Contacts of the strand formed by residues 323 - 330 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319D LEU* 3.5 4.1 - - - -
320D ARG* 2.9 32.6 + - + +
321D ASN* 3.9 17.7 - - + +
322D GLY* 1.3 82.8 + - - +
324D PRO* 1.4 76.2 - - + +
325D LEU* 3.8 7.6 + - + +
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Residues in contact with PRO 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D LEU 3.6 9.2 - - - +
319D LEU* 3.8 13.9 - - + -
322D GLY 4.1 4.9 - - - +
323D LYS* 1.4 89.8 - - + +
325D LEU* 1.3 71.1 + - - +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D LEU 3.6 0.2 - - - +
317D GLY* 3.8 1.9 - - - -
318D LEU* 2.9 48.0 + - + +
320D ARG* 3.7 50.3 - - + +
323D LYS* 4.2 9.4 - - + +
324D PRO* 1.3 83.4 - - - +
326D GLU* 1.3 64.8 + - - +
327D VAL* 4.8 6.7 - - + -
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D SER* 5.2 0.9 - - - -
292D GLY* 4.5 12.6 + - - -
315D LYS* 3.4 45.7 - - - +
316D LEU 3.4 4.0 - - - +
317D GLY* 3.9 19.1 + - - -
325D LEU* 1.3 75.8 - - - +
327D VAL* 1.3 65.1 + - - +
328D GLU 4.4 0.2 - - - -
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Residues in contact with VAL 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ALA* 3.4 43.3 - - + +
280D GLY 5.3 0.7 - - - +
281D VAL* 4.0 10.1 - - + -
314D VAL 3.6 0.7 - - - +
315D LYS* 3.5 4.1 - - - -
316D LEU* 2.7 46.2 + - + +
318D LEU* 4.2 19.5 - - + -
320D ARG* 5.3 6.5 - - - +
325D LEU* 4.8 9.0 - - + -
326D GLU* 1.3 82.4 - - - +
328D GLU* 1.3 61.0 + - - +
329D VAL* 3.8 9.5 + - + -
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Residues in contact with GLU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ALA* 3.4 16.1 - - - +
313D LYS* 3.6 43.7 + - + +
314D VAL 3.3 10.5 - - - +
315D LYS* 3.5 31.5 - - + +
327D VAL* 1.3 71.8 - - - +
329D VAL* 1.3 60.2 + - - +
330D THR 4.4 0.3 + - - -
122G SER* 4.4 16.9 + - - -
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D LEU* 3.8 20.4 - - + +
275D GLY* 3.5 25.6 - - - -
276D SER* 3.6 10.8 - - - +
279D ALA* 3.7 17.3 - - + -
281D VAL* 4.3 5.6 - - + -
312D THR 3.6 1.2 - - - +
313D LYS* 3.3 3.8 - - - -
314D VAL* 2.8 40.6 + - + +
316D LEU* 3.8 23.8 - - + -
327D VAL* 3.8 13.7 - - + +
328D GLU* 1.3 77.5 - - - +
330D THR* 1.3 70.9 + - - +
331D LEU* 4.8 0.7 - - + -
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Residues in contact with THR 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LEU 4.8 0.3 - - - +
275D GLY* 3.4 27.1 + - - -
311D GLY* 3.5 31.6 - - - +
312D THR 3.6 3.1 - - - +
313D LYS* 3.4 29.8 - - + +
328D GLU 4.4 0.4 + - - -
329D VAL* 1.3 73.9 - - - +
331D LEU* 1.3 64.8 + - - +
332D 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