Contacts of the strand formed by residues 323 - 330 (chain E) in PDB entry 3STJ
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 323 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319E LEU* 3.5 3.5 - - - -
320E ARG* 2.9 33.5 + - + +
321E ASN* 3.8 18.4 - - + +
322E GLY* 1.3 85.1 + - - +
324E PRO* 1.4 73.7 - - + +
325E LEU* 3.8 7.3 + - + +
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Residues in contact with PRO 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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318E LEU 3.6 8.7 - - - +
319E LEU* 3.8 13.4 - - + -
322E GLY 4.1 4.5 - - - +
323E LYS* 1.4 90.1 - - + +
325E LEU* 1.4 70.5 + - - +
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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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316E LEU 3.6 0.2 - - - +
317E GLY* 3.8 2.1 - - - -
318E LEU* 2.9 47.7 + - + +
320E ARG* 3.7 49.6 - - + +
323E LYS* 4.2 9.2 - - + +
324E PRO* 1.4 82.7 - - - +
326E GLU* 1.3 63.8 + - - +
327E VAL* 4.8 7.0 - - + -
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Residues in contact with GLU 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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289E SER* 5.2 0.7 - - - -
292E GLY* 4.5 12.5 + - - -
315E LYS* 3.4 45.2 - - - +
316E LEU 3.4 3.8 - - - +
317E GLY* 3.8 19.0 + - - -
325E LEU* 1.3 75.9 - - - +
327E VAL* 1.3 66.0 + - - +
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Residues in contact with VAL 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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279E ALA* 3.6 39.5 - - + +
280E GLY 5.4 1.1 - - - -
281E VAL* 4.2 13.5 - - + +
314E VAL 3.6 0.5 - - - +
315E LYS* 3.4 4.2 - - - -
316E LEU* 2.7 44.6 + - + +
318E LEU* 4.2 22.0 - - + -
320E ARG* 5.3 4.9 - - - +
325E LEU* 4.8 9.9 - - + -
326E GLU* 1.3 82.7 - - - +
328E GLU* 1.3 61.5 + - - +
329E VAL* 3.8 10.4 + - + -
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Residues in contact with GLU 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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120B ASN* 3.5 28.5 + - - -
121B PRO* 5.3 4.0 - - - +
279E ALA* 3.5 17.3 - - - +
313E LYS* 3.6 41.2 + - + +
314E VAL 3.3 10.8 - - - +
315E LYS* 3.5 31.1 - - + +
327E VAL* 1.3 71.4 - - - +
329E VAL* 1.3 61.8 + - - +
330E THR* 4.5 0.6 + - - +
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Residues in contact with VAL 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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242E LEU* 3.8 20.6 - - + +
275E GLY* 3.5 25.8 - - - -
276E SER* 3.6 10.8 - - - +
279E ALA* 3.7 17.0 - - + -
281E VAL* 4.2 5.2 - - + -
312E THR 3.6 1.0 - - - +
313E LYS* 3.3 3.1 - - - -
314E VAL* 2.8 40.6 + - + +
316E LEU* 3.8 23.8 - - + -
327E VAL* 3.8 13.5 - - + +
328E GLU* 1.3 77.5 - - - +
330E THR* 1.3 71.1 + - - +
331E LEU* 4.8 0.2 - - + -
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Residues in contact with THR 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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241E LEU 4.8 0.3 - - - +
275E GLY* 3.4 27.4 + - - -
311E GLY* 3.5 31.0 - - - +
312E THR 3.6 2.9 - - - -
313E LYS* 3.4 29.2 - - + +
328E GLU 5.7 0.2 - - - -
329E VAL* 1.3 74.6 - - - +
331E LEU* 1.3 64.4 + - - +
332E ASP* 3.7 2.9 + - - +
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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