Contacts of the strand formed by residues 323 - 330 (chain A) in PDB entry 1SLL
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 ILE 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASP* 3.7 23.1 - - + +
311A ALA 3.3 14.4 - - - +
312A ARG* 3.9 20.4 - - + +
313A TYR* 4.2 0.4 - - - -
317A HIS 3.7 22.0 - - - +
319A SER* 3.8 25.8 - - - +
321A SER* 4.2 11.2 - - - +
322A LYS* 1.3 83.0 + - - +
324A ASN* 1.3 80.2 + - - +
346A PHE* 5.3 0.3 - - - +
371A ALA 4.5 0.6 + - - +
372A SER* 3.5 12.7 - - - -
373A TYR* 3.0 37.7 + - - +
374A ILE* 4.2 3.6 - - + -
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Residues in contact with ASN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASP* 3.6 1.7 - - - -
311A ALA* 2.7 29.1 + - + -
313A TYR* 3.3 32.3 + - + +
322A LYS* 3.7 17.7 + - - +
323A ILE* 1.3 85.8 - - - +
325A ILE* 1.3 66.0 + - - +
342A LEU* 4.0 18.4 - - + +
344A LEU 3.6 7.6 - - - +
345A LYS* 3.2 34.8 - - + +
346A PHE* 3.2 9.9 + - - +
347A ASP* 5.8 0.2 + - - -
351A ALA* 4.4 4.6 - - - +
373A TYR* 4.5 2.7 - - - -
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 4.3 0.9 - - + -
309A ALA 3.6 4.0 - - - +
310A ASP* 3.5 26.2 - - - +
324A ASN* 1.3 78.6 - - - +
326A ALA* 1.3 69.1 + - - +
342A LEU* 3.3 11.2 - - - +
343A PRO* 3.3 18.4 - - - +
344A LEU* 2.9 21.9 + - + +
373A TYR* 3.7 32.3 - - + +
374A ILE* 4.0 3.4 - - - +
376A PRO* 4.0 24.9 - - + -
389A LEU* 4.0 23.6 - - + -
391A ALA* 3.8 15.7 - - + -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 3.7 23.6 - - + -
287A THR* 3.8 22.0 - - + -
292A PHE* 4.7 2.0 - - + -
308A ALA* 3.0 28.4 - - - +
309A ALA 2.9 14.7 + - - +
311A ALA* 4.4 8.5 - - + -
324A ASN 4.0 1.2 + - - -
325A ILE* 1.3 74.9 - - - +
327A PHE* 1.3 61.1 + - - +
341A THR 3.2 10.1 - - - +
342A LEU* 3.8 4.5 - - + -
343A PRO* 4.3 0.4 - - - -
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 3.7 2.9 - - - -
306A ILE* 3.8 45.1 - - + -
307A SER 3.3 18.4 - - - -
308A ALA* 4.7 3.1 - - + -
326A ALA* 1.3 76.8 - - - +
328A ALA* 1.3 70.4 + - - +
329A LYS* 4.6 5.6 - - + -
339A GLU 4.5 0.7 - - - +
340A PRO* 3.2 6.6 - - - +
341A THR* 2.9 43.3 + - - +
343A PRO* 3.5 22.7 - - + -
378A LEU* 4.4 9.9 - - + -
387A ILE* 4.2 3.1 - - + -
389A LEU* 5.4 2.9 - - + -
516A GLU 3.8 11.7 - - - -
517A GLY* 3.8 21.3 - - - -
520A TRP* 3.9 27.8 - + - -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 3.7 28.5 - - + +
281A PHE* 3.8 8.0 - - + -
306A ILE* 3.5 2.9 - - - +
307A SER* 2.8 37.3 + - - +
327A PHE* 1.3 84.3 - - - +
329A LYS* 1.3 60.7 + - - +
337A TRP* 3.9 4.0 - - + -
338A SER* 3.8 24.0 - - - +
340A PRO* 4.5 2.5 - - + -
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A THR* 4.1 17.3 - - + -
305A VAL 3.3 10.5 - - - +
306A ILE* 3.9 12.6 - - + -
327A PHE* 4.6 5.2 - - + -
328A ALA* 1.3 77.4 - - - +
330A SER* 1.3 59.0 + - - +
331A THR* 4.3 12.1 - - + +
337A TRP* 3.4 7.5 - - - -
338A SER* 2.9 41.7 + - - +
515A ASP 4.2 5.9 + - - -
516A GLU* 3.4 37.1 + - + +
517A GLY 5.3 0.6 - - - -
518A ALA* 4.9 7.1 - - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLY 4.4 0.5 - - - +
304A THR* 3.5 5.4 - - - +
305A VAL* 2.7 36.2 + - - +
329A LYS* 1.3 74.7 - - - +
331A THR* 1.3 61.4 + - - +
332A ASP* 2.7 27.4 + - - -
333A GLY 4.9 0.2 + - - -
334A GLY* 2.9 25.5 + - - -
336A THR 2.9 15.3 + - - -
337A TRP* 3.6 19.7 - - - -
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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