Contacts of the helix formed by residues 287 - 296 (chain B) in PDB entry 2BT4
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 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2405A TRS 3.7 3.4 - - - -
259B GLU* 2.5 28.0 + - - -
283B TYR* 2.9 35.8 + - - +
285B HIS 3.9 0.4 - - - -
286B THR* 1.3 69.3 + - - +
288B VAL* 1.3 62.5 + - - +
290B ILE* 2.9 32.2 + - - +
291B LEU* 3.3 17.0 + - - +
321B TYR* 4.0 10.9 - - - +
322B VAL* 4.9 1.7 - - - +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 3.7 18.8 - - + +
85A HIS* 4.4 9.0 - - + -
86A THR* 3.5 27.1 - - + +
116A PHE* 3.8 27.8 - - + -
117A ARG* 4.1 15.0 - - - +
286B THR 3.4 2.2 + - - -
287B SER* 1.3 74.3 - - - +
289B ALA* 1.3 56.8 + - - +
291B LEU* 3.2 8.2 + - + +
292B ASP* 2.8 30.3 + - - +
321B TYR* 3.7 34.3 - - + +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 4.0 14.8 - - + -
16A ASN* 3.3 11.2 + - - +
82A ALA* 3.5 16.2 - - + +
83A TYR* 3.8 33.4 - - + +
86A THR* 5.4 0.6 - - - +
259B GLU* 3.9 2.0 + - - +
263B VAL* 3.9 10.0 - - + +
287B SER* 3.1 6.8 - - - +
288B VAL* 1.3 78.1 - - - +
290B ILE* 1.3 56.9 + - - +
292B ASP 3.4 0.2 + - - -
293B ALA* 2.9 24.6 + - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU* 4.3 6.5 - - + +
262B LEU* 4.0 30.5 - - + -
263B VAL* 4.0 16.2 - - + -
266B ILE* 3.7 17.5 - - + -
278B ILE* 4.1 14.1 - - + -
280B PRO* 5.4 4.0 - - + -
283B TYR* 3.9 25.1 - - + -
287B SER* 2.9 25.7 + - - +
289B ALA* 1.3 75.0 - - - +
291B LEU* 1.3 64.9 + - - +
293B ALA* 3.2 6.5 + - - +
294B LEU* 2.9 26.4 + - + +
322B VAL* 4.0 20.4 - - + -
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.9 28.7 - - + -
117A ARG* 4.3 7.0 - - - +
287B SER 3.3 12.9 + - - +
288B VAL* 3.2 9.1 + - + +
290B ILE* 1.3 77.4 - - - +
292B ASP* 1.3 57.6 + - - +
294B LEU* 3.3 7.5 + - - +
295B ASN* 3.0 38.1 + - - +
321B TYR* 3.3 39.5 - - + +
322B VAL* 4.6 4.4 - - - +
324B GLN* 4.2 14.1 - - + +
325B ARG* 3.8 26.9 - - + +
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.2 19.7 + - + +
82A ALA* 3.5 10.5 - - - +
117A ARG* 2.8 33.6 + - - -
160A CA2 2.4 45.2 + - + +
288B VAL 2.8 21.3 + - - +
289B ALA 4.4 0.2 - - - -
291B LEU* 1.3 72.0 - - - +
293B ALA* 1.3 62.2 + - - +
295B ASN* 3.3 17.9 + - - +
296B THR* 3.3 17.8 + - - +
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Residues in contact with ALA 293 (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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16A ASN* 3.1 21.7 + - - +
263B VAL* 4.1 12.1 - - + -
266B ILE* 3.6 34.2 - - + +
267B HIS* 4.3 1.6 - - - +
289B ALA 2.9 13.2 + - - +
290B ILE* 3.2 10.1 + - - +
292B ASP* 1.3 74.5 - - - +
294B LEU* 1.3 61.6 + - - +
296B THR* 2.6 27.1 + - - -
297B CYS* 3.8 1.6 - - - -
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Residues in contact with LEU 294 (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 ILE* 3.9 17.5 - - + -
276B ILE* 3.8 33.2 - - + -
278B ILE* 4.4 5.8 - - + -
290B ILE* 2.9 28.7 + - + +
291B LEU* 3.7 4.7 - - - +
293B ALA* 1.3 75.0 - - - +
295B ASN* 1.3 61.7 + - - +
297B CYS* 3.0 22.6 + - - +
302B VAL* 4.2 24.7 - - + -
322B VAL* 3.8 33.2 - - + +
325B ARG* 3.3 30.4 + - + +
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Residues in contact with ASN 295 (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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23A ARG* 3.0 35.7 + - - +
117A ARG* 4.1 14.8 - - - +
291B LEU* 3.0 31.8 + - - +
292B ASP* 3.4 13.6 + - - +
293B ALA 3.2 0.4 - - - -
294B LEU* 1.3 77.3 - - - +
296B THR* 1.3 59.6 + - + +
297B CYS 3.3 1.2 + - - -
298B ASP* 3.9 2.4 + - - +
324B GLN 5.2 0.7 - - - +
325B ARG* 3.4 33.5 + - - +
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 4.7 5.4 - - + -
19A LEU* 3.6 28.9 - - + +
23A ARG* 3.6 12.9 + - - +
160A CA2 3.9 27.1 - - + -
267B HIS* 4.3 3.1 - - - -
270B ARG* 2.7 37.8 + - - -
292B ASP 3.3 14.3 + - - +
293B ALA* 2.6 20.9 + - - +
295B ASN* 1.3 76.5 - - + +
297B CYS* 1.3 54.0 + - - +
298B ASP* 3.0 17.4 + - - +
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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