Contacts of the helix formed by residues 262 - 274 (chain B) in PDB entry 1LFD
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 GLU 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B GLY 3.6 2.5 + - - +
261B GLN* 1.3 71.7 - - - +
263B GLU* 1.3 67.4 + - - +
264B TYR 3.1 1.3 + - - -
265B SER* 3.1 33.9 + - - -
268B ARG* 2.9 32.5 + - - +
44C THR* 5.1 1.7 - - - +
47C ARG* 3.5 22.7 - - + +
48C LYS* 3.3 31.6 - - + +
51C ASP* 3.6 25.6 - - + +
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLN* 3.0 20.6 - - + +
262B GLU* 1.3 80.6 - - - +
264B TYR* 1.3 83.6 + - + +
265B SER 3.5 0.2 - - - -
33C SER 5.3 0.4 - - - -
34C ILE* 3.4 23.5 - - - +
35C LEU* 2.6 44.8 + - + +
37C THR* 4.4 5.2 - - - +
48C LYS* 2.8 36.8 + - - +
52C LYS* 4.7 12.5 + - - +
233D ASP* 5.3 2.1 - - - +
234D PRO 5.9 1.6 - - - +
236D ILE* 4.4 8.0 - - + +
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.1 16.2 - - + -
35A LEU* 4.6 2.1 - - - +
235B THR 4.1 2.9 - - - -
236B ILE* 3.7 46.5 - - + +
259B ALA* 3.7 31.2 - - + +
261B GLN* 3.4 31.0 + - + -
262B GLU 3.1 0.8 - - - -
263B GLU* 1.3 93.1 - - + +
265B SER* 1.3 60.4 + - - +
266B ALA 3.4 3.5 + - - +
267B MET* 3.6 30.8 + - - +
268B ARG* 4.5 3.5 + - - +
271B TYR* 5.6 1.4 - - - -
35C LEU* 3.5 31.1 - - + +
37C THR* 5.5 5.8 - - + -
261D GLN* 5.6 2.9 + - - -
263D GLU* 4.5 5.2 + - - +
264D TYR* 4.4 9.2 + - - -
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Residues in contact with SER 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLU* 3.1 36.6 + - - -
263B GLU 3.5 0.8 - - - -
264B TYR* 1.3 73.6 - - - +
266B ALA* 1.3 63.1 + - - +
267B MET 3.0 6.1 - - - -
268B ARG* 3.1 50.6 + - - +
269B ASP* 4.7 0.5 + - - +
299B GLN* 4.9 0.7 - - - +
44C THR* 3.4 23.6 - - - +
48C LYS* 4.0 1.4 - - - +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR 3.4 1.0 - - - -
265B SER* 1.3 80.7 + - - +
267B MET* 1.3 62.5 + - + +
268B ARG 3.3 0.4 - - - -
269B ASP* 4.3 9.3 + - - +
270B GLN* 4.0 11.5 - - - +
37C THR* 3.7 17.0 - - + +
39C GLN* 4.7 19.5 - - + +
40C ASP* 3.1 27.6 - - - +
44C THR* 5.1 4.3 - - + -
48C LYS* 5.5 0.6 - - - +
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Residues in contact with MET 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.4 24.5 - - + -
236B ILE* 4.4 14.1 - - + +
237B GLU* 3.9 40.4 - - + +
264B TYR* 3.7 33.0 - - - +
265B SER 3.0 0.8 - - - -
266B ALA* 1.3 80.8 - - + +
268B ARG* 1.3 63.9 + - - +
269B ASP 3.4 0.7 - - - -
270B GLN* 3.3 21.9 + - - +
271B TYR* 3.2 31.4 + - + +
37C THR* 6.1 3.4 - - + -
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Residues in contact with ARG 268 (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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259B ALA 5.2 3.4 + - - -
260B GLY 4.4 3.8 + - - -
261B GLN 4.3 5.3 + - - -
262B GLU* 2.9 42.0 + - - +
264B TYR 4.7 1.8 + - - +
265B SER* 3.1 34.3 + - - +
267B MET* 1.3 78.1 - - - +
269B ASP* 1.3 64.6 + - - +
271B TYR* 3.5 28.3 + - + +
272B MET* 2.9 39.7 + - + +
296B TYR* 3.5 31.1 + - - -
299B GLN* 3.4 39.2 + - - +
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Residues in contact with ASP 269 (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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265B SER 4.7 0.5 + - - +
266B ALA 4.3 8.1 + - - +
267B MET 3.4 0.6 - - - -
268B ARG* 1.3 77.6 - - - +
270B GLN* 1.3 64.8 + - + +
272B MET 3.5 0.2 + - - -
273B ARG* 3.2 49.1 + - - +
299B GLN* 4.2 9.5 - - - +
303B VAL* 3.5 35.1 - - - +
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Residues in contact with GLN 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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266B ALA 4.0 7.1 - - - +
267B MET* 3.3 28.3 + - - +
268B ARG 3.3 0.6 - - - -
269B ASP* 1.3 78.5 - - + +
271B TYR* 1.3 61.5 + - - +
273B ARG* 3.5 21.0 + - - +
274B THR* 3.4 24.1 + - - +
39C GLN* 3.6 31.3 + - - +
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Residues in contact with TYR 271 (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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207B VAL* 3.7 14.7 - - + +
209B VAL* 3.7 29.1 - - + +
237B GLU* 4.9 7.6 - - + +
256B LEU* 3.4 27.5 - - + +
258B THR* 3.6 29.0 + - + -
259B ALA 5.1 2.6 + - - -
264B TYR 5.6 1.3 - - - -
267B MET* 3.2 25.6 + - + +
268B ARG* 3.5 34.7 + - + +
270B GLN* 1.3 76.4 - - - +
272B MET* 1.3 80.7 + - + +
274B THR* 3.5 7.1 + - - -
275B GLY* 2.9 27.5 + - - -
278B PHE* 4.1 2.5 - + - -
296B TYR* 4.1 9.9 - - - -
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Residues in contact with MET 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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209B VAL* 5.2 0.4 - - + -
268B ARG* 2.9 36.4 + - + +
269B ASP 3.9 3.1 - - - +
270B GLN 3.3 0.2 - - - -
271B TYR* 1.3 98.0 - - + +
273B ARG* 1.3 53.2 + - - +
275B GLY 3.7 0.3 - - - +
278B PHE* 3.4 14.0 - - + -
296B TYR* 4.1 14.1 - - + -
299B GLN* 3.6 44.9 - - + +
300B ILE* 3.7 38.4 - - + -
303B VAL* 3.9 16.6 - - + -
304B LYS* 2.7 40.5 + - + +
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Residues in contact with ARG 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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269B ASP* 3.2 54.6 + - - +
270B GLN* 3.6 19.2 - - - +
271B TYR 3.3 0.2 - - - -
272B MET* 1.3 78.0 - - - +
274B THR* 1.3 61.9 + - + +
303B VAL* 3.5 23.2 + - + +
304B LYS* 2.8 21.2 + - - +
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Residues in contact with THR 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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205B LYS* 3.3 30.5 - - - -
256B LEU* 5.7 1.9 - - - +
270B GLN 3.4 16.6 + - - +
271B TYR* 3.5 9.2 + - - +
273B ARG* 1.3 79.3 - - + +
275B GLY* 1.3 66.6 + - - +
276B GLU* 3.5 4.0 + - - +
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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