Contacts of the strand formed by residues 362 - 373 (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 ALA 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A GLN* 3.8 31.2 - - - +
351A TRP 3.3 5.8 - - - -
352A GLN* 4.0 5.8 - - + -
359A SER 4.4 0.7 - - - +
360A ARG* 4.2 15.7 - - - -
361A PRO* 1.3 75.6 - - - +
363A ILE* 1.3 62.9 + - - +
364A ARG* 4.0 12.9 - - - +
416A GLN 3.8 0.5 - - - +
417A MET* 3.2 7.6 - - - +
418A GLU 3.0 29.9 + - - +
58C PHE* 5.5 0.2 - - - -
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Residues in contact with ILE 363 (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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350A GLN* 3.3 4.9 - - - +
351A TRP* 2.8 42.1 + - + +
362A ALA* 1.3 78.3 - - - +
364A ARG* 1.3 66.3 + - - +
365A VAL* 5.6 3.1 - - + -
415A ALA* 5.9 0.7 - - + -
416A GLN 3.5 6.5 - - - +
417A MET* 4.5 4.9 - - + -
58C PHE* 4.3 6.1 - - + -
86C VAL* 3.9 32.1 - - + +
88C GLY* 3.9 11.7 - - - +
100C ILE* 3.6 51.8 - - + +
101C TRP* 4.3 4.9 - - - +
102C ALA* 4.4 15.0 - - + +
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Residues in contact with ARG 364 (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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33A ARG* 6.1 1.8 - - - +
34A LEU* 3.9 26.4 - - + +
37A GLU* 4.4 4.8 + - - -
311A ARG* 4.1 10.3 - - - +
348A ALA* 4.6 11.2 - - + -
349A GLN 3.5 5.6 - - - +
350A GLN* 3.3 31.1 + - + +
360A ARG* 3.3 22.2 - - - +
362A ALA* 4.1 7.9 - - + +
363A ILE* 1.3 80.0 - - - +
365A VAL* 1.3 64.3 + - - +
366A PHE* 4.2 6.7 - - + -
415A ALA* 3.1 7.3 - - - +
416A GLN* 2.8 70.7 + - + +
418A GLU* 2.8 43.8 + - - +
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Residues in contact with VAL 365 (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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348A ALA* 3.1 2.8 - - - -
349A GLN* 2.8 41.9 + - + +
351A TRP* 4.5 17.5 - - + -
363A ILE* 5.6 3.6 - - + -
364A ARG* 1.3 77.0 - - - +
366A PHE* 1.3 63.9 + - - +
414A GLY 3.4 9.4 - - - +
415A ALA* 4.3 13.2 - - + -
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Residues in contact with PHE 366 (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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11A ILE 4.8 0.4 - - - -
20A GLN* 3.5 30.1 - - - -
34A LEU* 6.0 1.3 - - + -
35A GLY* 3.5 37.9 - - - +
346A THR* 4.2 7.6 - - + -
347A LEU 3.2 10.8 - - - +
348A ALA* 3.9 11.4 - - + -
364A ARG* 4.7 8.1 - - + -
365A VAL* 1.3 79.6 - - - +
367A ALA* 1.3 65.3 + - - +
368A THR* 3.8 7.2 - - - -
412A THR* 4.0 6.3 - - - -
413A PHE* 3.2 15.8 - - - +
414A GLY* 2.9 65.1 + - - +
415A ALA* 3.8 13.5 - - - -
416A GLN* 4.4 11.9 - - + -
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Residues in contact with ALA 367 (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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345A ILE 4.0 0.7 - - - +
346A THR* 3.3 4.0 - - - +
347A LEU* 2.9 39.4 + - + +
366A PHE* 1.3 75.9 - - - +
368A THR* 1.3 62.4 + - - +
411A TRP* 5.6 6.5 - - + -
412A THR 3.3 9.6 - - - +
413A PHE* 4.5 6.3 - - + -
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Residues in contact with THR 368 (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* 4.3 14.6 - - + -
35A GLY* 2.8 24.0 + - - +
344A LYS* 3.9 21.3 - - + -
345A ILE 3.4 3.1 - - - -
346A THR* 2.7 30.7 + - - +
366A PHE* 3.8 0.7 - - - -
367A ALA* 1.3 73.8 - - - +
369A TYR* 1.3 67.2 + - - +
411A TRP* 3.0 8.7 - - - +
412A THR* 2.6 54.4 + - - +
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Residues in contact with TYR 369 (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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343A TYR* 4.0 22.5 + + - -
344A LYS* 3.4 2.4 - - - +
345A ILE* 2.7 58.0 + - + +
368A THR* 1.3 79.8 - - - +
370A ALA* 1.3 62.3 - - - +
371A LYS* 3.8 21.5 - - + +
409A ASP* 2.4 44.6 + - - -
410A GLU 3.6 12.8 - - - -
411A TRP* 4.3 13.2 - + + -
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Residues in contact with ALA 370 (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* 3.7 41.5 - - + -
342A GLN* 4.4 4.5 - - - +
343A TYR 3.4 9.2 - - - +
344A LYS* 4.2 7.4 - - + -
368A THR* 4.7 0.4 - - - +
369A TYR* 1.3 80.3 - - - +
371A LYS* 1.3 60.5 + - - +
372A TRP* 3.8 10.5 - - + -
409A ASP* 3.5 4.5 - - - +
410A GLU 2.9 33.0 + - - +
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Residues in contact with LYS 371 (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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341A ASN* 4.9 4.0 + - - +
342A GLN* 3.3 2.7 - - - -
343A TYR* 3.0 66.7 + - + +
369A TYR* 3.8 8.0 - - + +
370A ALA* 1.3 73.7 - - - +
372A TRP* 1.3 86.2 + - - +
373A ASP* 4.5 7.0 - - - +
407A ASP* 2.9 25.8 + - - -
408A SER* 3.3 13.2 + - - +
409A ASP* 3.0 22.1 - - - +
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Residues in contact with TRP 372 (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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21A GLN* 6.1 0.7 - - - -
23A PHE* 3.8 20.2 - + - -
341A ASN* 3.3 12.1 - - - +
342A GLN* 3.8 20.2 - - + +
370A ALA* 3.8 21.1 - - + -
371A LYS* 1.3 86.5 + - - +
373A ASP* 1.3 61.6 + - - +
374A GLU* 4.3 4.9 - - + -
405A ARG* 3.0 66.4 + - + +
406A GLY 3.4 14.6 - - - -
408A SER* 2.9 55.8 + - - +
409A ASP 3.8 19.1 - - - -
410A GLU* 3.8 9.4 - - + -
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Residues in contact with ASP 373 (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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339A LYS 4.1 2.6 - - - +
340A ASN* 3.6 2.3 - - - -
341A ASN* 2.9 50.9 + - - +
371A LYS* 4.5 6.2 - - - -
372A TRP* 1.3 77.4 - - - +
374A GLU* 1.3 62.9 + - - +
375A LYS* 3.5 35.2 + - - +
406A GLY 3.5 3.8 - - - -
407A ASP* 4.1 24.8 - - - +
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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