Contacts of the helix formed by residues 17 - 29 (chain A) in PDB entry 1YNU
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 1.3 62.5 + - - +
19A TYR* 3.0 5.0 - - - +
20A PHE* 2.7 42.5 + - - +
21A LEU* 2.8 32.7 + - - +
146A PRO* 5.6 2.0 - - - +
397A SER* 4.1 13.9 + - - +
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 1.3 80.2 + - - +
19A TYR* 1.3 57.2 + - - +
21A LEU* 4.0 13.2 - - - +
22A GLY* 2.9 26.9 + - - -
378A MET* 4.1 17.8 - - - +
381A TRP* 3.4 30.1 + - - -
391A ASN* 5.1 0.9 - - - +
392A ILE 5.6 0.5 - - - +
394A PRO* 3.6 28.9 - - - +
396A SER* 5.4 2.0 + - - -
397A SER* 4.4 4.3 + - - -
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER 3.0 0.8 - - - +
18A SER* 1.3 79.6 - - - +
20A PHE* 1.3 97.2 + + + +
22A GLY* 4.8 0.2 - - - -
23A TRP* 3.4 38.2 + + - +
44A GLY 3.6 19.3 - - - -
45A LEU* 3.7 11.2 - - + +
145A TYR* 3.7 19.4 + + - -
146A PRO* 3.8 25.1 - - + -
391A ASN* 5.2 3.0 + - - +
392A ILE 6.0 0.4 - - - -
393A SER* 3.6 23.6 - - - +
394A PRO* 5.3 1.6 - - - -
397A SER* 3.1 23.3 + - - +
407A ARG* 3.8 12.1 - - - -
600A PY4 2.7 27.5 + - - +
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 2.7 23.7 + - - +
19A TYR* 1.3 108.3 - + - +
21A LEU* 1.3 62.0 + - + +
23A TRP* 3.5 20.0 - + - +
24A GLN* 2.8 37.7 + - + +
145A TYR* 5.6 1.3 - - - -
146A PRO* 4.4 15.9 - - + -
147A GLY* 4.3 14.8 - - - -
150A ARG* 4.2 33.0 - - + -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 2.8 36.2 + - - +
18A SER* 3.3 14.1 + - - +
20A PHE* 1.3 74.9 - - + +
22A GLY* 1.3 59.3 + - - +
23A TRP 3.0 1.1 - - - -
24A GLN* 2.7 40.5 + - - +
25A GLU* 2.8 22.0 + - + +
381A TRP* 4.4 11.7 - - + -
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER 2.9 15.3 + - - -
21A LEU* 1.3 77.4 - - - +
23A TRP* 1.3 56.0 + - - +
25A GLU* 3.4 10.6 + - - +
26A TYR* 3.0 27.4 + - - +
40A ILE* 5.4 0.3 - - - +
381A TRP* 4.0 12.8 - - - -
385A VAL* 5.0 5.7 - - - +
391A ASN* 3.3 27.1 - - - +
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Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.4 49.9 + + - +
20A PHE* 3.5 24.9 - + - +
21A LEU 3.0 0.6 - - - -
22A GLY* 1.3 77.4 - - - +
24A GLN* 1.3 61.2 + - + +
26A TYR* 3.4 18.2 + + - +
27A GLU* 3.4 29.7 + - + +
42A GLN* 4.0 11.0 - - - +
45A LEU* 3.6 39.9 - - + +
145A TYR* 6.1 0.4 - - - -
391A ASN* 3.9 9.1 - - - +
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Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 2.8 29.1 + - - +
21A LEU* 2.7 29.4 + - - +
23A TRP* 1.3 73.4 - - + +
25A GLU* 1.3 67.1 + - - +
27A GLU* 3.4 11.1 + - - +
28A LYS* 3.1 39.2 + - - +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 2.8 23.1 + - + +
22A GLY* 3.6 11.4 - - - +
23A TRP 3.3 0.2 - - - -
24A GLN* 1.3 75.6 - - - +
26A TYR* 1.3 66.3 + - - +
28A LYS* 2.7 55.1 + - - +
29A ASN* 3.2 9.7 + - - +
40A ILE* 3.4 20.3 - - + +
381A TRP* 6.1 1.1 - - + -
385A VAL* 4.7 6.7 - - + -
386A TYR* 3.7 36.7 + - + +
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Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 3.0 13.7 + - - +
23A TRP* 3.4 17.0 - + - +
25A GLU* 1.3 77.5 - - - +
27A GLU* 1.3 64.6 + - + +
30A PRO* 2.7 62.7 - - + +
31A TYR* 4.0 6.0 + - + -
40A ILE* 3.3 45.7 - - + +
42A GLN* 3.7 47.0 - - + +
391A ASN* 4.8 2.9 - - - +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 3.4 33.0 + - - +
24A GLN* 3.4 12.0 + - - +
25A GLU 3.2 0.8 - - - -
26A TYR* 1.3 85.9 - - + +
28A LYS* 1.3 64.6 + - + +
29A ASN 3.1 2.2 - - - -
30A PRO* 3.3 14.9 - - - +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLN* 3.1 24.7 + - - +
25A GLU* 2.7 44.1 + - - +
27A GLU* 1.3 78.1 - - + +
29A ASN* 1.3 62.4 + - + +
30A PRO* 3.8 1.1 - - - +
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Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 3.2 7.8 + - - +
26A TYR 3.1 3.8 - - - -
28A LYS* 1.3 83.1 - - + +
30A PRO* 1.3 61.9 - - - +
36A ASN* 2.8 28.8 + - - +
38A ASN* 4.0 10.1 + - - +
39A GLY* 4.0 11.3 - - - -
40A ILE* 2.9 36.0 + - + +
389A HIS* 5.6 3.0 + - - -
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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