Contacts of the strand formed by residues 339 - 352 (chain A) in PDB entry 1AF6
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 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A ASN* 3.7 30.5 - - - +
331A VAL 3.2 4.0 - - - +
332A GLU* 2.6 41.9 + - + +
337A GLY 4.1 7.0 + - - +
338A ASP* 1.3 79.3 + - - +
340A ASN* 1.3 62.6 + - - +
341A ASN* 4.2 3.9 - - - +
373A ASP 4.1 3.1 - - - +
375A LYS* 3.3 31.6 + - + +
376A TRP* 3.8 0.4 - - - -
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Residues in contact with ASN 340 (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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25A THR* 3.9 11.2 - - + +
26A THR* 3.1 36.5 + - - +
329A ASP 3.9 0.2 - - - +
330A ASN* 3.3 3.6 + - - -
331A VAL 2.7 40.2 + - - +
339A LYS* 1.3 71.4 - - - +
341A ASN* 1.3 62.4 + - - +
373A ASP 3.6 2.9 - - - -
374A GLU* 3.0 13.6 - - + -
375A LYS 2.8 25.5 + - - -
376A TRP* 3.0 45.2 + - - +
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 4.4 3.6 - - - -
328A TYR* 4.0 14.5 - - + +
329A ASP 3.1 12.6 - - - +
330A ASN* 3.7 18.1 + - - +
339A LYS* 5.3 3.3 - - - +
340A ASN* 1.3 77.0 - - - +
342A GLN* 1.3 67.6 + - - +
343A TYR* 5.1 5.1 - - - +
371A LYS* 4.9 3.8 + - - +
372A TRP* 3.3 4.7 - - - +
373A ASP* 2.9 60.4 + - - +
374A GLU* 4.7 1.7 - - - +
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Residues in contact with GLN 342 (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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23A PHE* 3.3 35.0 + - - +
24A GLN* 4.1 0.8 - - - +
25A THR* 3.3 21.3 + - - +
31A LYS* 5.8 0.4 - - - +
327A GLY 3.8 0.7 - - - +
328A TYR* 3.3 7.9 - - - -
329A ASP* 2.9 40.2 + - + +
341A ASN* 1.3 79.6 - - - +
343A TYR* 1.3 73.6 + - - +
344A LYS* 4.6 10.1 - - - +
370A ALA* 4.4 3.4 - - - -
371A LYS 3.3 16.8 - - - +
372A TRP* 3.8 8.7 - - + +
405A ARG* 2.9 37.6 + - - +
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Residues in contact with TYR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ILE* 5.8 4.0 - - + -
327A GLY 3.2 8.3 - - - +
328A TYR* 4.2 16.4 - + + -
341A ASN* 5.5 5.4 - - - -
342A GLN* 1.3 78.4 - - - +
344A LYS* 1.3 62.1 + - - +
345A ILE* 4.0 29.2 - - + -
369A TYR* 4.0 20.9 + + - -
370A ALA* 3.4 1.9 - - - -
371A LYS* 3.0 67.9 + - + +
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Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 5.1 0.7 - - + -
32A TYR* 3.1 30.0 + - + +
34A LEU 2.7 24.4 + - - -
36A ASN* 3.8 18.8 - - - +
325A GLU* 2.6 35.6 + - - +
326A ILE* 3.4 5.5 - - - +
327A GLY 2.8 37.5 + - - +
342A GLN* 4.6 11.2 - - - +
343A TYR* 1.3 76.4 - - - +
345A ILE* 1.3 65.9 + - - +
346A THR* 3.1 18.1 + - - +
368A THR* 3.9 12.8 - - + -
369A TYR 3.4 9.6 - - - +
370A ALA* 4.2 11.0 - - + -
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Residues in contact with ILE 345 (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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324A MET* 5.2 11.0 - - + -
325A GLU 3.4 6.3 - - - +
326A ILE* 4.4 22.4 - - + -
343A TYR* 4.0 29.4 - - + -
344A LYS* 1.3 78.9 - - - +
346A THR* 1.3 72.7 + - - +
347A LEU* 6.1 1.1 - - + -
367A ALA 4.0 0.2 - - - +
368A THR* 3.4 1.4 - - - -
369A TYR* 2.7 56.6 + - + +
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Residues in contact with THR 346 (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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34A LEU* 3.1 33.2 + - + +
