Contacts of the strand formed by residues 362 - 373 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350C GLN* 3.8 31.0 - - - +
351C TRP 3.3 5.8 - - - -
352C GLN* 4.0 5.4 - - + -
359C SER 4.4 0.9 - - - +
360C ARG* 4.1 15.9 - - - -
361C PRO* 1.3 75.7 - - - +
363C ILE* 1.3 64.1 + - - +
364C ARG* 4.1 12.9 - - - +
416C GLN 3.8 0.3 - - - +
417C MET* 3.2 8.3 - - - +
418C GLU 3.0 29.5 + - - +
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Residues in contact with ILE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 4.3 9.2 - - + -
86B VAL* 3.9 33.2 - - + +
88B GLY 3.9 9.9 - - - +
100B ILE* 3.6 50.7 - - + +
101B TRP* 4.4 5.4 - - - +
102B ALA* 4.4 13.9 - - + +
350C GLN* 3.3 4.0 - - - -
351C TRP* 2.8 44.6 + - + +
362C ALA* 1.3 76.2 - - - +
364C ARG* 1.3 66.1 + - - +
365C VAL* 5.6 2.7 - - + -
415C ALA* 5.9 0.9 - - + -
416C GLN 3.5 5.6 - - - +
417C MET* 4.5 4.9 - - + -
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Residues in contact with ARG 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 6.1 1.6 - - - +
34C LEU* 3.8 26.6 - - + +
37C GLU* 4.4 4.6 + - - -
311C ARG* 4.0 10.3 - - - +
348C ALA* 4.6 11.4 - - + -
349C GLN 3.4 5.8 - - - +
350C GLN* 3.3 31.6 + - + +
360C ARG* 3.3 22.2 - - - +
362C ALA* 4.1 7.5 - - + +
363C ILE* 1.3 78.8 - - - +
365C VAL* 1.3 63.6 + - - +
366C PHE* 4.6 6.7 - - + -
415C ALA* 3.1 8.3 - - - +
416C GLN* 2.8 71.5 + - + +
418C GLU* 2.9 42.9 + - - +
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Residues in contact with VAL 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ALA* 3.1 3.1 - - - -
349C GLN* 2.8 40.7 + - + +
351C TRP* 4.3 19.3 - - + -
363C ILE* 5.6 3.8 - - + -
364C ARG* 1.3 78.6 - - - +
366C PHE* 1.3 64.1 + - - +
414C GLY 3.4 10.3 - - - +
415C ALA* 4.4 11.4 - - + -
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Residues in contact with PHE 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE 4.8 0.2 - - - -
20C GLN* 3.5 30.5 - - - -
34C LEU* 6.1 1.1 - - + -
35C GLY* 3.5 36.8 - - - +
346C THR* 4.2 7.4 - - + -
347C LEU 3.2 10.5 - - - +
348C ALA* 3.9 11.9 - - + -
364C ARG* 4.6 7.9 - - + -
365C VAL* 1.3 79.8 - - - +
367C ALA* 1.3 64.1 + - - +
368C THR* 3.8 7.4 - - - -
412C THR* 4.0 6.1 - - - -
413C PHE* 3.2 15.5 - - - +
414C GLY* 2.9 69.7 + - - +
415C ALA* 3.9 13.5 - - - -
416C GLN* 4.4 12.6 - - + -
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C ILE 4.0 0.3 - - - +
346C THR* 3.4 4.2 - - - +
347C LEU* 2.9 38.6 + - + +
366C PHE* 1.3 76.4 - - - +
368C THR* 1.3 62.8 + - - +
411C TRP* 5.5 7.0 - - + -
412C THR 3.3 9.0 - - - +
413C PHE* 4.5 6.3 - - + -
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Residues in contact with THR 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 4.2 15.5 - - + -
35C GLY* 2.9 22.8 + - - +
36C ASN* 5.2 0.2 - - + -
344C LYS* 3.9 21.5 - - + -
345C ILE 3.4 3.4 - - - -
346C THR* 2.7 31.2 + - - +
366C PHE* 3.8 1.0 - - - -
367C ALA* 1.3 73.5 + - - +
369C TYR* 1.3 66.4 + - - +
411C TRP* 3.0 8.0 - - - +
412C THR* 2.7 54.8 + - - +
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Residues in contact with TYR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C TYR* 4.0 16.8 + + - +
344C LYS* 3.4 2.4 - - - +
345C ILE* 2.7 62.4 + - + +
368C THR* 1.3 75.9 - - - +
370C ALA* 1.3 61.4 + - - +
371C LYS* 3.8 20.1 - - + +
409C ASP* 2.4 46.8 + - - -
410C GLU* 3.6 15.5 - - - -
411C TRP* 4.3 13.5 - + + -
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 3.6 41.1 - - + -
342C GLN* 4.4 4.5 - - - -
343C TYR 3.4 9.2 - - - +
344C LYS* 4.3 7.2 - - + -
368C THR* 4.6 0.4 - - - +
369C TYR* 1.3 79.9 - - - +
371C LYS* 1.3 60.7 + - - +
372C TRP* 3.8 10.6 - - + -
409C ASP* 3.5 4.3 - - - +
410C GLU 3.0 31.7 + - - +
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Residues in contact with LYS 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ASN* 4.9 3.1 + - - +
342C GLN* 3.3 3.0 - - - +
343C TYR* 3.0 68.5 + - + +
369C TYR* 3.8 7.6 - - + +
370C ALA* 1.3 73.1 - - - +
372C TRP* 1.3 87.0 + - - +
373C ASP* 4.5 7.0 - - - -
407C ASP* 2.9 26.1 + - - -
408C SER* 3.3 12.6 + - - +
409C ASP* 3.0 22.4 - - - +
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Residues in contact with TRP 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 6.1 0.2 - - - -
23C PHE* 3.9 17.7 - + - -
341C ASN* 3.3 13.5 - - - +
342C GLN* 3.8 18.4 - - + +
370C ALA* 3.8 20.9 - - + -
371C LYS* 1.3 87.1 + - - +
373C ASP* 1.3 62.0 + - - +
374C GLU* 4.3 5.4 - - + -
405C ARG* 3.1 65.2 + - + +
406C GLY 3.4 13.9 - - - -
407C ASP* 3.5 0.2 - - - -
408C SER* 2.9 58.1 + - - +
409C ASP 3.8 20.2 - - - -
410C GLU* 3.8 11.2 - - + -
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Residues in contact with ASP 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C LYS 4.1 2.4 - - - +
340C ASN* 3.6 2.6 - - - -
341C ASN* 2.9 47.6 + - - +
371C LYS* 4.5 6.2 - - - -
372C TRP* 1.3 77.6 - - - +
374C GLU* 1.3 63.2 + - - +
375C LYS* 3.7 34.5 + - - +
406C GLY 3.5 2.9 - - - -
407C ASP* 4.1 24.1 - - - +
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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
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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