Contacts of the helix formed by residues 260 - 268 (chain B) in PDB entry 1N1E
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 GLY 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ALA* 3.6 16.6 - - - -
210B LYS* 5.3 0.2 - - - +
238B LEU* 4.2 6.7 - - - -
241B ILE* 4.9 2.0 - - - +
254B ALA 3.3 9.8 + - - -
255B VAL* 3.4 12.6 - - - -
258B LEU 3.3 0.2 - - - -
259B ALA* 1.3 78.6 - - - +
261B LEU* 1.3 67.3 + - - +
262B GLY 3.2 1.2 + - - -
263B ASP 3.4 0.9 + - - -
264B LEU* 2.8 29.4 + - - +
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Residues in contact with LEU 261 (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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234A ILE* 4.2 18.4 - - + -
235A MET* 4.2 22.2 - - - -
238A LEU* 3.5 21.1 - - + -
256A PHE* 4.0 11.0 - - + -
261A LEU* 3.2 38.6 - - + -
265A GLN* 6.3 0.2 - - + -
234B ILE* 5.4 1.9 - - + +
238B LEU* 3.9 13.9 - - + +
255B VAL 2.9 16.6 + - - +
256B PHE* 3.9 11.9 - - + +
257B GLY 3.2 7.4 + - - +
260B GLY* 1.3 71.1 - - - +
262B GLY* 1.3 65.9 + - - +
264B LEU* 3.9 3.2 - - - +
265B GLN* 3.0 33.3 + - + +
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Residues in contact with GLY 262 (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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231A ALA* 3.7 11.5 - - - +
235A MET* 4.5 3.1 - - - -
154B PRO* 3.6 16.7 - - - +
257B GLY 3.0 12.9 + - - -
258B LEU* 3.5 9.9 - - - -
261B LEU* 1.3 83.6 - - - +
263B ASP* 1.3 57.7 + - - +
265B GLN* 3.4 7.9 - - - +
266B LEU* 3.1 27.9 + - - +
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Residues in contact with ASP 263 (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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125B LYS* 2.6 29.0 + - - +
153B GLY* 3.3 21.3 + - - +
154B PRO* 3.9 10.5 - - - +
207B SER* 4.5 2.3 + - - -
210B LYS* 3.3 22.9 + - + +
258B LEU 2.9 11.8 + - - +
259B ALA 3.4 20.1 - - - +
260B GLY 3.4 0.4 + - - -
262B GLY* 1.3 72.6 - - - +
264B LEU* 1.3 66.7 + - - +
266B LEU* 3.4 1.7 + - - +
267B THR* 2.9 43.1 + - - -
401B NDE 3.8 5.0 + - - -
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Residues in contact with LEU 264 (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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210B LYS* 3.8 24.5 - - + +
213B LEU* 3.7 27.1 - - + -
234B ILE* 3.4 38.8 - - + +
237B GLY 4.4 1.1 - - - -
238B LEU* 3.8 30.7 - - + +
241B ILE* 4.2 5.6 - - + -
260B GLY 2.8 21.0 + - - +
261B LEU* 3.9 2.9 - - - +
263B ASP* 1.3 76.4 - - - +
265B GLN* 1.3 62.2 + - - +
267B THR* 4.0 0.3 - - - -
268B CYS* 3.1 50.1 + - - -
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Residues in contact with GLN 265 (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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227A LEU 4.7 1.8 + - - -
230A ARG* 4.6 3.7 - - - +
231A ALA* 3.1 32.4 - - + +
234A ILE* 3.4 33.3 - - + +
265A GLN* 3.4 24.9 - - + +
269A SER* 4.0 5.0 + - - -
234B ILE* 4.1 24.9 - - + -
261B LEU* 3.0 19.4 + - + +
262B GLY* 3.4 11.7 - - - +
264B LEU* 1.3 77.7 - - - +
266B LEU* 1.3 75.8 + - - +
268B CYS 3.6 0.5 + - - -
269B SER* 2.6 34.2 + - - -
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Residues in contact with LEU 266 (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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227A LEU* 3.4 40.6 - - + +
228A ASN* 3.6 12.8 - - - +
231A ALA* 4.3 1.1 - - + -
154B PRO* 3.4 30.1 - - + -
155B SER 3.5 10.3 - - - +
156B PHE* 3.6 39.9 - - + +
262B GLY 3.1 19.0 + - - +
263B ASP* 3.6 9.2 - - - +
264B LEU 3.3 0.2 - - - -
265B GLN* 1.3 87.0 - - - +
267B THR* 1.3 61.1 + - - +
269B SER* 3.2 14.3 + - - -
270B SER* 3.8 7.8 + - - -
401B NDE 4.6 1.3 - - - +
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Residues in contact with THR 267 (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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156B PHE* 4.2 7.1 - - - -
210B LYS* 2.9 31.5 + - + +
211B ASN* 4.0 2.2 - - - +
214B ALA* 3.5 17.7 - - + +
263B ASP* 2.9 23.0 + - - -
264B LEU 4.1 1.8 - - - -
266B LEU* 1.3 80.0 - - - +
268B CYS* 1.3 60.7 + - - +
269B SER 3.2 1.3 + - - -
270B SER 3.9 1.0 - - - +
273B SER* 3.1 39.4 + - - +
276B PHE* 3.7 9.2 - - - +
401B NDE 3.3 16.4 + - - +
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Residues in contact with CYS 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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214B ALA* 3.8 23.1 - - - +
217B SER* 2.6 33.9 + - - +
230B ARG* 3.4 5.9 + - - -
233B LEU* 3.9 19.7 - - - -
234B ILE* 3.7 22.7 - - + -
264B LEU* 3.1 41.5 + - - +
267B THR* 1.3 76.2 - - - +
269B SER* 1.3 58.0 + - - +
270B SER 3.7 0.9 - - - -
276B PHE* 3.4 10.9 - - - -
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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