Contacts of the helix formed by residues 335 - 346 (chain A) in PDB entry 2CSX
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 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A VAL 3.8 1.1 - - - -
292A GLU* 3.4 27.1 - - - -
333A ASP* 3.3 19.7 + - - -
334A PHE* 1.3 80.5 - - - +
336A LYS* 1.3 65.9 + - - +
337A LYS* 4.0 5.5 + - - +
338A ALA* 3.2 20.1 + - - +
339A ILE* 3.1 29.9 + - - +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.2 14.5 + - - +
313A TYR* 3.7 26.2 + - - +
335A SER* 1.3 72.5 - - - +
337A LYS* 1.3 67.3 + - - +
338A ALA 3.1 0.2 + - - -
339A ILE* 4.0 2.3 - - - +
340A LEU* 3.1 53.3 + - + +
497A GLY* 4.2 21.1 + - - -
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Residues in contact with LYS 337 (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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292A GLU* 5.3 1.5 + - - +
335A SER* 3.4 6.1 + - - +
336A LYS* 1.3 78.8 - - - +
338A ALA* 1.3 57.8 + - - +
340A LEU* 3.9 5.0 - - - +
341A ASN* 3.0 36.3 + - - +
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Residues in contact with ALA 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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321A PHE* 4.0 10.8 - - + -
325A GLU* 3.6 21.5 - - - +
333A ASP* 4.7 3.1 - - - +
335A SER* 3.2 22.2 + - - +
336A LYS 3.2 0.6 - - - -
337A LYS* 1.3 78.4 - - - +
339A ILE* 1.3 66.6 + - - +
341A ASN* 3.1 9.1 + - - +
342A ARG* 3.0 25.5 + - - +
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Residues in contact with ILE 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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313A TYR* 3.6 32.1 - - + -
317A GLU 5.4 0.9 - - - +
318A VAL* 5.4 2.7 - - - -
321A PHE* 3.8 40.8 - - + -
334A PHE* 3.0 44.9 - - + -
335A SER 3.1 19.4 + - - +
336A LYS 4.1 2.0 - - - +
338A ALA* 1.3 74.4 - - - +
340A LEU* 1.3 55.5 + - - +
342A ARG* 2.9 4.0 + - - +
343A ILE* 2.7 59.5 + - + +
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Residues in contact with LEU 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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313A TYR* 4.3 23.6 - - + -
336A LYS* 3.1 37.9 + - + +
337A LYS* 3.9 4.3 - - - +
339A ILE* 1.3 78.9 - - - +
341A ASN* 1.3 63.7 + - - +
343A ILE* 4.2 9.0 - - + -
344A ASN* 2.9 45.3 + - - +
495A ARG* 5.1 3.8 - - + -
496A GLU* 4.1 8.3 - - - +
497A GLY* 3.8 38.6 - - - +
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Residues in contact with ASN 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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337A LYS* 3.0 24.3 + - - +
338A ALA* 3.2 11.7 - - - +
339A ILE 3.1 0.2 - - - -
340A LEU* 1.3 77.2 - - - +
342A ARG* 1.3 66.1 + - + +
344A ASN* 5.2 0.7 - - - -
345A GLY* 2.7 36.7 + - - +
346A GLU* 4.2 0.7 + - - +
25C C 3.9 31.0 + - - +
26C G 4.7 12.3 + - - -
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Residues in contact with ARG 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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320A TYR* 4.4 11.7 - - + -
321A PHE* 3.7 16.8 - - + -
324A ARG* 2.5 43.5 - - - +
325A GLU* 2.8 32.0 + - - +
338A ALA 3.0 11.9 + - - +
339A ILE 2.9 7.0 + - - +
341A ASN* 1.3 88.0 + - - +
343A ILE* 1.3 61.4 + - + +
346A GLU* 3.2 36.6 + - - +
347A LEU* 3.3 22.1 + - - +
24C G 5.2 4.8 + - - -
25C C 5.2 16.1 + - - -
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Residues in contact with ILE 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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313A TYR* 3.8 16.8 - - + +
317A GLU* 3.4 47.6 - - + +
320A TYR* 6.4 0.4 - - + -
321A PHE* 5.9 0.7 - - + -
339A ILE* 2.7 46.8 + - + +
340A LEU* 3.9 9.9 - - + +
342A ARG* 1.3 73.4 - - + +
344A ASN* 1.3 67.1 + - - +
347A LEU* 3.2 16.9 + - + +
348A ALA* 2.8 28.0 + - + +
492A PHE* 5.4 2.9 - - + -
493A PRO 4.9 12.3 - - - +
495A ARG* 5.3 10.5 - - + +
496A GLU 6.2 0.2 - - - +
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Residues in contact with ASN 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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340A LEU* 2.9 34.2 + - - +
341A ASN* 5.2 0.7 - - - -
343A ILE* 1.3 80.2 - - - +
345A GLY* 1.3 60.6 + - - +
346A GLU 3.3 0.2 + - - -
348A ALA* 3.4 3.4 - - - +
349A ASN* 3.0 38.4 + - - +
494A LYS* 3.2 47.7 - - + +
495A ARG 4.1 0.5 + - - -
496A GLU* 3.7 27.2 + - - +
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Residues in contact with GLY 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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341A ASN* 2.7 24.3 + - - -
344A ASN* 1.3 74.1 - - - +
346A GLU* 1.3 61.3 + - - +
349A ASN* 3.3 25.4 + - - +
350A GLU* 3.7 15.9 - - - +
39C G 4.6 1.7 + - - -
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Residues in contact with GLU 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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320A TYR* 2.8 27.6 + - - +
324A ARG* 2.7 42.5 + - - -
341A ASN 5.0 0.4 - - - +
342A ARG* 3.2 34.6 + - - +
344A ASN 3.3 0.2 - - - -
345A GLY* 1.3 82.8 - - - +
347A LEU* 1.3 64.5 + - - +
348A ALA 3.5 0.7 - - - -
350A GLU* 3.1 18.7 + - - +
351A ILE* 2.9 32.8 + - - +
406A LEU* 4.0 20.2 - - + +
25C C 6.0 1.1 - - - +
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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