Contacts of the helix formed by residues 335 - 348 (chain A) in PDB entry 2V5E
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 ASN 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A PHE* 4.4 2.6 - - - -
267A CYS* 3.2 29.3 + - - +
269A PRO* 4.2 9.1 - - - +
331A PHE* 2.6 47.4 + - - +
332A PHE 3.9 8.7 + - - +
333A LYS 3.7 2.6 + - - -
334A ASP* 1.3 72.5 + - - +
336A THR* 1.3 57.1 + - - +
337A CYS* 3.1 6.4 + - - +
338A LEU* 2.9 30.8 + - + +
339A LYS* 2.9 30.2 + - - +
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Residues in contact with THR 336 (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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269A PRO* 4.5 8.4 - - - +
276A ASN* 3.5 36.1 - - - +
334A ASP* 4.0 8.1 + - - -
335A ASN* 1.3 70.2 + - - +
337A CYS* 1.3 65.0 + - - +
339A LYS* 4.4 18.4 + - - +
340A ASN* 3.0 34.7 + - - +
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Residues in contact with CYS 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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266A ASN 4.0 4.3 - - - -
267A CYS* 3.5 31.9 - - - +
269A PRO* 3.8 9.2 - - + +
276A ASN 3.6 14.8 + - - +
277A CYS* 2.0 52.7 - - - -
285A CYS* 4.2 5.8 - - - -
335A ASN* 3.1 9.2 + - - +
336A THR* 1.3 79.0 - - - +
338A LEU* 1.3 56.0 - - - +
340A ASN* 3.6 3.4 - - - +
341A ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 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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263A PHE* 4.0 13.2 - - + -
267A CYS* 4.4 0.9 - - + -
285A CYS* 3.8 26.4 - - - -
286A LEU* 4.5 5.8 - - + -
289A TYR* 3.8 35.7 - - + -
307A LEU 5.9 0.7 - - - +
309A VAL* 3.7 29.8 - - + -
332A PHE 4.6 5.4 - - - +
335A ASN* 2.9 23.3 + - + +
337A CYS* 1.3 76.7 - - - +
339A LYS* 1.3 57.4 + - - +
341A ALA* 3.2 2.8 + - - +
342A ILE* 2.9 51.6 + - + +
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Residues in contact with LYS 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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307A LEU* 3.7 34.0 - - + +
335A ASN 2.9 18.3 + - - +
336A THR* 4.0 15.8 + - + +
338A LEU* 1.3 76.4 - - - +
340A ASN* 1.3 63.6 + - - +
342A ILE* 3.4 3.7 + - - -
343A GLN* 2.9 51.8 + - - +
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Residues in contact with ASN 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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274A VAL 4.9 2.8 + - - -
275A SER 3.2 20.5 + - - +
276A ASN* 3.4 20.8 - - - +
282A TYR* 3.5 18.8 + - + +
336A THR* 3.0 24.9 + - - +
337A CYS 3.6 3.6 - - - +
339A LYS* 1.3 79.6 - - - +
341A ALA* 1.3 54.5 + - - +
343A GLN* 3.4 17.2 + - - +
344A ALA* 2.7 35.9 + - - +
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Residues in contact with ALA 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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282A TYR* 3.5 36.5 - - + +
285A CYS* 4.4 6.3 - - - -
286A LEU* 3.6 30.4 - - + +
337A CYS 2.9 17.0 + - - +
338A LEU* 3.5 8.5 - - - +
340A ASN* 1.3 77.9 - - - +
342A ILE* 1.3 57.1 + - - +
344A ALA* 3.4 2.6 + - - +
345A PHE 3.1 22.0 + - - -
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Residues in contact with ILE 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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213A PHE* 3.6 55.4 - - + +
286A LEU* 3.8 10.1 - - + -
289A TYR* 5.0 3.8 - - + -
301A TYR* 4.0 20.2 - - + +
307A LEU* 4.1 28.7 - - + +
309A VAL* 5.3 1.8 - - + -
338A LEU* 2.9 40.8 + - + +
339A LYS* 3.9 5.4 - - - +
341A ALA* 1.3 74.0 - - - +
343A GLN* 1.3 65.4 + - - +
345A PHE* 3.2 6.3 + - - +
346A GLY* 3.0 20.1 + - - -
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Residues in contact with GLN 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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215A SER* 6.5 0.7 - - - -
307A LEU* 3.7 16.8 - - + +
339A LYS* 2.9 36.8 + - - +
340A ASN* 3.6 23.3 - - - +
342A ILE* 1.3 75.5 - - - +
344A ALA* 1.3 57.3 + - - +
346A GLY* 3.2 3.3 + - - -
347A ASN* 2.9 40.7 + - - +
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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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282A TYR* 3.6 28.3 - - + -
340A ASN 2.7 21.6 + - - +
341A ALA 3.5 6.1 - - - +
342A ILE 3.2 0.4 - - - -
343A GLN* 1.3 73.8 - - - +
345A PHE* 1.3 61.5 + - - +
347A ASN* 3.4 9.2 + - - +
348A GLY 3.3 16.6 + - - -
349A SER* 3.4 24.1 + - - +
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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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205A ALA 4.7 2.9 - - - -
206A LYS* 4.3 12.6 - - - -
209A TYR* 3.4 41.5 - + + -
210A GLY* 3.4 29.4 - - - -
213A PHE* 3.6 26.0 - - + -
214A CYS* 4.7 1.8 - - - -
286A LEU* 3.9 15.5 - - + +
341A ALA 3.1 14.7 + - - +
342A ILE 3.2 6.5 + - - +
344A ALA* 1.3 74.8 - - - +
346A GLY* 1.3 65.5 + - - +
347A ASN 3.3 0.7 + - - -
348A GLY* 3.4 13.7 + - - +
349A SER* 4.6 5.8 - - - +
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Residues in contact with GLY 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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153A ASN* 4.8 3.1 + - - -
213A PHE 4.2 11.9 - - - -
214A CYS* 5.2 1.1 - - - -
215A SER* 3.3 32.6 + - - -
342A ILE 3.0 14.3 + - - -
343A GLN* 3.2 4.5 + - - -
345A PHE* 1.3 79.7 - - - +
347A ASN* 1.3 62.7 + - - +
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Residues in contact with ASN 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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215A SER* 5.7 2.1 - - - -
343A GLN* 2.9 29.9 + - - +
344A ALA* 3.7 9.3 - - - +
345A PHE 3.2 0.4 - - - -
346A GLY* 1.3 81.2 - - - +
348A GLY* 1.3 57.7 + - - +
349A SER* 4.9 1.3 - - - +
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Residues in contact with GLY 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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344A ALA 3.3 2.6 + - - -
345A PHE 3.4 10.5 + - - -
347A ASN* 1.3 79.3 - - - +
349A SER* 1.3 66.2 + - - +
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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