Contacts of the helix formed by residues 321 - 334 (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 ASP 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A LEU* 3.4 23.2 - - + +
318A SER* 2.9 16.4 + - - +
320A ASN* 1.3 85.5 + - - +
322A LEU* 1.3 58.8 + - - +
323A GLU 3.3 2.7 - - - -
324A ASP* 3.2 17.5 + - + +
325A CYS* 2.8 27.9 + - - +
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Residues in contact with LEU 322 (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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315A CYS* 3.4 36.3 - - + +
318A SER* 3.5 17.4 - - - +
319A GLY 3.7 9.4 + - - +
320A ASN 3.4 3.0 - - - -
321A ASP* 1.3 77.2 - - - +
323A GLU* 1.3 56.8 + - - +
325A CYS* 3.5 0.4 - - - +
326A LEU* 2.9 48.2 + - + +
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Residues in contact with GLU 323 (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 ASN 4.8 3.1 + - - +
321A ASP 3.3 0.8 - - - -
322A LEU* 1.3 78.3 - - - +
324A ASP* 1.3 60.9 + - - +
326A LEU* 3.5 7.0 + - - +
327A LYS* 3.0 31.8 + - + +
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Residues in contact with ASP 324 (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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244A LEU* 4.2 13.9 - - + +
321A ASP* 3.2 21.6 + - + +
323A GLU* 1.3 76.4 - - - +
325A CYS* 1.3 65.0 + - - +
327A LYS* 3.4 14.0 + - - +
328A PHE* 3.0 22.7 + - - +
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Residues in contact with CYS 325 (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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242A ASN* 3.8 12.1 - - - -
243A CYS* 3.8 16.8 - - - -
244A LEU* 3.7 18.1 - - + +
315A CYS* 2.1 59.3 - - + -
318A SER* 3.7 14.1 - - - +
321A ASP 2.8 19.6 + - - +
322A LEU 3.5 4.9 - - - +
324A ASP* 1.3 72.7 - - - +
326A LEU* 1.3 56.0 + - - +
328A PHE* 3.1 5.9 + - - +
329A LEU 2.9 24.3 + - - -
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Residues in contact with LEU 326 (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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315A CYS* 4.0 18.4 - - + -
322A LEU* 2.9 46.0 + - + +
323A GLU* 3.9 6.5 - - + +
325A CYS* 1.3 70.1 - - - +
327A LYS* 1.3 57.4 + - - +
329A LEU* 4.4 8.1 - - + +
330A ASN* 2.7 59.3 + - - +
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Residues in contact with LYS 327 (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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264A PHE* 5.0 1.9 - - + -
323A GLU* 3.0 20.2 + - + +
324A ASP* 3.5 14.5 + - - +
325A CYS 3.3 0.2 - - - -
326A LEU* 1.3 75.9 - - - +
328A PHE* 1.3 60.9 + - - +
330A ASN* 4.4 3.3 - - - +
331A PHE* 3.2 24.6 + - + +
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Residues in contact with PHE 328 (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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243A CYS* 3.7 33.2 - - + -
244A LEU* 4.5 8.1 - - + -
247A GLN* 3.4 38.8 - - + +
260A LEU* 4.2 6.5 - - + -
264A PHE* 3.5 34.0 - + - -
297A MET* 3.7 35.4 - - + -
311A PRO* 4.5 4.5 - - + -
313A CYS* 4.7 0.2 - - - -
324A ASP 3.0 13.1 + - - +
325A CYS 3.3 8.5 - - - +
327A LYS* 1.3 76.5 - - - +
329A LEU* 1.3 64.9 + - - +
331A PHE* 3.3 17.2 + - - +
332A PHE* 3.4 30.9 - + - -
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Residues in contact with LEU 329 (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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243A CYS* 3.8 17.9 - - - -
310A ALA* 4.1 4.0 - - + -
311A PRO* 3.9 23.3 - - + -
313A CYS 4.1 6.1 - - - +
314A ASP* 4.2 24.0 - - + -
315A CYS* 4.2 14.4 - - + +
325A CYS 2.9 16.4 + - - +
326A LEU* 3.9 10.1 - - + +
328A PHE* 1.3 79.4 - - - +
330A ASN* 1.3 61.6 + - - +
332A PHE* 3.2 8.8 + - - +
333A LYS* 3.1 55.9 + - + +
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Residues in contact with ASN 330 (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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326A LEU* 2.7 46.7 + - - +
327A LYS* 4.4 3.6 - - - +
329A LEU* 1.3 72.0 - - - +
331A PHE* 1.3 60.6 + - - +
332A PHE 3.1 1.6 - - - -
333A LYS* 3.6 20.3 + - - +
334A ASP* 2.8 42.1 + - + +
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Residues in contact with PHE 331 (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* 3.6 23.6 - + - -
264A PHE* 3.4 64.4 - + + -
267A CYS 3.5 18.8 - - - -
268A GLN* 3.6 27.4 - - - -
269A PRO* 3.7 16.2 - - + -
327A LYS* 3.2 15.1 + - + +
328A PHE 3.3 12.8 - - - +
329A LEU 3.2 0.6 - - - -
330A ASN* 1.3 78.5 - - - +
332A PHE* 1.3 55.9 + - - +
334A ASP 5.0 0.9 - - - -
335A ASN* 2.6 44.9 + - - +
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Residues in contact with PHE 332 (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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260A LEU* 4.3 2.9 - - + -
263A PHE* 3.5 33.7 - + - -
264A PHE* 4.1 8.7 - + - -
289A TYR* 4.8 4.5 - + - -
292A LEU* 3.8 17.3 - - + -
297A MET* 4.0 21.8 - - + -
299A PRO* 4.5 15.3 - - + -
309A VAL* 3.1 32.0 + - + +
310A ALA* 3.9 6.5 - - - -
311A PRO* 3.6 26.0 - - + -
328A PHE* 3.4 42.8 - + - -
329A LEU* 3.2 8.6 + - - +
330A ASN 3.1 0.2 - - - -
331A PHE* 1.3 80.0 - - - +
333A LYS* 1.3 64.6 + - - +
334A ASP 3.5 0.6 + - - -
335A ASN* 3.9 8.7 + - - +
338A LEU* 4.6 1.4 - - - +
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Residues in contact with LYS 333 (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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302A VAL* 5.4 7.0 - - + -
308A SER* 3.2 29.8 + - - +
309A VAL 3.2 14.6 - - - +
310A ALA* 3.9 16.6 - - + -
314A ASP* 6.1 0.4 - - - +
329A LEU* 3.1 43.2 + - + +
330A ASN* 3.4 17.6 + - - +
332A PHE* 1.3 80.3 - - - +
334A ASP* 1.3 59.5 + - + +
335A ASN 3.7 1.3 + - - -
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Residues in contact with ASP 334 (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* 5.5 3.3 - - - +
330A ASN* 2.8 30.4 + - + +
331A PHE* 5.0 0.9 - - - -
333A LYS* 1.3 75.6 - - + +
335A ASN* 1.3 58.4 + - - +
336A THR* 4.0 7.9 + - - -
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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