Contacts of the helix formed by residues 320 - 330 (chain E) in PDB entry 7V3X
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 320 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319E GLU* 1.3 77.5 - - - +
321E ARG* 1.3 59.7 + - - +
322E ALA* 4.0 10.2 + - - +
323E GLN* 3.4 21.0 + - - +
324E LEU* 3.0 26.0 + - - +
348E CYS* 3.9 6.3 - - - -
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Residues in contact with ARG 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E SER* 1.3 70.3 - - - +
322E ALA* 1.3 55.2 - - - +
324E LEU* 3.6 5.6 - - - +
325E LEU* 2.8 47.1 + - + +
339E GLU* 3.7 27.4 + - - -
346E ILE* 3.4 51.6 + - + +
347E VAL* 5.0 0.4 - - - +
348E CYS* 3.4 26.7 - - - +
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Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E SER* 3.2 10.9 - - - +
321E ARG* 1.3 77.4 - - - +
323E GLN* 1.3 57.4 - - - +
325E LEU* 3.2 12.0 + - - +
326E ARG* 3.0 27.3 + - - +
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Residues in contact with GLN 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E GLU* 3.7 24.3 - - + +
320E SER* 3.4 18.8 + - - +
322E ALA* 1.3 75.7 - - - +
324E LEU* 1.3 56.4 + - - +
326E ARG* 3.7 30.9 - - - +
327E ASN* 2.8 59.0 + - - +
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Residues in contact with LEU 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E THR* 4.2 15.7 - - + -
314E LEU* 3.9 24.9 - - + -
316E ALA* 3.3 33.7 - - + -
319E GLU* 3.6 38.6 - - + +
320E SER 3.0 17.1 + - - +
321E ARG* 3.6 5.6 - - - +
323E GLN* 1.3 74.5 - - - +
325E LEU* 1.3 59.1 + - - +
327E ASN* 4.3 3.5 - - + +
328E ALA* 3.0 32.6 + - - +
335E PHE* 4.9 5.8 - - + -
346E ILE* 4.2 16.2 - - + -
348E CYS* 4.2 0.4 - - - -
378E ASP* 6.3 1.3 - - + -
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Residues in contact with LEU 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E ARG* 2.8 39.6 + - + +
322E ALA* 3.2 8.3 + - - +
324E LEU* 1.3 71.4 - - - +
326E ARG* 1.3 57.9 + - - +
328E ALA* 3.7 4.0 - - - +
329E TYR* 2.9 30.9 + - - +
335E PHE* 3.4 29.5 - - + +
336E GLU* 3.4 27.4 - - + +
339E GLU* 4.0 17.9 - - - +
346E ILE* 5.1 2.5 - - + -
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Residues in contact with ARG 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E ALA 3.0 14.9 + - - +
323E GLN* 3.7 27.5 + - - +
324E LEU 3.3 0.2 - - - -
325E LEU* 1.3 74.9 - - - +
327E ASN* 1.3 86.3 + - - +
329E TYR* 3.2 6.0 + - - +
330E SER* 3.0 39.7 + - - +
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Residues in contact with ASN 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E THR* 6.4 1.3 - - + -
319E GLU* 3.2 25.6 + - - +
323E GLN* 2.8 34.8 + - - +
324E LEU* 4.3 3.8 - - + +
326E ARG* 1.3 102.2 + - - +
328E ALA* 1.3 60.9 + - - +
330E SER* 3.6 8.5 + - - -
331E TRP* 3.3 43.6 + - + -
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Residues in contact with ALA 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E SER* 4.9 3.4 - - - +
324E LEU 3.0 22.0 + - - +
325E LEU 3.7 2.9 - - - +
327E ASN* 1.3 73.6 - - - +
329E TYR* 1.3 52.6 + - - +
331E TRP* 2.8 29.3 + - - +
332E GLY 2.5 22.9 - - - +
333E MET* 3.3 6.5 - - + +
335E PHE* 3.2 42.0 - - + -
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Residues in contact with TYR 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E LEU 2.9 20.1 + - - +
326E ARG* 3.2 6.7 + - - +
328E ALA* 1.3 74.7 - - - +
330E SER* 1.3 61.5 + - - +
331E TRP 3.1 0.2 - - - -
332E GLY* 3.0 21.3 + - - +
333E MET 3.4 7.6 + - - +
334E ASP* 3.8 32.8 - - + -
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Residues in contact with SER 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E ARG* 3.0 23.5 + - - +
327E ASN* 3.8 9.4 - - - -
328E ALA 3.2 0.4 - - - -
329E TYR* 1.3 76.6 - - - +
331E TRP* 1.3 61.9 + - - +
332E GLY 3.4 2.8 + - - -
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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