Contacts of the helix formed by residues 337 - 352 (chain K) in PDB entry 1IA0
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 337 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ARG* 4.7 0.6 - - - +
18K ARG* 6.2 0.5 - - - +
19K GLU* 3.2 15.4 + - - +
98K GLN* 3.1 33.8 + - - +
332K SER* 2.7 31.4 + - - +
334K ALA* 3.1 6.1 + - - +
336K ILE* 1.3 96.7 - - - +
338K TYR* 1.3 63.7 + - - +
340K GLU* 3.2 12.4 + - - +
341K THR* 2.8 28.2 + - - +
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Residues in contact with TYR 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K ILE* 3.8 8.5 - - + -
37K ILE* 3.7 24.7 - - + -
38K VAL 3.3 29.4 - - - -
39K ASN* 3.4 41.1 + - + +
40K PRO* 3.6 13.9 - - + -
41K LYS* 4.2 11.2 - - - -
45K GLU* 4.9 0.2 + - - -
48K LYS* 3.9 18.2 - - - +
334K ALA 3.9 1.2 + - - -
335K ASP 3.2 16.6 + - - +
336K ILE 3.4 1.8 + - - -
337K ASN* 1.3 76.4 - - - +
339K ASP* 1.3 77.5 + - - +
341K THR* 3.2 1.9 + - - -
342K LEU* 2.8 58.4 + - + +
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Residues in contact with ASP 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B MET* 4.3 11.7 - - + +
420B GLU* 2.9 32.0 - - - +
41K LYS* 3.3 29.2 + - - -
336K ILE 5.5 0.2 + - - -
337K ASN 3.5 0.8 - - - -
338K TYR* 1.3 88.2 - - - +
340K GLU* 1.3 75.4 + - - +
342K LEU* 3.4 5.7 + - - +
343K SER* 3.1 23.9 + - - -
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Residues in contact with GLU 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B MET* 4.5 15.4 - - + +
98K GLN* 3.3 43.2 + - + +
253K GLU* 4.5 19.7 - - + -
336K ILE 4.2 3.6 - - - +
337K ASN* 3.3 23.2 - - - +
339K ASP* 1.3 84.9 + - - +
341K THR* 1.3 62.9 + - - +
343K SER* 3.4 7.3 + - - -
344K THR* 3.1 25.9 + - - -
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Residues in contact with THR 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K ILE* 5.5 1.6 - - + -
28K ILE* 4.0 13.0 - - + -
37K ILE* 3.9 17.0 - - + -
98K GLN* 4.4 2.6 + - - -
331K LEU* 4.1 20.4 - - + +
332K SER* 3.6 30.3 + - - +
334K ALA 4.9 1.0 + - - -
337K ASN* 2.8 27.8 + - - +
338K TYR* 3.7 3.1 - - - -
340K GLU* 1.3 74.0 - - - +
342K LEU* 1.3 67.8 + - - +
344K THR* 3.2 6.6 + - - -
345K LEU* 3.0 25.0 + - + +
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Residues in contact with LEU 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ILE* 4.0 18.3 - - + +
48K LYS* 3.9 22.2 - - + -
50K PHE* 3.9 24.5 - - + -
338K TYR* 2.8 44.9 + - + +
339K ASP* 3.7 6.5 - - - +
341K THR* 1.3 75.8 - - - +
343K SER* 1.3 57.9 + - - +
345K LEU* 3.2 4.6 + - - +
346K ARG* 2.9 65.4 + - - +
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Residues in contact with SER 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLU* 4.3 13.7 + - - +
416B MET* 4.1 16.2 - - - +
96K TYR* 5.2 2.1 + - - -
339K ASP 3.1 18.1 + - - -
340K GLU 3.5 5.6 - - - -
341K THR 3.2 0.2 - - - -
342K LEU* 1.3 79.0 - - - +
344K THR* 1.3 57.1 + - - +
346K ARG* 3.3 9.2 + - - +
347K TYR* 2.9 50.0 + - - -
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Residues in contact with THR 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K TYR* 4.0 22.1 - - + -
97K GLY* 4.0 1.3 - - - -
98K GLN* 4.0 17.8 + - - +
252K SER* 4.0 8.7 + - - -
327K MET* 5.0 0.2 - - - +
329K ALA* 3.7 20.2 - - + -
330K ALA 3.9 8.2 + - - +
331K LEU* 3.6 24.9 - - + -
340K GLU 3.1 14.6 + - - -
341K THR* 3.2 9.5 + - - -
343K SER* 1.3 75.7 - - - +
