Contacts of the helix formed by residues 319 - 333 (chain B) in PDB entry 2XT6
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 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320B ALA* 1.4 61.2 + - - +
321B GLU* 4.4 3.4 - - - +
322B SER* 2.6 37.2 + - - +
323B GLY* 3.1 10.2 + - - -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLY* 1.4 70.3 - - - +
321B GLU* 1.4 51.7 + - - +
322B SER 3.1 4.5 - - - -
323B GLY* 2.9 4.7 + - - -
324B ASP* 2.8 35.6 + - - +
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Residues in contact with GLU 321 (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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319B GLY 4.4 3.1 - - - +
320B ALA* 1.4 75.5 - - - +
322B SER* 1.4 56.5 + - - +
324B ASP* 3.7 10.4 - - - +
325B PHE* 3.1 27.0 + - - +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER* 4.5 22.1 + - - -
319B GLY* 2.6 37.5 + - - +
320B ALA 3.1 0.2 - - - -
321B GLU* 1.4 78.5 - - - +
323B GLY* 1.3 59.1 + - - +
324B ASP 3.2 0.2 - - - -
325B PHE* 3.4 7.7 + - - +
326B LEU* 3.3 28.5 + - - +
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Residues in contact with GLY 323 (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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129B ARG* 3.0 29.3 + - - -
319B GLY 3.1 6.1 + - - -
320B ALA* 2.9 8.7 + - - -
322B SER* 1.3 82.1 + - - +
324B ASP* 1.4 57.7 + - - +
326B LEU* 4.0 9.5 + - - +
327B ARG* 3.6 3.6 + - - +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ALA 2.8 14.9 + - - +
321B GLU* 3.7 12.1 - - - +
322B SER 3.2 0.2 - - - -
323B GLY* 1.4 73.9 - - - +
325B PHE* 1.3 54.9 + - - +
326B LEU 3.3 1.6 - - - -
327B ARG* 3.2 14.4 + - - +
328B THR* 2.6 42.4 + - - -
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Residues in contact with PHE 325 (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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165B ILE* 3.9 39.3 - - + -
253B ILE* 5.4 8.1 - - + -
278B ILE* 3.7 30.7 - - + -
321B GLU 3.1 18.1 + - - +
322B SER* 3.4 9.6 + - - +
324B ASP* 1.3 75.7 - - - +
326B LEU* 1.4 57.8 + - + +
328B THR* 3.3 11.2 + - + -
329B ILE* 3.1 42.8 + - + +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL 4.2 8.7 - - - +
129B ARG* 3.3 43.5 - - + +
131B ILE* 3.6 5.4 - - - +
278B ILE* 4.4 8.1 - - + -
308B LEU* 3.7 40.2 - - + +
309B THR* 3.9 20.9 - - - +
310B SER* 4.8 5.8 - - - +
322B SER 3.3 16.4 + - - +
323B GLY* 4.1 9.0 - - - +
324B ASP 3.3 0.2 - - - -
325B PHE* 1.4 78.4 - - + +
327B ARG* 1.4 55.6 + - - +
329B ILE* 3.7 18.4 - - + +
330B HIS* 3.2 18.7 + - - +
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Residues in contact with ARG 327 (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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129B ARG* 3.3 38.0 - - - +
323B GLY 3.6 6.1 + - - +
324B ASP* 3.2 20.5 + - - +
326B LEU* 1.4 75.6 - - - +
328B THR* 1.4 58.5 + - - +
329B ILE 3.3 0.2 - - - -
330B HIS* 3.3 15.8 + - - +
331B GLN* 3.1 46.0 + - + +
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Residues in contact with THR 328 (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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167B GLN 6.0 4.3 - - - +
324B ASP* 2.6 30.4 + - - -
325B PHE* 3.3 13.7 + - + -
327B ARG* 1.4 72.4 - - - +
329B ILE* 1.4 63.3 + - - +
331B GLN* 3.6 13.6 + - + +
332B LEU* 3.2 37.5 + - + +
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Residues in contact with ILE 329 (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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131B ILE* 4.0 4.9 - - + -
161B LEU* 5.8 5.6 - - + +
164B ALA* 5.0 6.5 - - + +
165B ILE* 4.0 38.6 - - + +
278B ILE* 4.6 6.3 - - + -
308B LEU* 3.8 28.5 - - + -
325B PHE* 3.1 39.0 + - + +
326B LEU* 3.7 18.8 - - + +
328B THR* 1.4 73.2 - - - +
330B HIS* 1.4 64.6 + - - +
332B LEU* 3.2 19.1 + - + +
333B LEU* 3.3 29.2 + - + +
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Residues in contact with HIS 330 (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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129B ARG* 3.0 26.7 + - - -
130B ALA 3.7 15.5 - - - -
131B ILE* 3.4 21.1 - - + +
132B PRO* 3.0 35.9 - - + +
326B LEU 3.2 11.2 + - - +
327B ARG* 3.3 26.7 - - - +
329B ILE* 1.4 79.1 - - - +
331B GLN* 1.3 60.2 + - - +
332B LEU 3.5 0.2 + - - -
333B LEU* 3.6 6.1 + - - +
334B LEU* 3.5 29.3 - - + +
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Residues in contact with GLN 331 (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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327B ARG* 3.1 28.1 + - + +
328B THR* 3.7 17.5 - - - +
330B HIS* 1.3 77.7 - - - +
332B LEU* 1.4 74.3 + - - +
334B LEU* 3.6 8.6 + - - +
335B ASP* 2.8 43.8 + - - +
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Residues in contact with LEU 332 (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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164B ALA* 3.3 45.1 - - + +
167B GLN* 4.2 17.0 - - + -
328B THR* 3.2 26.1 + - + +
329B ILE* 3.2 9.1 + - + +
331B GLN* 1.4 83.3 - - - +
333B LEU* 1.4 55.3 + - - +
334B LEU 3.2 4.9 - - - -
335B ASP* 3.2 25.7 + - - +
338B PHE* 3.2 45.5 - - + -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.9 26.2 - - + -
132B PRO 5.1 2.0 - - - +
133B ALA* 5.7 0.7 - - + -
135B LEU* 3.4 16.3 - - - +
136B MET* 3.8 47.9 + - + -
160B LEU* 4.5 17.5 - - + +
161B LEU* 4.8 4.9 - - + -
164B ALA* 4.7 7.0 - - + -
308B LEU* 5.3 3.6 - - + -
329B ILE* 3.3 29.3 + - + +
330B HIS 3.6 4.2 + - - +
331B GLN 3.5 0.4 - - - -
332B LEU* 1.4 73.1 - - - +
334B LEU* 1.3 65.1 + - + +
335B ASP 3.6 0.7 - - - -
338B PHE* 4.7 7.9 - - + -
339B PHE* 3.3 23.3 - - + -
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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