Contacts of the strand formed by residues 339 - 352 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ASN* 3.9 29.6 - - - +
331B VAL 3.2 3.8 - - - +
332B GLU* 2.9 37.3 + - + +
337B GLY 4.1 7.8 + - - +
338B ASP* 1.3 79.6 - - - +
340B ASN* 1.3 63.1 + - - +
341B ASN* 4.2 3.0 - - - +
373B ASP 4.1 3.3 - - - +
375B LYS* 3.4 30.9 + - + +
376B TRP* 3.8 0.4 - - - -
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Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.9 10.6 - - + +
26B THR* 3.0 36.2 + - - +
330B ASN* 3.3 3.3 + - - -
331B VAL* 2.6 42.2 + - + +
339B LYS* 1.3 71.6 - - - +
341B ASN* 1.3 61.6 + - - +
373B ASP 3.6 2.7 - - - -
374B GLU* 3.0 15.2 - - + +
375B LYS 2.9 24.8 + - - -
376B TRP* 3.0 46.2 + - - +
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 4.5 2.9 - - - -
328B TYR* 4.0 14.5 - - + +
329B ASP 3.1 12.3 - - - +
330B ASN* 3.7 17.1 + - - +
339B LYS* 5.3 3.3 - - - +
340B ASN* 1.3 76.0 - - - +
342B GLN* 1.3 69.3 + - - +
343B TYR* 5.1 4.9 - - - +
371B LYS* 4.9 3.8 + - - +
372B TRP* 3.3 4.5 - - - +
373B ASP* 2.9 59.8 + - - +
374B GLU* 4.7 1.9 - - - +
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.3 35.0 + - - +
24B GLN* 4.1 0.8 - - - +
25B THR* 3.2 23.5 + - - +
31B LYS* 5.8 0.6 - - - +
32B TYR* 6.2 0.6 - - - +
327B GLY 3.9 0.7 - - - +
328B TYR* 3.3 6.4 - - - -
329B ASP* 2.8 42.6 + - + +
341B ASN* 1.3 77.2 - - - +
343B TYR* 1.3 71.9 + - - +
344B LYS* 4.3 11.7 - - - +
370B ALA* 4.4 3.8 - - - -
371B LYS 3.3 16.8 - - - +
372B TRP* 3.9 8.3 - - + +
405B ARG* 3.0 38.1 + - - +
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Residues in contact with TYR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 5.8 4.3 - - + -
327B GLY 3.2 8.5 - - - +
328B TYR* 4.2 15.9 - + + -
341B ASN* 5.5 5.4 - - - -
342B GLN* 1.3 78.5 - - - +
344B LYS* 1.3 62.5 + - - +
345B ILE* 3.9 31.0 - - + -
369B TYR* 4.0 20.5 + + - -
370B ALA* 3.4 1.4 - - - -
371B LYS* 3.0 66.1 + - + +
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 5.1 0.9 - - + -
32B TYR* 3.1 25.3 + - + +
34B LEU 2.6 28.5 + - - -
36B ASN* 3.7 24.7 - - - +
325B GLU* 2.7 27.9 + - - +
326B ILE* 3.4 5.4 - - - +
327B GLY 2.8 37.9 + - - +
342B GLN* 4.6 11.9 - - - +
343B TYR* 1.3 75.4 - - - +
345B ILE* 1.3 65.6 + - - +
346B THR* 3.0 17.5 + - - +
368B THR* 3.8 16.4 - - + -
369B TYR 3.4 10.1 - - - +
370B ALA* 4.2 10.8 - - + +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B MET* 5.2 10.5 - - + -
325B GLU 3.4 6.1 - - - +
326B ILE* 4.4 22.7 - - + -
343B TYR* 3.9 30.1 - - + -
344B LYS* 1.3 78.9 - - - +
346B THR* 1.3 69.7 + - - +
347B LEU* 6.2 1.1 - - + -
367B ALA 4.1 0.5 - - - +
368B THR* 3.4 1.2 - - - -
369B TYR* 2.7 54.9 + - + +
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.0 41.4 + - + +
