 65.4 + - - +
271B GLN* 3.3 18.8 + - - +
272B GLU* 2.9 29.7 + - - +
273B ILE* 3.2 15.2 + - - +
323B GLU 4.0 9.6 - - - -
327B PHE* 4.0 6.1 - - - -
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Residues in contact with ILE 270 (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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269B SER* 1.3 73.5 - - - +
271B GLN* 1.3 85.3 + - - +
273B ILE* 3.3 18.2 + - + -
274B ASP* 2.8 28.0 + - - +
310B TYR* 5.3 0.2 - - - +
315B THR* 3.7 23.6 - - + +
316B LEU* 3.8 17.0 - - + +
319B ASN* 3.6 41.3 - - + +
320B LEU 5.9 1.8 - - - +
323B GLU 4.8 0.2 + - - -
327B PHE* 3.6 26.2 - - + -
328B LYS 4.0 3.6 - - - +
329B ILE* 4.7 1.6 - - + -
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Residues in contact with GLN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 3.1 18.1 + - - +
270B ILE* 1.3 98.6 - - - +
272B GLU* 1.3 58.6 + - - +
274B ASP* 3.1 8.8 + - - +
275B ALA* 2.8 32.3 + - - +
316B LEU* 3.8 15.7 + - + +
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Residues in contact with GLU 272 (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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183B PHE* 3.4 13.9 - - + -
266B ARG* 2.5 33.9 + - - -
267B ASP 4.6 0.2 - - - +
268B THR* 2.9 27.2 - - + +
269B SER* 2.9 21.6 + - - +
271B GLN* 1.3 76.0 - - - +
273B ILE* 1.3 62.4 + - - +
275B ALA* 3.5 6.1 + - - +
276B ALA* 3.1 18.4 + - - +
279B ARG* 5.6 0.2 + - - -
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Residues in contact with ILE 273 (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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178B LEU* 4.1 9.6 - - + -
183B PHE* 3.8 31.1 - - + -
262B PHE* 4.2 14.1 - - + -
268B THR* 4.5 4.3 - - - +
269B SER 3.2 12.8 + - - +
270B ILE* 3.6 15.3 - - + +
272B GLU* 1.3 76.8 - - - +
274B ASP* 1.3 63.9 + - - +
276B ALA* 3.3 3.5 + - - +
277B LEU* 3.0 32.5 + - + +
310B TYR* 5.4 1.1 - - - +
327B PHE* 3.7 38.6 - - + -
329B ILE* 3.6 27.8 - - + -
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Residues in contact with ASP 274 (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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270B ILE 2.8 17.5 + - - +
271B GLN* 3.4 5.1 - - - +
273B ILE* 1.3 78.0 - - - +
275B ALA* 1.3 64.1 + - - +
277B LEU* 3.5 1.9 + - - +
278B LYS* 3.1 47.6 + - - +
310B TYR* 2.5 35.6 + - - +
312B SER* 2.5 26.2 + - - -
316B LEU* 4.0 20.0 - - + +
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Residues in contact with ALA 275 (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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271B GLN 2.8 19.6 + - - +
272B GLU* 3.8 7.0 - - - +
274B ASP* 1.3 75.7 + - - +
276B ALA* 1.3 57.3 + - - +
278B LYS* 3.5 7.0 + - - +
279B ARG* 3.0 40.0 + - - +
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Residues in contact with ALA 276 (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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177B VAL* 4.2 4.2 - - + +
181B GLU* 4.1 9.3 - - + +
183B PHE* 3.5 33.4 - - + -
272B GLU 3.1 11.9 + - - +
273B ILE 3.5 2.2 - - - +
274B ASP 3.3 0.2 - - - -
275B ALA* 1.3 75.8 - - - +
277B LEU* 1.3 66.2 + - - +
279B ARG* 3.3 29.9 + - - +
280B ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 277 (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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174B ILE* 4.0 22.0 - - + +
177B VAL* 3.7 30.3 - - + -
178B LEU* 5.4 3.4 - - + +
273B ILE* 3.0 33.7 + - + +
274B ASP 3.9 3.6 - - - +
276B ALA* 1.3 75.8 - - + +
278B LYS* 1.3 58.6 + - - +
280B ALA* 3.2 2.8 + - - +
281B SER* 2.9 30.2 + - - -
289B LEU* 3.7 19.2 - - + +
291B TYR* 5.5 0.9 - - - -
310B TYR* 3.6 47.3 - - + -
329B ILE* 4.1 13.0 - - + -
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Residues in contact with LYS 278 (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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274B ASP* 3.1 40.3 + - - +
275B ALA* 3.7 6.3 - - - +
276B ALA 3.2 0.2 - - - -
277B LEU* 1.3 77.6 - - - +
279B ARG* 1.3 61.7 + - - +
281B SER* 2.8 23.2 + - - -
282B LYS* 3.1 19.4 + - - +
291B TYR* 3.7 45.1 - - + +
293B ASP* 4.9 8.3 + - - +
310B TYR* 4.5 3.8 - - + -
312B SER* 3.3 24.4 + - - -
316B LEU* 5.2 2.8 - - - +
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Residues in contact with ARG 279 (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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181B GLU* 2.6 37.0 + - - +
183B PHE* 5.7 1.0 - - - -
275B ALA* 3.0 27.4 + - - +
276B ALA* 3.6 25.3 - - - +
278B LYS* 1.3 76.4 - - - +
280B ALA* 1.3 55.3 + - - +
282B LYS* 3.4 10.3 + - - +
283B THR* 2.7 41.3 + - + +
284B TYR* 6.2 0.9 - - + -
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Residues in contact with ALA 280 (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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177B VAL* 3.9 17.9 - - + -
181B GLU* 4.6 0.6 + - - +
276B ALA 2.9 18.6 + - - +
277B LEU 3.6 4.9 - - - +
279B ARG* 1.3 75.4 - - - +
281B SER* 1.3 63.0 + - - +
283B THR* 3.1 11.4 + - - -
284B TYR* 3.4 34.6 + - + +
285B MET* 2.8 31.5 + - + -
289B LEU* 4.6 0.2 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU 2.9 14.1 + - - -
278B LYS 2.8 14.4 + - - -
280B ALA* 1.3 76.0 - - - +
282B LYS* 1.3 57.9 + - - +
285B MET* 4.1 5.4 - - - +
286B LYS* 3.1 29.1 + - - +
287B GLY 4.7 0.2 + - - -
289B LEU* 3.0 35.9 - - - +
290B GLY* 3.9 8.0 - - - -
291B TYR* 3.1 24.6 - - - -
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Residues in contact with LYS 282 (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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278B LYS* 3.1 19.8 + - - +
279B ARG* 3.7 9.6 - - - +
280B ALA 3.2 0.2 - - - -
281B SER* 1.3 85.3 + - - +
283B THR* 1.3 64.0 + - + +
286B LYS* 4.4 18.6 + - - +
291B TYR* 3.4 29.3 + - + -
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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