345K LEU* 1.3 58.3 + - - +
347K TYR* 3.2 2.6 + - - +
348K ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K VAL* 4.3 2.5 - - + -
28K ILE* 4.5 5.6 - - + -
35K THR* 4.1 11.4 - - + -
37K ILE* 4.0 38.6 - - + -
50K PHE* 4.0 22.5 - - + -
52K PHE* 3.8 29.2 - - + -
331K LEU* 3.7 29.6 - - + -
341K THR* 3.0 23.5 + - + +
342K LEU* 3.2 6.7 + - - +
344K THR* 1.3 78.6 - - - +
346K ARG* 1.3 57.1 + - - +
348K ALA* 3.3 5.7 + - - +
349K ASP* 2.9 28.6 + - - +
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Residues in contact with ARG 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 5.8 1.8 - - - +
419B THR* 5.1 13.9 - - - +
48K LYS* 3.7 22.6 - - - +
50K PHE* 4.1 18.0 - - + -
342K LEU* 2.9 53.7 + - - +
343K SER* 3.7 8.7 - - - +
345K LEU* 1.3 72.7 - - - +
347K TYR* 1.3 64.7 + - - +
349K ASP* 3.4 7.7 + - - +
350K ARG* 3.2 49.0 + - - +
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Residues in contact with TYR 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLU* 4.1 29.8 + - + +
96K TYR* 4.0 28.5 - + + -
279K GLY* 3.5 41.7 - - - -
282K ILE* 4.0 18.5 - - + +
283K SER* 3.7 3.6 + - - -
327K MET* 4.5 5.4 - - + +
343K SER* 2.9 41.5 + - - +
344K THR 3.8 3.4 - - - +
346K ARG* 1.3 76.8 - - - +
348K ALA* 1.3 62.2 + - - +
350K ARG* 2.9 36.1 + - - +
351K ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K VAL* 3.7 20.8 - - + +
10K VAL* 4.1 2.2 - - + -
52K PHE* 3.6 21.3 - - + -
327K MET* 4.0 12.7 - - + +
329K ALA* 4.0 19.3 - - + -
344K THR 2.9 17.3 + - - +
345K LEU 3.7 2.5 - - - +
347K TYR* 1.3 76.5 - - - +
349K ASP* 1.3 64.6 + - - +
351K ALA 3.5 0.3 + - - -
352K LYS* 3.2 21.8 + - - +
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Residues in contact with ASP 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K PHE* 4.1 24.8 - - + +
51K SER 5.3 0.3 + - - -
52K PHE* 3.7 3.2 - - + -
345K LEU 2.9 16.5 + - - +
346K ARG* 3.5 8.9 - - - +
347K TYR 3.2 0.2 - - - -
348K ALA* 1.3 78.6 - - - +
350K ARG* 1.3 62.2 + - - +
352K LYS* 2.5 55.4 + - - +
353K GLN* 3.5 20.7 + - - +
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Residues in contact with ARG 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282K ILE* 4.1 7.9 - - + -
283K SER* 3.5 23.7 + - - +
286K ALA* 3.3 23.2 - - + +
346K ARG* 3.2 39.7 + - - +
347K TYR* 2.9 54.0 + - - +
348K ALA 3.3 0.2 - - - -
349K ASP* 1.3 75.9 - - + +
351K ALA* 1.3 61.4 + - - +
352K LYS 3.1 2.2 - - - -
353K GLN* 2.9 37.2 + - - +
354K ILE* 3.7 0.9 + - - +
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Residues in contact with ALA 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 3.7 14.3 - - + +
8K VAL* 4.0 7.6 - - + -
94K PHE* 5.4 2.2 - - + -
282K ILE* 3.8 13.1 - - + +
327K MET* 3.7 26.5 - - + -
347K TYR 3.1 17.4 + - - +
348K ALA 3.8 3.1 - - - +
349K ASP 3.4 0.2 - - - -
350K ARG* 1.3 75.8 - - - +
352K LYS* 1.3 58.1 - - - +
353K GLN 3.0 0.2 - - - -
354K ILE* 2.9 41.6 + - + +
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Residues in contact with LYS 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K SER* 4.4 9.0 - - - -
6K VAL 3.9 9.9 - - - +
8K VAL* 3.6 20.6 - - + +
51K SER* 2.7 35.5 + - - +
52K PHE* 3.9 13.2 - - + -
53K ASP* 4.8 10.3 - - - +
348K ALA 3.2 6.9 + - - +
349K ASP* 2.5 45.4 + - - +
351K ALA* 1.3 77.3 - - - +
353K GLN* 1.3 59.9 + - + +
354K ILE 3.7 3.8 + - - +
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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