Contacts of the strand formed by residues 333 - 345 (chain N) in PDB entry 5IYB
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 ASN 333 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331N THR 5.6 0.2 - - - -
332N GLU* 1.3 78.6 - - - +
334N VAL* 1.3 58.0 + - - +
359N ASN* 3.1 19.0 - - - +
360N LEU* 3.2 15.8 - - + -
361N ASN* 2.3 45.5 + - - +
362N GLY 4.1 1.2 + - - -
90O VAL* 4.0 23.2 - - + +
92O LYS 3.9 4.6 + - - +
93O VAL* 3.2 28.4 - - + +
94O LYS* 3.4 3.3 + - - +
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Residues in contact with VAL 334 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330N ASP 5.8 1.6 - - - +
332N GLU 3.6 3.8 + - - +
333N ASN* 1.3 74.4 - - - +
335N VAL* 1.3 80.6 + - - +
336N VAL* 4.7 13.2 - - + +
359N ASN* 3.2 41.0 + - + +
8O ASN* 5.2 7.4 - - - +
94O LYS* 3.4 27.6 - - + +
96O VAL* 5.9 2.9 - - + -
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Residues in contact with VAL 335 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334N VAL* 1.3 82.1 - - - +
336N VAL* 1.3 68.0 + - - +
337N CYS* 4.6 12.1 - - - -
353N LEU* 6.3 0.7 - - + -
357N ILE 3.9 10.8 - - - +
358N MET* 4.1 20.2 - - + -
360N LEU* 4.6 2.9 - - + -
367N PHE* 4.6 11.7 - - + -
81O PHE* 4.1 23.6 - - + -
93O VAL* 3.6 19.5 - - + -
94O LYS 3.0 12.5 + - - +
95O ILE* 3.4 15.7 - - + +
96O VAL 3.3 21.7 + - - +
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Residues in contact with VAL 336 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334N VAL* 4.7 13.0 - - + -
335N VAL* 1.3 78.5 - - - +
337N CYS* 1.3 61.3 + - - +
356N GLY* 3.7 0.5 + - - -
357N ILE* 3.0 47.6 + - + +
5O LEU* 3.9 31.0 - - + +
6O TYR* 4.9 5.5 - - + -
8O ASN* 4.3 16.4 - - - +
9O THR* 3.7 29.6 - - + -
96O VAL* 3.8 11.2 - - + +
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Residues in contact with CYS 337 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335N VAL* 4.6 5.2 - - + -
336N VAL* 1.3 76.5 - - - +
338N GLN* 1.3 77.5 + - - +
353N LEU* 4.2 20.4 - - - -
355N ASP 3.1 21.1 - - - +
356N GLY* 3.8 8.3 - - - +
367N PHE* 3.9 9.2 - - + -
5O LEU* 3.4 13.2 - - - +
6O TYR* 5.5 2.9 - - - -
95O ILE* 4.2 13.7 - - - -
96O VAL 3.2 9.6 + - - -
97O ALA* 3.3 29.0 - - - -
98O CYS 3.4 5.2 + - - -
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Residues in contact with GLN 338 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N CYS* 1.3 80.9 - - - +
339N TYR* 1.3 60.6 + - - +
353N LEU* 3.5 11.6 - - - +
354N LYS* 2.9 45.1 + - + +
355N ASP* 3.2 28.3 + - + +
3O TYR* 2.7 49.7 + - + -
6O TYR* 3.3 21.3 + - + +
45O ASN* 4.4 2.8 + - - -
97O ALA* 4.0 4.7 - - - -
98O CYS* 3.1 24.2 - - - +
99O ASP* 4.0 7.8 - - - +
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Residues in contact with TYR 339 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338N GLN* 1.3 75.9 - - - +
340N ASP* 1.3 65.6 + - - +
341N LYS* 5.4 0.4 - - - -
342N ILE* 4.1 20.4 - - + -
353N LEU* 3.9 16.6 - - + -
354N LYS* 3.4 16.6 - - - -
67O PHE* 4.2 2.2 - + - -
70O ASN* 2.7 45.2 + - - -
72O TRP* 3.5 31.0 - + + -
97O ALA* 3.2 35.2 - - + -
98O CYS 3.3 15.7 + - - -
99O ASP* 3.5 21.0 + - + +
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Residues in contact with ASP 340 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339N TYR* 1.3 78.9 - - - +
341N LYS* 1.3 69.5 + - - +
352N HIS* 2.7 24.6 + - + +
353N LEU* 3.9 7.6 - - - +
354N LYS* 3.4 33.2 + - + +
369N LYS* 6.0 2.5 - - - -
99O ASP* 5.4 1.0 - - - +
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Residues in contact with LYS 341 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339N TYR* 3.8 1.3 - - - +
340N ASP* 1.3 86.9 - - - +
342N ILE* 1.3 76.4 + - - +
343N HIS* 5.2 4.5 - - + -
351N PHE* 4.0 0.2 - - - -
352N HIS* 2.8 67.8 + - + +
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Residues in contact with ILE 342 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339N TYR* 4.1 21.3 - - + -
341N LYS* 1.3 90.6 - - - +
343N HIS* 1.3 66.8 + - - +
349N TRP* 4.5 17.0 - - + -
350N LYS 3.9 3.4 - - - +
351N PHE* 4.4 16.4 - - + -
353N LEU* 4.5 11.4 - - + -
72O TRP* 3.6 52.9 - - + +
74O PHE* 4.5 15.0 - - + -
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Residues in contact with HIS 343 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341N LYS* 5.2 8.3 - - + -
342N ILE* 1.3 78.5 + - - +
344N ARG* 1.3 79.0 + - - +
345N SER* 3.6 15.1 + - - -
349N TRP* 3.7 9.4 - - - -
350N LYS* 2.9 58.4 + - + +
352N HIS* 5.3 4.9 - - + +
7X G 4.9 0.7 - - - -
8X C 2.4 46.8 + - - -
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Residues in contact with ARG 344 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343N HIS* 1.3 90.5 + - - +
345N SER* 1.3 70.4 + - - +
346N LYS* 3.5 31.3 + - - +
348N LYS 3.5 6.1 - - - +
349N TRP* 3.4 45.8 - - + -
350N LYS* 5.8 0.2 - - - -
203P ARG* 3.0 27.4 - - - +
78Y T 3.9 18.0 + - - -
79Y T 2.3 46.8 + - - -
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Residues in contact with SER 345 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343N HIS* 3.6 6.4 + - - -
344N ARG* 1.3 78.9 + - - +
346N LYS* 1.3 66.1 + - - +
348N LYS* 2.7 46.0 + - - +
350N LYS* 5.9 4.4 + - - +
8X C 3.4 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