Contacts of the helix formed by residues 34 - 44 (chain 3) in PDB entry 1YIT
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 34 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24330 A 3.5 26.9 - - - +
24340 A 3.6 28.8 + - - +
24510 G 3.3 33.2 + - - +
24520 G 4.0 15.7 + - - +
303 GLN* 5.8 2.0 - - - +
313 THR* 3.0 30.5 - - - +
323 GLY 4.7 1.6 - - - +
333 MET* 1.3 78.8 - - - +
353 TRP* 1.3 67.4 + - - +
363 ILE* 3.2 5.4 - - + -
373 ASP* 2.7 28.2 + - - +
383 ARG* 3.2 11.1 + - - +
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Residues in contact with TRP 35 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2170 C 5.0 0.8 + - - -
2180 C 3.5 23.2 + - - -
2190 G 4.9 0.2 - - - -
2200 C 3.6 19.4 - + - +
3950 A 4.0 15.6 + - - -
3960 U 3.8 22.0 - - - -
24310 C 5.7 1.3 - - - -
24320 C 4.1 11.9 - - - -
24520 G 3.1 27.8 + - - +
343 LYS* 1.3 73.1 - - - +
363 ILE* 1.3 89.2 + - + +
383 ARG* 3.0 28.7 + - - +
393 GLN* 3.0 48.6 + - + -
423 ARG* 4.0 8.3 - - - +
513 LYS* 5.8 1.1 - - - -
48L LYS* 3.3 29.2 - - - -
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Residues in contact with ILE 36 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24320 C 3.4 42.8 - - - +
24330 A 3.7 20.1 + - - +
343 LYS* 4.2 2.2 - - + -
353 TRP* 1.3 97.5 - - + +
373 ASP* 1.3 78.2 + - - +
393 GLN* 3.4 23.0 + - - +
403 ARG* 3.1 23.1 + - + +
513 LYS* 3.8 20.4 - - - +
523 PHE* 4.2 10.8 - - + -
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Residues in contact with ASP 37 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303 GLN* 4.0 15.2 + - - -
323 GLY* 3.3 36.1 + - - +
333 MET* 3.2 4.1 + - - -
343 LYS* 2.7 41.3 + - - +
363 ILE* 1.3 84.5 - - - +
383 ARG* 1.3 63.9 + - + +
403 ARG* 3.6 9.6 + - - +
413 GLU* 3.5 25.9 + - - +
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Residues in contact with ARG 38 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3960 U 2.8 91.8 + - - +
3970 A 5.7 0.2 - - - +
24510 G 3.0 25.0 + - - -
24520 G 4.6 2.8 - - - -
323 GLY 6.0 0.2 - - - +
333 MET* 4.0 11.3 + - - +
343 LYS 3.2 7.6 + - - +
353 TRP* 3.0 39.1 + - - +
373 ASP* 1.3 77.4 - - + +
393 GLN* 1.3 60.3 + - - +
413 GLU* 3.0 13.6 + - - +
423 ARG* 2.8 37.1 + - - +
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Residues in contact with GLN 39 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2180 C 2.8 34.7 + - - +
2190 G 3.1 25.8 + - - -
353 TRP* 3.0 41.1 + - + +
363 ILE* 3.4 13.5 + - - +
383 ARG* 1.3 76.0 - - - +
403 ARG* 1.3 55.6 + - - +
423 ARG* 3.3 17.2 - - - +
433 ASN* 2.7 56.8 + - - +
513 LYS* 4.4 2.6 + - - -
523 PHE* 3.3 19.2 - - + -
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Residues in contact with ARG 40 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363 ILE* 3.1 13.3 + - + +
373 ASP* 3.6 13.7 - - - +
383 ARG 3.1 0.4 - - - -
393 GLN* 1.3 77.3 - - - +
413 GLU* 1.3 65.8 + - + +
443 SER* 2.7 36.4 + - - +
513 LYS 5.1 0.6 + - - -
523 PHE* 3.4 66.4 + - + +
543 LYS 5.0 5.7 + - - -
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Residues in contact with GLU 41 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19230 G 4.6 13.0 + - - +
323 GLY 4.8 7.6 - - - +
373 ASP* 3.5 17.4 + - - +
383 ARG* 3.0 11.4 + - - +
403 ARG* 1.3 83.8 - - + +
423 ARG* 1.3 66.7 + - - +
443 SER* 3.6 13.5 + - - +
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Residues in contact with ARG 42 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2170 C 5.6 0.2 + - - -
2180 C 4.7 7.0 + - - -
3900 G 5.7 0.5 + - - -
3910 U 5.5 3.3 - - - +
3950 A 3.3 47.0 + - - +
3960 U 2.8 44.8 + - - -
85680 NA 3.7 15.9 - - - -
353 TRP* 4.0 7.1 - - - +
383 ARG* 2.8 22.0 + - - +
393 GLN* 3.3 30.6 - - - +
413 GLU* 1.3 76.2 - - - +
433 ASN* 1.3 70.2 + - - +
443 SER 3.4 4.5 + - - +
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Residues in contact with ASN 43 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700 U 5.0 11.4 + - - +
2180 C 3.1 36.6 + - - +
2190 G 4.5 5.1 + - - -
393 GLN* 2.7 39.0 + - - +
423 ARG* 1.3 82.8 - - - +
443 SER* 1.3 61.1 + - - +
453 GLY 3.5 2.8 + - - -
493 ASP* 4.4 6.4 - - - +
523 PHE* 3.7 17.5 - - + -
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Residues in contact with SER 44 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3890 G 4.7 9.8 + - - +
3900 G 4.5 3.0 + - - -
403 ARG* 2.7 30.1 + - - +
413 GLU* 3.7 12.0 - - - +
423 ARG 3.3 4.1 - - - +
433 ASN* 1.3 77.7 - - - +
453 GLY* 1.3 57.9 + - - +
493 ASP* 3.3 24.5 + - - -
523 PHE* 3.9 15.2 - - - +
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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
------------------------------------------------------------
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