Contacts of the helix formed by residues 4 - 18 (chain 2) in PDB entry 1YI2
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 SER 4 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210 U 4.4 9.5 + - - -
1220 C 5.8 3.1 - - - -
14860 A 6.0 1.3 - - - +
16750 C 4.5 4.5 - - - -
16760 G 4.4 2.7 - - - -
22 LYS 4.0 1.2 + - - -
32 LYS* 1.3 76.3 - - - +
52 LYS* 1.3 65.9 + - - +
62 ALA* 3.5 8.0 + - - +
72 THR* 3.3 26.0 + - - -
82 LYS* 3.0 22.2 + - - +
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Residues in contact with LYS 5 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220 C 3.6 20.8 + - - +
1230 U 3.1 33.4 + - - +
16740 C 4.9 0.2 + - - -
16750 C 3.4 45.8 + - - +
16760 G 4.0 7.9 - - - +
42 SER* 1.3 74.5 - - - +
62 ALA* 1.3 58.9 + - - +
82 LYS* 3.5 3.5 - - - +
92 LYS* 3.1 38.2 + - + +
30S ASP* 2.7 45.0 + - - +
31S ARG* 4.9 0.4 - - - +
56S ASN* 3.8 20.2 - - + +
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Residues in contact with ALA 6 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210 U 3.4 39.9 - - - +
1220 C 3.5 33.9 + - - +
42 SER* 3.2 3.1 + - - +
52 LYS* 1.3 76.7 - - - +
72 THR* 1.3 66.8 + - - +
82 LYS 3.1 1.6 - - - -
92 LYS* 3.0 14.4 + - - +
102 ARG* 3.1 21.9 + - - +
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Residues in contact with THR 7 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200 A 3.5 18.8 + - + +
1210 U 4.6 0.3 + - - -
14170 G 5.3 4.9 - - + +
32 LYS* 3.8 18.2 - - + -
42 SER* 3.3 25.7 + - - -
62 ALA* 1.3 77.3 - - - +
82 LYS* 1.3 58.3 + - - +
102 ARG* 3.1 15.8 + - - +
112 LEU* 2.9 42.9 + - + +
492 GLU* 3.2 21.2 + - - +
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Residues in contact with LYS 8 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14460 U 4.8 10.9 + - - -
16760 G 3.3 19.7 + - - +
16770 U 2.5 42.1 + - - +
32 LYS* 3.9 16.4 - - + -
42 SER 3.0 17.7 + - - +
52 LYS 3.5 7.2 - - - +
72 THR* 1.3 75.5 - - - +
92 LYS* 1.3 61.0 + - + +
112 LEU* 3.4 4.9 + - - +
122 ALA* 2.9 29.1 + - - +
55S GLN* 5.5 1.0 - - - +
56S ASN* 2.6 32.5 + - + +
57S THR* 4.0 11.3 - - - +
58S MET* 3.6 31.7 - - - +
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Residues in contact with LYS 9 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530 C 4.0 33.3 + - - +
540 G 4.9 2.3 + - - -
1220 C 3.6 39.9 + - - +
52 LYS* 3.1 26.0 + - + +
62 ALA* 3.0 6.3 + - - +
82 LYS* 1.3 75.8 - - + +
102 ARG* 1.3 60.4 + - + +
122 ALA* 3.1 9.7 - - - +
132 LYS* 2.8 29.0 + - - +
30S ASP* 3.9 22.9 + - - +
57S THR 6.1 0.2 - - - -
60S GLY* 4.7 22.6 - - - +
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Residues in contact with ARG 10 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520 A 4.6 3.5 + - - +
530 C 3.7 29.5 + - - +
1200 A 3.8 6.7 + - - -
1210 U 2.3 71.8 + - - -
1220 C 5.6 1.6 + - - +
181 LYS* 4.3 20.1 - - - +
62 ALA* 3.1 18.3 + - - +
72 THR* 3.4 15.7 + - - +
92 LYS* 1.3 75.5 - - + +
112 LEU* 1.3 64.8 + - - +
132 LYS* 3.2 7.2 + - - +
142 LEU* 2.9 32.6 + - + +
492 GLU* 2.8 52.6 + - - +
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Residues in contact with LEU 11 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14170 G 3.4 72.2 + - + +
