Contacts of the strand formed by residues 323 - 330 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319J LEU* 3.5 3.6 - - - -
320J ARG* 3.0 33.1 + - + +
321J ASN* 3.8 17.9 - - + +
322J GLY* 1.4 82.5 + - - +
324J PRO* 1.4 75.2 - - + +
325J LEU* 3.8 7.7 + - + +
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Residues in contact with PRO 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318J LEU 3.6 9.9 - - - +
319J LEU* 3.8 13.4 - - + -
322J GLY 4.1 5.6 - - - +
323J LYS* 1.4 89.2 - - + +
325J LEU* 1.3 70.2 + - - +
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Residues in contact with LEU 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317J GLY* 3.8 2.1 - - - -
318J LEU* 2.9 49.1 + - + +
320J ARG* 3.8 49.4 - - + +
323J LYS* 4.2 9.9 - - + +
324J PRO* 1.3 82.0 - - - +
326J GLU* 1.3 63.7 + - - +
327J VAL* 4.8 6.5 - - + -
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Residues in contact with GLU 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289J SER* 5.3 0.9 - - - -
292J GLY* 4.5 12.1 + - - -
315J LYS* 3.4 44.8 - - - +
316J LEU 3.4 4.2 - - - +
317J GLY* 3.9 18.9 + - - -
325J LEU* 1.3 77.2 - - - +
327J VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279J ALA* 3.4 43.7 - - + +
280J GLY 5.0 7.4 - - - +
281J VAL* 4.2 9.0 - - + -
314J VAL 3.6 0.5 - - - +
315J LYS* 3.5 3.8 - - - -
316J LEU* 2.7 46.8 + - + +
318J LEU* 4.2 20.4 - - + -
320J ARG* 5.3 1.8 - - - +
325J LEU* 4.8 9.2 - - + -
326J GLU* 1.3 82.9 - - - +
328J GLU* 1.3 61.9 + - - +
329J VAL* 3.8 9.9 + - + -
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Residues in contact with GLU 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D ASN* 4.4 16.3 + - - +
279J ALA* 3.3 17.5 - - - +
313J LYS* 3.6 45.0 + - + +
314J VAL 3.3 11.7 - - - +
315J LYS* 3.5 31.3 - - + +
326J GLU 4.4 0.2 - - - -
327J VAL* 1.3 71.6 - - - +
329J VAL* 1.3 60.2 + - - +
330J THR* 4.4 0.7 + - - -
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Residues in contact with VAL 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J LEU* 3.8 26.5 - - + +
275J GLY* 3.5 25.1 - - - -
276J SER* 3.6 5.2 - - - +
279J ALA* 3.8 16.8 - - + -
281J VAL* 4.4 5.4 - - + -
312J THR 3.6 1.2 - - - +
313J LYS* 3.3 4.1 - - - -
314J VAL* 2.8 40.0 + - + +
316J LEU* 3.8 28.3 - - + -
327J VAL* 3.8 10.1 - - + +
328J GLU* 1.3 76.4 - - - +
330J THR* 1.3 71.1 + - - +
331J LEU* 4.8 1.1 - - + -
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Residues in contact with THR 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241J LEU 4.8 0.2 - - - +
242J LEU 5.4 0.2 - - - +
275J GLY* 3.4 25.9 + - - -
311J GLY* 3.4 31.4 - - - +
312J THR 3.6 2.7 - - - -
313J LYS* 3.4 30.5 + - + +
328J GLU 5.5 0.3 + - - -
329J VAL* 1.3 75.9 - - - +
331J LEU* 1.3 64.9 + - - +
332J ASP* 3.7 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