Contacts of the helix formed by residues 337 - 349 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A HIS* 4.6 1.1 - - - -
333A LYS* 3.7 26.4 + - - +
334A THR* 3.0 18.1 + - + +
336A ALA* 1.3 77.4 - - + +
338A LYS* 1.3 64.1 + - - +
339A ALA* 3.3 2.2 - - - -
340A GLU* 3.0 38.7 + - + +
341A TRP* 3.0 20.1 + - - +
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A HIS* 3.6 49.6 + - + +
170A ASN* 4.0 20.2 - - - +
334A THR 4.0 0.2 + - - -
335A ARG 3.1 17.7 + - - +
336A ALA 3.2 2.9 + - - +
337A LYS* 1.3 76.7 - - - +
339A ALA* 1.3 59.0 + - - +
341A TRP* 3.0 4.0 + - - +
342A GLN* 2.8 59.0 + - + +
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ALA 4.9 1.9 + - - +
337A LYS 3.3 0.8 - - - -
338A LYS* 1.3 79.5 - - - +
340A GLU* 1.3 57.1 + - - +
342A GLN* 3.4 14.9 + - - +
343A ASP* 3.0 39.8 + - - +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LYS* 3.0 43.1 + - + +
339A ALA* 1.3 78.4 - - - +
341A TRP* 1.3 58.9 + - - +
343A ASP* 3.4 7.1 + - - +
344A ALA* 3.0 29.6 + - + +
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Residues in contact with TRP 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 6.2 0.9 - - + -
29A VAL* 3.6 29.2 - - + -
33A MET* 3.9 15.0 - - + -
160A PHE* 3.2 37.1 - + - -
161A PRO* 3.0 28.8 + - + -
162A ILE 3.6 11.0 - - - -
164A GLN* 3.4 22.9 - - + +
165A TYR* 3.6 34.8 - - + -
168A HIS* 3.3 31.2 - + + +
337A LYS* 3.0 11.3 + - + +
338A LYS 3.0 7.3 + - - +
340A GLU* 1.3 75.1 - - - +
342A GLN* 1.3 86.4 + - + +
344A ALA* 3.2 4.5 + - - -
345A PHE* 3.0 19.7 + + + -
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 5.3 2.6 + - + +
32A GLU* 4.0 7.9 + - - +
33A MET* 3.6 47.4 - - + +
338A LYS* 2.8 43.7 + - + +
339A ALA* 3.5 21.9 + - - +
341A TRP* 1.3 88.0 - - + +
343A ASP* 1.3 65.7 + - - +
345A PHE* 3.1 4.0 + - - +
346A LYS* 3.0 32.5 + - - +
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ALA* 3.0 25.9 + - - +
340A GLU* 3.7 6.9 - - - +
342A GLN* 1.3 78.0 - - - +
344A ALA* 1.3 57.8 + - - +
346A LYS* 3.4 19.4 + - - +
347A LYS* 3.0 28.2 + - - +
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Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 5.1 2.3 - - - +
160A PHE* 3.6 18.2 - - + -
161A PRO* 6.1 0.2 - - + -
340A GLU* 3.0 18.7 + - + +
341A TRP* 3.2 6.7 + - - +
343A ASP* 1.3 73.9 - - - +
345A PHE* 1.3 60.5 + - - +
347A LYS* 3.4 9.2 + - - +
348A ALA* 3.0 27.2 + - - +
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 6.1 3.8 - - + -
30A ILE* 3.7 38.4 - - + -
33A MET* 3.8 28.5 - - + -
63A ILE* 4.1 5.8 - - + -
97A LEU* 4.5 22.0 - - + -
135A ILE* 4.9 2.0 - - + -
160A PHE* 3.4 40.5 - + + -
162A ILE* 5.8 2.5 - - + -
341A TRP* 3.0 9.1 + + - +
342A GLN 3.5 8.3 - - - +
344A ALA* 1.3 75.6 - - - +
346A LYS* 1.3 67.1 + - + +
348A ALA* 2.9 16.3 + - + +
349A ILE* 3.1 50.8 + - + +
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Residues in contact with LYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A MET* 3.2 49.5 + - - +
35A LEU* 4.3 22.1 - - + +
342A GLN* 3.0 20.8 + - - +
343A ASP* 3.7 20.7 + - - +
345A PHE* 1.3 76.6 - - - +
347A LYS* 1.3 58.1 + - - +
349A ILE* 3.2 15.4 + - - +
351A LEU* 2.7 49.0 + - + +
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LYS* 4.2 3.3 + - - -
158A GLU* 3.2 26.8 + - - +
343A ASP 3.0 17.4 + - - +
344A ALA* 3.7 8.1 - - - +
345A PHE 3.2 0.2 - - - -
346A LYS* 1.3 77.0 - - - +
348A ALA* 1.3 62.0 + - - +
350A ASP* 3.1 17.3 + - - +
351A LEU 3.8 11.8 + - - +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 3.7 3.3 - - - -
133A LYS* 2.8 29.5 + - - +
135A ILE* 4.0 25.6 - - + +
158A GLU* 3.6 24.0 - - - +
160A PHE* 4.7 7.6 - - + -
344A ALA 3.0 13.6 + - - +
345A PHE* 2.9 16.6 + - + +
347A LYS* 1.3 79.1 - - - +
349A ILE* 1.3 56.4 + - - +
350A ASP 3.2 1.3 + - - -
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.3 15.0 - - + -
35A LEU* 4.4 2.9 - - + -
61A ARG* 2.8 34.0 + - + -
63A ILE* 4.2 15.3 - - + -
95A TYR* 3.6 23.8 - - + -
135A ILE* 3.9 19.3 - - + -
345A PHE* 3.1 42.5 + - + +
346A LYS* 3.4 12.6 - - - +
347A LYS 3.2 0.2 - - - -
348A ALA* 1.3 79.2 - - - +
350A ASP* 1.3 57.6 + - - +
351A LEU* 3.4 26.7 + - + +
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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