14180 U 4.8 2.8 + - - -
32 LYS* 4.0 17.3 - - + -
72 THR* 2.9 29.0 + - + +
82 LYS 3.8 4.7 - - - +
102 ARG* 1.3 76.2 - - + +
122 ALA* 1.3 63.3 + - - +
142 LEU* 3.2 22.4 + - + +
152 ASP* 2.9 22.5 + - - +
472 THR* 4.4 8.3 - - - +
482 ASP 5.8 1.3 - - - +
492 GLU* 5.5 5.4 - - - +
58S MET* 4.1 12.2 - - + +
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Residues in contact with ALA 12 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540 G 5.9 0.4 - - - +
82 LYS 2.9 14.6 + - - +
92 LYS* 3.1 13.0 - - - +
112 LEU* 1.3 76.8 - - - +
132 LYS* 1.3 63.2 + - - +
152 ASP* 3.0 14.2 + - - +
162 ASN* 3.0 13.2 + - - +
57S THR 4.8 0.2 - - - +
58S MET* 3.4 39.7 - - - +
59S ASP 4.1 4.0 - - - -
60S GLY* 3.8 15.0 - - - +
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Residues in contact with LYS 13 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530 C 3.5 47.5 - - - +
540 G 2.7 46.8 + - - +
610 G 5.1 4.0 + - - -
92 LYS 2.8 16.1 + - - +
102 ARG* 3.2 8.9 + - - +
122 ALA* 1.3 72.2 - - - +
142 LEU* 1.3 59.4 + - + +
162 ASN* 3.0 10.3 + - + +
172 GLN* 2.8 52.7 + - + +
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Residues in contact with LEU 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14180 U 5.3 0.2 - - - +
102 ARG* 2.9 21.8 + - + +
112 LEU* 3.4 21.3 - - + +
132 LYS* 1.3 76.4 - - + +
152 ASP* 1.3 62.4 + - - +
172 GLN* 3.4 22.7 + - + +
182 ASN* 3.1 22.5 + - - +
402 ARG* 3.8 24.6 + - - +
472 THR* 3.7 33.2 - - + -
482 ASP 5.2 2.7 - - - +
492 GLU* 5.6 3.4 - - - +
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Residues in contact with ASP 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14180 U 3.9 45.4 + - + +
14190 U 5.1 1.0 + - - -
112 LEU 2.9 12.4 + - - +
122 ALA* 3.0 10.7 + - - +
142 LEU* 1.3 76.7 - - - +
162 ASN* 1.3 65.9 + - - +
182 ASN* 3.2 22.7 + - - +
192 SER* 4.2 1.0 + - - -
402 ARG* 4.2 0.6 - - - +
80762 MG 3.9 18.7 - - - -
58S MET* 4.9 12.2 - - + +
59S ASP* 5.5 1.6 - - - +
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Residues in contact with ASN 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600 A 3.3 33.6 + - - +
122 ALA 3.0 10.4 + - - +
132 LYS* 3.0 12.4 + - + +
152 ASP* 1.3 76.0 + - - +
172 GLN* 1.3 65.9 + - + +
182 ASN 3.0 2.7 + - - -
192 SER* 3.0 23.2 + - - -
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Residues in contact with GLN 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600 A 3.6 16.3 + - - +
610 G 3.1 27.2 + - - +
620 C 5.6 1.0 + - - -
132 LYS* 2.8 41.8 + - + +
142 LEU* 3.6 32.9 + - + +
162 ASN* 1.3 73.5 - - + +
182 ASN* 1.3 56.7 + - - +
192 SER 2.9 6.5 + - - +
362 ASN* 3.6 19.2 + - - +
382 LYS* 4.4 34.6 - - + +
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Residues in contact with ASN 18 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14180 U 5.0 2.6 + - - -
14410 G 5.6 2.9 + - - -
142 LEU 3.1 13.3 + - - +
152 ASP* 3.3 20.8 - - - +
162 ASN 3.0 1.4 - - - -
172 GLN* 1.3 75.6 - - - +
192 SER* 1.3 58.5 + - - -
362 ASN* 5.3 0.4 - - - +
382 LYS 4.8 4.9 - - - +
392 ARG* 3.8 12.1 - - - +
402 ARG* 2.4 56.0 + - + +
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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