324B MET* 3.2 9.4 - - - +
325B GLU* 2.8 43.0 + - - +
344B LYS* 3.0 17.3 + - - -
345B ILE* 1.3 79.0 + - - +
347B LEU* 1.3 68.5 + - - +
366B PHE* 4.2 9.6 - - + -
367B ALA 3.4 7.2 - - - +
368B THR* 2.7 26.6 + - - +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B THR* 4.0 20.2 - - + -
323B VAL 3.7 8.3 - - - +
324B MET* 3.9 27.1 - - + -
345B ILE* 6.2 1.3 - - + -
346B THR* 1.3 74.0 - - - +
348B ALA* 1.3 65.3 + - - +
366B PHE* 3.2 2.6 - - - -
367B ALA* 2.9 37.8 + - + +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.3 16.8 - - + -
322B THR* 3.4 7.6 - - - +
323B VAL* 2.7 50.0 + - + +
346B THR 4.3 0.2 - - - -
347B LEU* 1.3 77.3 - - - +
349B GLN* 1.3 64.2 + - - +
350B GLN* 5.3 0.2 - - + -
364B ARG* 4.6 13.2 - - + -
365B VAL 3.1 12.3 - - - +
366B PHE* 3.9 11.4 - - + -
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B TRP* 3.9 8.0 + - - -
320B MET* 3.8 20.6 - - + +
321B SER 3.4 10.0 + - - +
322B THR* 2.5 35.4 + - - +
348B ALA* 1.3 72.6 - - - +
350B GLN* 1.3 62.9 + - - +
351B TRP* 3.9 29.4 - - + -
364B ARG* 3.4 2.3 - - - -
365B VAL* 2.8 39.0 + - + +
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 5.3 1.4 - - - +
313B MET* 4.1 6.1 - - - +
320B MET* 3.3 6.6 - - - +
321B SER* 2.8 51.6 + - - +
323B VAL* 3.9 23.9 - - + +
348B ALA* 5.0 1.7 - - + +
349B GLN* 1.3 77.5 - - - +
351B TRP* 1.3 73.1 + - - +
352B GLN* 3.1 32.1 + - - +
356B SER 5.3 1.0 + - - -
357B ILE* 5.8 2.0 + - - +
359B SER 5.2 1.6 + - - -
360B ARG* 5.5 3.3 + - - +
362B ALA* 3.8 12.2 - - + +
363B ILE 3.3 11.2 - - - +
364B ARG* 3.3 33.5 + - + +
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Residues in contact with TRP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 4.1 6.9 - - + -
91A LEU* 4.1 33.2 + - + -
92A ILE* 4.2 23.1 - - + +
100A ILE* 3.8 30.7 - - + -
319B ILE* 3.2 9.6 - - + +
320B MET* 3.7 41.0 - - + +
349B GLN* 3.9 30.5 - - + -
350B GLN* 1.3 75.0 - - - +
352B GLN* 1.3 61.4 + - - +
361B PRO 4.1 0.2 - - - +
362B ALA* 3.3 1.2 - - - -
363B ILE* 2.8 47.9 + - + +
365B VAL* 4.4 19.1 - - + -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.7 7.7 - - - -
313B MET* 3.7 17.8 - - - +
315B LYS* 6.0 0.8 - - - +
317B THR 5.0 0.8 + - - -
318B PRO 3.5 4.9 + - - -
319B ILE* 2.9 51.8 + - - +
320B MET 4.0 1.2 + - - +
321B SER* 2.9 23.1 + - - -
350B GLN* 3.1 24.8 + - - +
351B TRP* 1.3 74.8 - - - +
353B ALA* 1.3 57.4 + - - +
354B GLY 2.8 32.8 + - - +
355B ASP* 4.2 1.6 - - - +
356B SER 4.2 4.0 - - - +
359B SER* 3.9 20.6 - - - +
361B PRO 3.2 12.1 - - - +
362B ALA* 4.0 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
------------------------------------------------------------
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