Contacts of the helix formed by residues 256 - 265 (chain B) in PDB entry 3HOT
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 ALA 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA* 3.8 23.8 - - + -
252B PRO 3.5 2.4 + - - -
253B SER 3.7 4.0 + - - +
254B HIS 3.5 2.0 - - - -
255B THR* 1.3 76.1 - - - +
257B ARG* 1.3 66.8 + - - +
258B ALA* 4.1 4.3 - - + +
259B VAL* 3.0 12.9 + - + +
260B ARG* 2.9 25.1 + - - +
7G G 3.5 24.2 - - - +
8G T 3.6 10.5 - - - +
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Residues in contact with ARG 257 (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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255B THR 3.8 1.4 + - - -
256B ALA* 1.3 71.2 - - - +
258B ALA* 1.3 62.0 + - - +
260B ARG* 3.0 46.6 + - - +
261B ASP* 3.0 42.7 + - - +
8G T 3.2 27.3 + - - +
9G A 4.2 20.0 + - - -
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 5.0 7.9 - - + -
220B GLN* 2.9 20.6 + - - +
256B ALA* 3.1 7.4 - - + +
257B ARG* 1.3 80.5 - - - +
259B VAL* 1.3 53.5 + - + +
261B ASP* 3.4 5.6 + - - +
262B THR* 2.6 35.2 + - - -
8G T 4.5 1.5 + - - +
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Residues in contact with VAL 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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216B ALA* 3.9 21.5 - - + +
219B TYR* 3.7 27.1 - - + -
220B GLN* 3.9 5.2 - - + +
223B LEU* 3.8 17.9 - - + -
253B SER 3.4 23.1 - - - +
254B HIS 4.1 9.6 - - - +
256B ALA* 3.0 15.8 + - + +
258B ALA* 1.3 71.2 - - - +
260B ARG* 1.3 58.9 + - - +
261B ASP 3.0 1.3 - - - -
262B THR* 2.8 7.4 + - - -
263B LEU* 2.7 44.7 + - + +
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Residues in contact with ARG 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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254B HIS 5.1 2.9 - - - +
255B THR* 3.5 26.7 - - - +
256B ALA 2.9 11.1 + - - +
257B ARG* 3.0 62.7 + - - +
259B VAL* 1.3 77.2 - - - +
261B ASP* 1.3 61.9 + - - +
263B LEU* 3.9 12.3 - - + +
264B GLU* 3.2 25.8 + - - +
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Residues in contact with ASP 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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257B ARG* 3.0 44.4 + - - +
258B ALA* 3.6 5.4 - - - +
259B VAL 3.0 0.8 - - - -
260B ARG* 1.3 83.2 + - - +
262B THR* 1.3 61.3 - - - +
264B GLU* 3.1 29.2 - - - +
265B THR* 3.2 17.5 + - - -
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Residues in contact with THR 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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220B GLN* 2.5 51.7 + - + +
223B LEU* 5.5 4.0 - - + -
224B ILE* 4.8 15.0 - - + -
258B ALA 2.6 9.6 + - - -
259B VAL* 2.8 11.0 + - - -
261B ASP* 1.3 73.7 - - - +
263B LEU* 1.3 66.8 + - - +
265B THR* 3.1 16.1 + - - -
266B LEU* 3.3 26.6 + - + +
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Residues in contact with LEU 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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223B LEU* 4.0 25.4 - - + -
246B PHE* 4.1 13.2 - - + -
248B HIS* 4.4 11.2 - - + +
254B HIS 5.1 1.8 - - - +
259B VAL* 2.7 41.6 + - + +
260B ARG* 3.9 11.4 - - + +
262B THR* 1.3 73.2 - - - +
264B GLU* 1.3 63.7 + - - +
266B LEU* 2.8 24.2 + - - +
267B ASN 3.2 7.1 + - - -
268B TRP* 3.8 27.4 + - + +
270B VAL* 4.0 32.1 - - + -
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Residues in contact with GLU 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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260B ARG 3.2 16.1 + - - +
261B ASP* 3.1 30.5 - - - +
262B THR 3.1 0.4 - - - -
263B LEU* 1.3 78.2 - - - +
265B THR* 1.3 60.1 + - + +
267B ASN* 3.0 28.2 + - - +
268B TRP 5.6 2.2 - - - +
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Residues in contact with THR 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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261B ASP 3.2 15.9 + - - -
262B THR* 3.1 8.0 + - - -
264B GLU* 1.3 77.6 - - + +
266B LEU* 1.3 59.5 + - - +
267B ASN* 3.4 1.1 - - - -
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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