Contacts of the strand formed by residues 323 - 330 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319F LEU* 3.5 3.9 - - - -
320F ARG* 2.9 31.5 + - + +
321F ASN* 3.8 18.2 - - + +
322F GLY* 1.3 85.6 + - - +
324F PRO* 1.4 75.9 - - + +
325F LEU* 3.8 7.4 + - + +
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Residues in contact with PRO 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F LEU 3.6 9.4 - - - +
319F LEU* 3.8 13.4 - - + -
322F GLY 4.1 4.7 - - - +
323F LYS* 1.4 90.7 - - + +
325F LEU* 1.3 70.4 + - - +
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Residues in contact with LEU 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F GLY* 3.8 2.3 - - - -
318F LEU* 2.9 47.5 + - + +
320F ARG* 3.7 50.3 - - + +
323F LYS* 4.2 9.6 - - + +
324F PRO* 1.3 81.2 - - - +
326F GLU* 1.3 62.1 + - - +
327F VAL* 4.7 9.9 - - + -
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Residues in contact with GLU 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F SER* 5.2 0.9 - - - -
292F GLY* 4.6 12.3 + - - -
315F LYS* 3.4 44.7 - - - +
316F LEU 3.4 4.0 - - - +
317F GLY* 3.8 18.1 + - - -
325F LEU* 1.3 76.1 - - - +
327F VAL* 1.3 65.6 + - - +
328F GLU 4.5 0.2 + - - -
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Residues in contact with VAL 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F ALA* 3.4 44.0 - - + +
280F GLY 5.2 5.2 - - - +
281F VAL* 4.0 11.2 - - + -
314F VAL 3.6 0.9 - - - +
315F LYS* 3.5 4.4 - - - -
316F LEU* 2.7 44.5 + - + +
318F LEU* 4.3 21.8 - - + -
320F ARG* 5.3 2.5 - - - +
325F LEU* 4.7 9.2 - - + -
326F GLU* 1.3 81.7 - - - +
328F GLU* 1.3 57.9 + - - +
329F VAL* 3.8 10.2 + - + -
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Residues in contact with GLU 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F ALA* 3.3 17.2 - - - +
313F LYS* 3.6 44.6 + - + +
314F VAL 3.3 11.4 - - - +
315F LYS* 3.6 31.3 + - + +
327F VAL* 1.3 71.4 - - - +
329F VAL* 1.3 61.1 + - - +
330F THR* 5.7 0.4 - - - -
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Residues in contact with VAL 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F LEU* 3.8 20.4 - - + +
275F GLY* 3.5 25.6 - - - -
276F SER* 3.5 12.3 - - - +
279F ALA* 3.8 17.0 - - + -
281F VAL* 4.3 5.8 - - + -
312F THR 3.6 1.2 - - - +
313F LYS* 3.3 3.5 - - - -
314F VAL* 2.8 38.2 + - + +
316F LEU* 3.8 24.5 - - + -
327F VAL* 3.8 13.5 - - + +
328F GLU* 1.3 76.4 - - - +
330F THR* 1.3 73.0 + - - +
331F LEU* 4.8 0.7 - - + -
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Residues in contact with THR 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F GLY* 3.4 26.8 + - - -
311F GLY* 3.5 31.6 - - - +
312F THR 3.6 2.9 - - - -
313F LYS* 3.4 29.5 - - + +
328F GLU 4.4 0.6 + - - -
329F VAL* 1.3 74.3 - - - +
331F LEU* 1.3 64.5 + - - +
332F ASP* 3.6 3.1 + - - +
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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