35A GLY* 4.2 4.0 - - - -
324A MET* 3.1 10.8 - - - +
325A GLU* 2.8 41.6 + - - +
344A LYS* 3.1 26.2 + - - -
345A ILE* 1.3 78.5 - - - +
347A LEU* 1.3 66.8 + - - +
366A PHE* 4.2 6.1 - - + -
367A ALA 3.3 7.9 - - - +
368A THR* 2.7 26.1 + - - +
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Residues in contact with LEU 347 (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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322A THR* 4.0 20.2 - - + -
323A VAL 3.7 7.9 - - - +
324A MET* 3.9 27.1 - - + -
345A ILE* 6.1 1.1 - - + -
346A THR* 1.3 74.7 - - - +
348A ALA* 1.3 66.3 + - - +
366A PHE* 3.2 2.4 - - - -
367A ALA* 2.9 38.5 + - + +
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Residues in contact with ALA 348 (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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34A LEU* 4.3 17.9 - - + -
322A THR* 3.4 7.5 - - - +
323A VAL* 2.7 49.7 + - + +
347A LEU* 1.3 76.0 - - - +
349A GLN* 1.3 63.8 + - - +
350A GLN* 4.1 0.4 - - + -
364A ARG* 4.6 13.2 - - + -
365A VAL 3.1 11.4 - - - +
366A PHE* 3.9 11.7 - - + -
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Residues in contact with GLN 349 (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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316A TRP* 3.9 7.4 + - - -
320A MET* 3.8 20.0 - - - +
321A SER 3.3 11.2 + - - +
322A THR* 2.6 34.6 + - - +
348A ALA* 1.3 72.1 - - - +
350A GLN* 1.3 62.8 + - - +
351A TRP* 3.9 30.0 - - + -
364A ARG* 3.5 2.4 - - - -
365A VAL* 2.8 38.2 + - + +
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Residues in contact with GLN 350 (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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34A LEU* 5.4 1.4 - - - +
313A MET* 4.1 7.1 - - - +
319A ILE 3.8 0.3 - - - +
320A MET* 3.3 6.9 - - - +
321A SER* 2.8 52.1 + - - +
323A VAL* 4.0 23.4 - - + +
348A ALA* 5.0 1.9 - - + +
349A GLN* 1.3 76.9 - - - +
351A TRP* 1.3 72.8 + - - +
352A GLN* 3.1 31.3 + - - +
356A SER 5.3 1.0 + - - -
357A ILE* 5.7 1.8 + - - +
359A SER 5.3 1.2 + - - -
360A ARG* 5.5 3.9 + - - +
362A ALA* 3.8 12.8 - - + +
363A ILE 3.3 10.3 - - - +
364A ARG* 3.3 32.8 + - + +
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Residues in contact with TRP 351 (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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319A ILE* 3.2 10.1 - - + +
320A MET* 3.7 40.1 - - + +
349A GLN* 3.9 30.7 - - + -
350A GLN* 1.3 74.9 - - - +
352A GLN* 1.3 60.2 + - - +
362A ALA* 3.3 1.4 - - - -
363A ILE* 2.8 48.0 + - + +
365A VAL* 4.5 19.5 - - + -
58C PHE* 4.1 6.4 - - + -
91C LEU* 4.1 33.7 + - + -
92C ILE* 4.2 24.9 - - + +
100C ILE* 3.8 32.3 - - + -
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Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 3.7 19.2 - - - +
315A LYS* 6.0 0.6 - - - +
317A THR 5.0 1.2 + - - -
318A PRO 3.4 12.7 + - - -
319A ILE* 2.8 43.7 + - - +
320A MET 4.1 1.0 - - - +
321A SER* 2.9 23.0 + - - -
350A GLN* 3.1 23.3 + - - +
351A TRP* 1.3 74.8 - - - +
353A ALA* 1.3 58.1 + - - +
354A GLY 2.7 33.1 + - - +
355A ASP* 4.2 1.6 - - - +
356A SER 4.2 3.6 - - - +
359A SER* 3.9 17.5 - - - +
361A PRO 3.2 12.3 - - - +
362A ALA* 4.0 6.3 - - + -
58C PHE* 3.6 7.5 - - - -
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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