Contacts of the helix formed by residues 335 - 346 (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 ASP 335 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.4 2.0 - - - +
331B GLN* 2.8 36.7 + - - +
332B LEU* 3.2 23.9 + - - +
333B LEU 3.6 0.6 - - - -
334B LEU* 1.4 75.8 - - - +
336B ASP* 1.3 79.1 + - - +
337B ASP* 3.2 23.4 + - - +
338B PHE* 3.7 12.1 + - + +
339B PHE* 3.2 27.0 + - - -
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Residues in contact with ASP 336 (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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135B LEU* 5.8 1.5 - - - +
334B LEU 5.1 2.4 - - - +
335B ASP* 1.3 74.1 + - - +
337B ASP* 1.3 58.1 + - - +
339B PHE* 2.9 9.7 + - - +
340B ASP* 2.7 39.4 + - - +
354B ARG* 3.5 47.2 + - - +
355B TRP* 4.6 9.0 + - - +
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Residues in contact with ASP 337 (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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335B ASP* 3.2 10.7 + - - +
336B ASP* 1.3 82.6 - - - +
338B PHE* 1.4 55.8 + - - +
340B ASP* 3.3 17.5 - - - +
341B GLU* 2.9 29.8 + - - +
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Residues in contact with PHE 338 (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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160B LEU* 3.6 26.5 - - + -
163B TYR* 3.7 29.5 - + - -
164B ALA* 3.9 20.9 - - + -
167B GLN* 4.5 7.0 - - + -
332B LEU* 3.2 43.5 - - + +
333B LEU* 4.7 6.3 - - + -
335B ASP* 3.7 17.0 + - + +
336B ASP 3.1 0.2 + - - -
337B ASP* 1.4 74.2 - - - +
339B PHE* 1.4 80.6 + + - +
341B GLU* 3.3 5.2 + - - +
342B ILE* 3.1 51.8 + - + +
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Residues in contact with PHE 339 (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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135B LEU* 3.9 13.5 - - + -
136B MET* 4.3 21.8 - - + -
139B ASN* 3.6 31.4 - - + +
140B ARG 5.6 0.2 - - - -
143B ILE* 4.8 6.7 - - + -
160B LEU* 5.5 5.6 - - + -
332B LEU 4.0 0.2 - - - -
333B LEU* 3.3 36.6 - - + -
335B ASP 3.2 19.1 - - - +
336B ASP* 2.9 7.8 + - - +
338B PHE* 1.4 98.0 - + - +
340B ASP* 1.3 64.2 + - - +
342B ILE* 4.3 13.5 - - + -
343B PHE* 3.1 36.2 + + + +
352B PRO* 3.5 20.8 - - + +
353B VAL 5.2 0.4 - - - +
354B ARG* 4.9 0.9 - - - +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASP* 2.7 33.5 + - - +
337B ASP* 3.2 22.4 + - - +
339B PHE* 1.3 73.9 - - - +
341B GLU* 1.4 63.2 + - - +
343B PHE* 3.6 0.9 + - - +
344B ARG* 3.0 51.4 + - + +
352B PRO* 3.9 3.8 - - - +
354B ARG* 2.7 31.4 + - - -
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Residues in contact with GLU 341 (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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163B TYR* 6.0 5.6 - - + +
224B PHE* 5.3 2.0 - - + -
337B ASP 2.9 17.7 + - - +
338B PHE* 3.3 3.8 + - - +
340B ASP* 1.4 76.7 - - - +
342B ILE* 1.4 58.2 + - - +
344B ARG* 3.3 28.4 + - - +
345B GLU* 2.9 48.3 + - - +
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Residues in contact with ILE 342 (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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143B ILE* 3.9 27.4 - - + -
155B ILE* 6.0 0.2 - - + -
160B LEU* 5.0 7.4 - - + -
163B TYR* 4.7 5.8 - - + -
224B PHE* 3.8 51.8 - - + +
338B PHE* 3.1 53.1 + - + +
339B PHE* 3.9 15.5 - - + +
341B GLU* 1.4 71.5 - - + +
343B PHE* 1.4 61.0 + - + +
345B GLU* 3.3 4.3 + - - +
346B LEU* 3.1 37.3 + - + +
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Residues in contact with PHE 343 (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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139B ASN* 3.4 25.4 - - - -
142B VAL* 3.6 28.9 - - + -
143B ILE* 3.6 34.1 - - + -
339B PHE* 3.1 29.4 + + - +
340B ASP 3.8 4.5 - - - +
342B ILE* 1.4 77.3 - - + +
344B ARG* 1.4 67.3 + - - +
346B LEU* 3.0 3.1 + - - +
347B GLY 2.9 24.8 + - - -
348B ILE* 2.9 38.8 + - + -
350B TYR* 3.3 21.8 - - + -
351B GLU 4.3 1.6 - - - -
352B PRO* 3.6 28.7 - - + -
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Residues in contact with ARG 344 (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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340B ASP* 3.0 47.9 + - + +
341B GLU* 3.3 25.8 + - - +
343B PHE* 1.4 78.4 - - - +
345B GLU* 1.3 59.3 + - - +
347B GLY* 3.5 11.2 + - - +
348B ILE 3.1 24.9 + - - -
349B PRO* 3.8 11.1 + - - +
350B TYR 3.1 14.5 + - - -
351B GLU* 4.1 4.4 - - - +
352B PRO* 3.5 20.6 - - - +
354B ARG* 4.9 0.6 - - - +
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Residues in contact with GLU 345 (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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163B TYR* 5.3 0.5 + - - -
223B ARG* 3.3 42.5 + - + +
224B PHE* 3.7 16.0 + - + +
225B GLY* 3.2 33.4 - - - +
341B GLU* 2.9 35.2 + - - +
342B ILE 3.4 5.8 - - - +
344B ARG* 1.3 76.3 - - - +
346B LEU* 1.4 60.4 + - - +
347B GLY 3.4 1.4 + - - -
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Residues in contact with LEU 346 (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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143B ILE* 3.8 29.6 - - + -
146B HIS* 4.7 2.9 + - - -
147B LEU* 4.3 23.3 - - + +
151B ARG* 5.9 2.6 - - - +
155B ILE* 4.0 13.5 - - + -
224B PHE* 4.0 4.5 - - + -
225B GLY* 5.4 1.1 - - - -
228B ILE* 3.8 27.8 - - + -
342B ILE* 3.1 34.2 + - + +
343B PHE 3.0 5.4 + - - +
345B GLU* 1.4 78.0 - - + +
347B GLY* 1.3 61.7 + - - +
348B ILE* 3.3 17.9 + - + +
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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