Contacts of the strand formed by residues 348 - 360 (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 LYS 348 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344N ARG* 3.5 2.6 - - - +
345N SER* 2.7 48.7 + - - +
346N LYS* 5.4 1.8 - - + -
347N ASN* 1.3 90.5 - - - +
349N TRP* 1.3 60.7 + - - +
350N LYS* 5.2 8.0 - - + +
373N ASP* 5.2 6.1 - - - +
374N ALA 3.5 4.9 - - - +
375N GLU* 3.5 26.4 + - + +
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Residues in contact with TRP 349 (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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342N ILE* 4.5 16.2 - - + -
343N HIS 3.7 16.6 - - - -
344N ARG* 3.4 37.5 - - + +
346N LYS 4.9 0.2 + - - -
347N ASN* 3.5 19.5 + - - +
348N LYS* 1.3 74.7 - - - +
350N LYS* 1.3 64.6 + - - +
351N PHE* 3.4 28.7 - + + -
373N ASP* 3.0 10.2 - - - +
374N ALA* 2.4 44.4 + - + +
375N GLU 4.6 0.4 - - - -
376N TRP* 3.6 15.7 - + + +
62O LEU* 3.5 32.4 - - + +
65O TYR* 4.3 31.9 - + - -
72O TRP* 4.9 5.6 - + - -
74O PHE* 5.1 4.9 - + - -
191P GLU* 4.4 8.3 - - - -
203P ARG* 4.3 11.0 - - - -
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Residues in contact with LYS 350 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341N LYS 4.3 0.2 - - - +
342N ILE 3.9 1.0 - - - -
343N HIS* 2.9 61.7 + - + +
344N ARG* 5.8 0.4 - - - -
345N SER* 5.9 4.5 + - - +
348N LYS* 5.2 8.7 - - + +
349N TRP* 1.3 76.7 - - - +
351N PHE* 1.3 66.6 - - - +
352N HIS* 4.3 11.4 - - - +
372N GLY 3.3 10.5 - - - +
373N ASP* 3.5 26.5 - - + +
7X G 3.7 40.6 + - - -
8X C 4.9 5.1 + - - -
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Residues in contact with PHE 351 (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 4.0 2.5 - - - -
342N ILE* 4.4 13.7 - - + -
349N TRP* 3.4 46.9 - + + -
350N LYS* 1.3 81.5 - - - +
352N HIS* 1.3 65.5 + - - +
353N LEU* 4.0 12.8 - - + -
370N ALA 4.4 0.2 - - - -
371N ILE* 3.4 5.7 - - - +
372N GLY* 2.7 40.5 + - - +
373N ASP 4.4 0.2 - - - -
374N ALA* 3.4 27.8 - - + -
58O PHE* 3.4 37.5 - + + -
62O LEU* 5.0 7.0 - - + -
74O PHE* 4.4 22.4 - + - -
76O LEU* 4.1 13.7 - - + -
95O ILE* 6.5 0.4 - - + -
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Residues in contact with HIS 352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339N TYR* 4.0 0.2 - - - -
340N ASP* 2.7 35.6 + - + +
341N LYS* 2.8 62.7 + - + +
342N ILE* 4.7 0.2 - - - +
343N HIS* 5.3 4.9 - - + +
350N LYS* 4.6 13.0 - - + +
351N PHE* 1.3 81.8 + - - +
353N LEU* 1.3 58.5 + - - +
370N ALA 3.6 3.4 - - - -
371N ILE* 4.0 32.2 - - + +
372N GLY 5.6 0.6 + - - -
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Residues in contact with LEU 353 (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* 6.3 1.1 - - + -
337N CYS* 4.2 20.2 - - - -
338N GLN 3.5 16.4 - - - +
339N TYR* 3.9 15.9 - - + -
340N ASP* 3.9 4.8 - - - +
342N ILE* 4.5 10.5 - - + -
351N PHE* 4.4 6.7 - - + -
352N HIS* 1.3 77.8 - - - +
354N LYS* 1.3 65.2 + - - +
367N PHE* 4.5 6.7 - - + -
369N LYS* 3.6 6.4 - - - +
370N ALA* 2.6 44.0 + - + +
371N ILE* 5.5 0.9 - - - +
58O PHE* 3.7 31.9 - - + -
74O PHE* 6.0 4.0 - - + -
95O ILE* 5.4 10.8 - - + -
97O ALA* 4.8 4.0 - - + -
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Residues in contact with LYS 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338N GLN* 2.9 38.1 + - + +
