Contacts of the helix formed by residues 337 - 349 (chain B) in PDB entry 1SXQ
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 LYS 337 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B HIS* 4.6 0.6 - - - -
333B LYS 4.0 12.6 - - - +
334B THR* 3.1 14.8 + - + +
335B ARG 3.0 1.6 - - - -
336B ALA* 1.3 89.7 + - - +
338B LYS* 1.3 62.6 + - - +
339B ALA* 3.3 3.6 - - - +
340B GLU* 3.3 31.0 + - + +
341B TRP* 3.3 18.9 + - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 6.1 1.3 - - - -
32B GLU* 4.8 3.6 + - - +
168B HIS* 2.9 53.5 + - + +
169B MET 4.6 0.2 - - - -
170B ASN* 2.8 33.7 - - - +
335B ARG 3.1 16.3 + - - +
336B ALA 3.3 2.8 + - - +
337B LYS* 1.3 78.4 - - - +
339B ALA* 1.3 58.5 + - - +
341B TRP* 3.0 4.7 + - - +
342B GLN* 2.9 56.6 + - + +
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Residues in contact with ALA 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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336B ALA 5.1 1.3 + - - +
337B LYS 3.3 1.7 - - - -
338B LYS* 1.3 78.7 - - - +
340B GLU* 1.3 59.0 + - + +
342B GLN* 3.3 15.2 + - - +
343B ASP* 2.9 37.4 + - - +
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Residues in contact with GLU 340 (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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337B LYS* 3.3 42.7 + - + +
338B LYS 3.3 0.6 - - - -
339B ALA* 1.3 78.6 - - + +
341B TRP* 1.3 58.3 + - - +
343B ASP* 3.3 8.3 + - - +
344B ALA* 2.9 31.4 + - - +
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Residues in contact with TRP 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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26B LEU* 6.3 0.2 - - + -
29B VAL* 3.6 36.8 - - + -
33B MET* 3.8 16.4 - - + -
160B PHE* 3.2 38.2 - + - -
161B PRO* 3.0 30.6 + - + -
162B ILE 3.7 10.5 - - - -
164B GLN* 3.4 20.6 - - - +
165B TYR* 3.6 28.0 - - + -
168B HIS* 3.3 32.1 - + + +
337B LYS 3.3 9.8 + - - +
338B LYS 3.0 9.1 + - - +
340B GLU* 1.3 78.7 - - - +
342B GLN* 1.3 82.6 + - + +
344B ALA* 3.2 4.1 + - - -
345B PHE* 3.0 20.6 + + + -
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Residues in contact with GLN 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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29B VAL* 5.3 2.2 + - - +
32B GLU* 4.0 7.1 + - - +
33B MET* 3.7 46.1 - - + +
338B LYS* 2.9 42.8 + - + +
339B ALA* 3.6 21.0 + - - +
341B TRP* 1.3 92.4 - - + +
343B ASP* 1.3 66.6 + - - +
345B PHE* 3.2 2.8 + - - +
346B LYS* 3.0 32.6 + - - +
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Residues in contact with ASP 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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339B ALA* 2.9 23.7 + - - +
340B GLU* 3.6 9.8 - - - +
341B TRP 3.3 0.2 - - - -
342B GLN* 1.3 77.9 - - - +
344B ALA* 1.3 58.5 + - - +
346B LYS* 3.3 18.9 + - - +
347B LYS* 2.9 27.9 + - - +
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Residues in contact with ALA 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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158B GLU* 4.8 2.3 - - - +
160B PHE* 3.6 19.2 - - + -
340B GLU 2.9 17.7 + - - +
341B TRP* 3.6 6.3 - - - +
343B ASP* 1.3 75.4 - - - +
345B PHE* 1.3 60.6 + - - +
347B LYS* 3.3 10.3 + - - +
348B ALA* 2.9 27.5 + - - +
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Residues in contact with PHE 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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26B LEU* 5.9 4.7 - - + -
30B ILE* 3.7 38.6 - - + -
33B MET* 3.7 29.8 - - + -
35B LEU* 5.0 0.7 - - + -
63B ILE* 4.1 6.3 - - + -
97B LEU* 4.6 22.2 - - + -
135B ILE* 4.9 2.9 - - + -
160B PHE* 3.3 41.4 - + + -
162B ILE* 5.7 2.9 - - + -
341B TRP* 3.0 10.3 + + + +
342B GLN 3.2 7.6 + - - +
344B ALA* 1.3 76.0 - - - +
346B LYS* 1.3 63.8 + - + +
348B ALA* 3.0 15.8 + - + +
349B ILE* 3.1 50.7 + - + +
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Residues in contact with LYS 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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33B MET* 3.1 51.4 + - - +
35B LEU* 4.3 21.2 - - + +
342B GLN* 3.0 21.0 + - - +
343B ASP* 3.5 19.3 + - - +
345B PHE* 1.3 76.6 - - - +
347B LYS* 1.3 59.2 + - - +
349B ILE* 3.2 15.0 + - - +
351B LEU* 2.8 44.8 + - + +
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Residues in contact with LYS 347 (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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133B LYS* 4.2 2.9 + - - -
158B GLU* 4.6 14.9 - - - +
343B ASP 2.9 15.1 + - - +
344B ALA* 3.6 11.4 - - - +
345B PHE 3.2 0.2 - - - -
346B LYS* 1.3 76.3 - - - +
348B ALA* 1.3 63.3 + - - +
350B ASP* 3.0 18.2 + - - +
351B LEU 3.9 11.0 + - - +
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Residues in contact with ALA 348 (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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95B TYR* 3.6 3.8 - - - -
133B LYS* 2.9 28.9 + - - +
135B ILE* 4.1 26.9 - - + +
158B GLU* 3.9 23.8 + - - +
160B PHE* 4.8 8.7 - - + -
344B ALA 2.9 14.5 + - - +
345B PHE* 3.0 14.1 + - + +
347B LYS* 1.3 77.8 - - - +
349B ILE* 1.3 57.4 + - + +
350B ASP 3.2 1.4 + - - -
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Residues in contact with ILE 349 (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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3B ILE* 4.1 16.8 - - + -
35B LEU* 4.4 2.7 - - + -
61B ARG* 2.8 30.4 + - + -
63B ILE* 4.2 14.8 - - + -
95B TYR* 3.6 23.1 - - + -
135B ILE* 4.0 19.1 - - + -
345B PHE* 3.1 43.0 + - + +
346B LYS* 3.4 12.6 - - - +
347B LYS 3.2 0.2 - - - -
348B ALA* 1.3 76.6 - - - +
350B ASP* 1.3 63.3 + - - +
351B LEU* 3.5 26.9 - - + +
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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