Contacts of the helix formed by residues 258 - 269 (chain B) in PDB entry 4U7D
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 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B TRP* 6.1 2.5 - - + -
256B THR 4.2 1.0 - - - -
257B ALA* 1.3 75.0 - - - +
259B ASN* 1.3 62.8 + - + +
260B HIS* 3.0 16.8 - - + +
261B VAL* 2.7 42.2 + - + +
262B LEU* 2.9 13.7 + - - +
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Residues in contact with ASN 259 (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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257B ALA 4.1 0.8 + - - -
258B THR* 1.3 77.8 - - + +
260B HIS* 1.3 67.5 + - + +
262B LEU* 3.7 12.8 + - - +
263B THR* 3.0 40.4 + - - -
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Residues in contact with HIS 260 (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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225B SER* 4.5 0.2 + - - -
227B TRP* 4.2 34.3 - + + -
258B THR* 3.0 10.3 - - + +
259B ASN* 1.3 85.9 - - + +
261B VAL* 1.3 61.6 + - - +
262B LEU 3.5 0.2 - - - -
263B THR* 4.1 8.3 - - + -
264B ASP* 3.1 32.3 + - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B HIS* 3.9 31.9 - - + +
225B SER* 3.7 22.0 - - - -
227B TRP* 4.1 25.8 - - + +
228B GLY* 4.5 7.9 - - - +
256B THR 4.9 3.6 - - - +
257B ALA* 5.0 1.3 - - - -
258B THR* 2.7 34.1 + - + +
260B HIS* 1.3 80.0 - - + +
262B LEU* 1.3 59.4 + - + +
264B ASP* 3.5 2.4 + - - +
265B ALA* 3.0 26.4 + - + +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.5 32.9 - - + -
112B VAL* 3.8 23.6 - - + -
221B VAL* 4.6 7.4 - - + -
254B THR* 4.4 12.6 - - + -
257B ALA* 3.8 22.9 - - + +
258B THR 2.9 16.2 + - - +
259B ASN* 3.9 13.0 - - - +
261B VAL* 1.3 74.2 - - + +
263B THR* 1.3 58.1 + - - +
264B ASP 3.0 1.6 - - - -
265B ALA* 3.1 1.0 + - - -
266B GLN* 2.8 37.8 + - - +
276B THR* 3.9 23.8 - - + +
278B THR* 5.7 0.2 - - - +
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Residues in contact with THR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 3.0 28.2 + - - -
260B HIS* 4.2 8.3 - - + -
261B VAL 3.4 0.2 - - - -
262B LEU* 1.3 78.5 - - - +
264B ASP* 1.3 66.9 + - - +
266B GLN* 3.6 11.5 + - - +
267B LYS* 3.2 35.6 + - + +
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Residues in contact with ASP 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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225B SER* 3.2 29.1 + - - +
226B GLN 5.3 0.2 + - - -
227B TRP* 3.3 19.7 + - - -
260B HIS* 3.1 20.1 + - - +
261B VAL 3.5 3.5 + - - +
262B LEU 3.0 0.6 - - - -
263B THR* 1.3 83.2 - - - +
265B ALA* 1.3 60.3 + - - +
266B GLN 3.2 1.1 - - - -
267B LYS* 3.0 9.6 + - - +
268B ILE* 2.8 37.0 + - + +
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Residues in contact with ALA 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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110B PHE* 4.0 8.7 - - + -
221B VAL* 3.9 40.4 - - + +
224B CYS* 4.2 15.6 - - + +
261B VAL* 3.0 17.8 + - + +
262B LEU* 3.7 4.7 - - + +
264B ASP* 1.3 75.6 - - - +
266B GLN* 1.3 57.8 + - - +
268B ILE* 3.9 0.8 - - - +
269B LEU* 3.0 36.6 + - - +
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Residues in contact with GLN 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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110B PHE* 3.7 14.6 - - + -
262B LEU 2.8 18.4 + - - +
263B THR* 3.6 11.5 + - - +
265B ALA* 1.3 77.8 - - - +
267B LYS* 1.3 59.5 + - + +
269B LEU 3.9 0.2 + - - -
270B CYS 3.4 1.4 + - - -
271B ILE* 2.8 60.0 + - + +
272B GLU* 3.4 33.5 + - - +
274B CYS* 3.7 28.5 - - + +
276B THR* 5.2 3.5 + - - -
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Residues in contact with LYS 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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263B THR* 3.2 24.7 - - + +
264B ASP* 3.0 11.7 + - - +
266B GLN* 1.3 76.3 - - + +
268B ILE* 1.3 66.6 + - + +
269B LEU 3.1 1.6 - - - -
270B CYS* 3.0 18.9 + - - +
271B ILE 5.2 0.7 - - - -
272B GLU* 5.3 8.5 + - - -
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Residues in contact with ILE 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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224B CYS* 4.2 26.0 - - + +
225B SER* 5.9 0.7 - - - -
235B TYR 3.5 25.4 - - - +
236B LYS* 3.7 35.8 - - + +
239B GLY* 3.1 19.5 - - - +
264B ASP* 2.8 28.8 + - + +
265B ALA* 3.9 6.1 - - - +
267B LYS* 1.3 73.0 - - + +
269B LEU* 1.3 59.0 + - + +
270B CYS* 3.2 4.6 + - - -
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Residues in contact with LEU 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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110B PHE* 4.2 4.5 - - + -
218B VAL* 4.7 14.6 - - + -
221B VAL* 3.7 28.3 - - + -
224B CYS* 4.6 11.7 - - - -
235B TYR 4.9 0.4 - - - +
238B LEU* 3.7 35.8 - - + +
239B GLY* 3.7 11.6 - - - +
241B LEU* 5.6 0.4 - - + -
242B LYS* 3.9 13.3 + - - +
250B LEU* 4.4 18.3 - - + +
265B ALA 3.0 20.0 + - - +
268B ILE* 1.3 77.3 - - - +
270B CYS* 1.3 72.7 + - - +
271B ILE* 3.6 27.1 + - + +
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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