Contacts of the helix formed by residues 58 - 68 (chain D) in PDB entry 1S4Y
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 PHE 58 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 5.2 3.6 - + - -
25B TRP* 3.7 34.3 - + - -
28B TRP* 3.9 25.4 - + - -
35B TYR* 5.1 0.2 - - - -
91B MET* 4.1 16.2 - - + -
105B ILE* 3.9 19.7 - - + -
106B GLN 4.6 4.6 + - - +
107B ASN* 4.3 9.3 + - - +
108B MET* 3.3 43.5 - - + -
59D HIS* 1.3 57.3 + - - +
60D SER* 2.8 29.3 + - - +
61D THR* 2.8 28.1 + - - +
62D VAL* 2.8 27.3 + - + +
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 4.8 0.7 - - - -
37B ALA* 2.9 33.5 + - + +
38B ASN 3.0 16.4 + - - -
39B TYR* 4.6 8.1 - - + -
86B LEU* 4.9 6.3 - - + -
107B ASN 3.4 18.8 + - - +
108B MET* 2.9 29.3 - - - +
110B VAL* 3.2 23.9 - - + +
58D PHE* 1.3 72.3 - - - +
60D SER* 1.4 59.5 + - - +
62D VAL* 4.2 10.1 - - + -
63D ILE* 2.8 46.0 + - + +
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PHE* 3.0 22.1 + - - +
59D HIS* 1.4 78.9 - - - +
61D THR* 1.3 58.9 + - - -
63D ILE* 3.5 2.9 - - - +
64D ASN* 3.1 25.7 + - - +
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TRP* 4.5 14.1 - - - -
58D PHE* 2.8 24.0 + - - -
60D SER* 1.3 75.3 - - - +
62D VAL* 1.3 60.8 + - - -
64D ASN* 3.9 4.5 - - - +
65D HIS* 2.7 35.4 + - - +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 3.9 25.6 - - + -
23B ILE* 4.5 6.5 - - + -
25B TRP* 4.2 22.7 - - + -
35B TYR* 3.2 25.4 - - + +
58D PHE* 2.8 31.1 + - + +
59D HIS* 3.2 5.6 + - + +
61D THR* 1.3 72.1 - - - +
63D ILE* 1.3 67.2 + - - +
65D HIS* 4.0 1.6 + - - +
66D TYR* 2.9 52.4 + - + -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D HIS* 2.8 29.7 + - + +
60D SER* 3.5 3.8 - - - +
62D VAL* 1.3 81.7 - - - +
64D ASN* 1.3 52.6 + - + +
66D TYR* 2.8 7.8 + - - +
67D ARG* 2.8 32.0 + - - +
116D SER* 5.2 9.9 - - - +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D SER 3.1 16.6 + - - +
61D THR* 4.7 3.1 - - - +
63D ILE* 1.3 75.3 - - - +
65D HIS* 1.3 57.5 + - - +
67D ARG* 3.5 12.5 - - + +
68D MET* 3.1 39.6 + - + +
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 4.1 28.5 + - + +
25B TRP* 3.6 41.3 + + + -
61D THR* 2.7 23.7 + - - +
62D VAL 4.5 2.4 + - - -
64D ASN* 1.3 76.8 - - - +
66D TYR* 1.3 66.4 + - - +
67D ARG 3.1 0.8 + - - -
68D MET* 4.9 3.8 - - - -
69D ARG* 2.7 85.7 + - - +
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Residues in contact with TYR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 4.6 23.0 - + - -
18B VAL* 4.2 20.5 - - + +
19B SER 4.6 1.0 + - - -
22B ASP* 4.2 13.5 - - - +
23B ILE* 3.0 37.1 - - + +
62D VAL* 2.9 40.6 + - + +
63D ILE* 2.8 16.5 + - - +
65D HIS* 1.3 75.4 - - - +
67D ARG* 1.4 47.3 + - - -
69D ARG* 3.5 2.8 - - - +
70D GLY* 2.5 43.3 + - - -
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE 2.8 16.3 + - - +
64D ASN* 3.5 15.9 - - - +
65D HIS 3.1 1.0 - - - -
66D TYR* 1.4 68.1 - - - +
68D MET* 1.3 60.1 + - + +
69D ARG 2.9 10.2 + - - -
70D GLY* 3.5 9.3 + - - +
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D SER 5.8 3.8 - - - +
64D ASN* 3.1 24.1 + - + +
65D HIS* 4.1 3.3 + - - +
67D ARG* 1.3 71.1 - - - +
69D ARG* 1.3 67.4 + - + +
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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