339N TYR 3.4 15.6 + - - -
340N ASP* 3.4 31.3 + - + +
353N LEU* 1.3 78.7 - - - +
355N ASP* 1.3 80.2 + - - +
367N PHE* 4.3 0.7 - - - -
368N SER 3.1 13.2 - - - +
369N LYS* 3.9 12.8 - - + +
370N ALA 4.3 0.4 - - - +
99O ASP* 3.0 35.4 + - - -
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Residues in contact with ASP 355 (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* 3.1 9.7 - - - +
338N GLN* 3.2 36.9 + - - +
354N LYS* 1.3 91.8 - - - +
356N GLY* 1.3 59.6 + - - +
367N PHE* 3.0 24.0 - - - -
368N SER* 2.6 28.0 + - - +
3O TYR* 4.9 0.3 + - - -
6O TYR* 4.3 4.5 - - - +
45O ASN* 5.4 0.9 - - - +
48O LEU* 5.0 10.3 - - + +
49O ALA* 4.8 18.8 - - - +
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Residues in contact with GLY 356 (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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336N VAL 3.7 6.7 + - - -
337N CYS* 3.9 5.7 - - - +
355N ASP* 1.3 80.6 - - - +
357N ILE* 1.3 65.3 + - - +
366N ILE* 3.2 9.1 - - - +
367N PHE* 3.0 44.5 + - - +
6O TYR* 4.5 6.7 + - - -
48O LEU* 4.5 6.9 - - - +
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Residues in contact with ILE 357 (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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14N TYR* 4.5 17.3 - - + +
335N VAL* 3.9 0.9 - - - +
336N VAL* 3.0 42.4 + - + +
356N GLY* 1.3 78.6 - - - +
358N MET* 1.3 70.0 + - - +
359N ASN* 6.3 0.2 - - + -
364N ASP* 5.6 1.1 - - + -
365N TYR 3.4 9.0 - - - +
366N ILE* 4.4 5.8 - - + -
367N PHE* 4.7 0.4 - - - -
6O TYR* 3.9 23.8 - - + -
9O THR* 4.5 14.4 - - + -
11O LEU* 5.2 10.3 - - + -
44O ILE* 5.0 7.9 - - + -
48O LEU* 3.9 34.5 - - + -
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Residues in contact with MET 358 (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 4.2 3.6 - - - -
335N VAL* 4.1 15.7 - - + +
357N ILE* 1.3 83.0 - - - +
359N ASN* 1.3 60.3 + - - +
360N LEU* 4.2 18.4 - - + -
364N ASP* 3.3 5.4 - - - +
365N TYR* 2.6 62.5 + - + +
366N ILE 4.8 2.9 - - - +
367N PHE* 3.5 34.1 - - + -
56O VAL* 4.1 27.8 - - + -
81O PHE* 4.1 24.7 - - + -
88O ILE* 5.4 2.5 - - + -
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Residues in contact with ASN 359 (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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333N ASN* 3.1 25.3 - - - +
334N VAL* 3.2 29.2 + - + +
357N ILE* 6.3 0.2 - - + -
358N MET* 1.3 74.5 - - - +
360N LEU* 1.3 63.7 + - - +
362N GLY* 3.6 22.0 + - - -
363N ARG 3.1 6.4 + - - -
364N ASP* 2.4 29.0 + - - +
10O THR* 4.8 17.4 + - + +
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Residues in contact with LEU 360 (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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333N ASN* 3.2 17.3 - - + +
335N VAL* 4.6 8.7 - - + -
358N MET* 4.3 6.7 - - + -
359N ASN* 1.3 87.2 - - - +
361N ASN* 1.3 73.9 + - - +
362N GLY 3.3 0.7 - - - -
363N ARG* 3.0 21.0 + - - +
365N TYR* 3.6 23.3 + - + -
81O PHE* 3.4 42.0 - - + -
88O ILE* 3.4 37.9 - - + +
90O VAL* 4.8 8.3 - - + -
93O VAL* 5.5 1.3 - - + -
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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