Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 5Y03
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 CYS 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLY 4.8 0.7 - - - +
18A SER* 1.3 75.8 - - - +
20A VAL* 1.3 65.4 + - - +
21A ILE* 3.8 27.0 - - + +
92A CYS* 3.8 21.3 - - - -
93A ILE 3.4 8.3 - - - -
94A TYR* 4.1 21.8 - - + -
136A CYS 3.6 1.2 - - - +
137A VAL* 3.2 6.0 - - - -
138A CYS* 2.8 42.2 + - + +
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Residues in contact with VAL 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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14A LEU* 4.0 24.7 - - + -
19A CYS* 1.3 73.4 - - - +
21A ILE* 1.3 60.8 + - - +
22A ILE* 4.0 26.0 - - + -
40A PHE* 3.8 27.1 - - + -
91A LEU 3.5 1.9 - - - +
92A CYS* 3.1 4.9 - - - +
93A ILE* 2.8 42.6 + - + +
95A VAL* 5.6 1.3 - - + -
124A VAL* 4.5 19.5 - - + -
135A VAL* 4.5 8.5 - - + -
136A CYS 3.4 7.2 - - - +
137A VAL* 4.6 10.8 - - + +
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Residues in contact with ILE 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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19A CYS* 3.8 30.1 - - + +
20A VAL* 1.3 73.5 - - - +
22A ILE* 1.3 62.5 + - - +
23A LYS* 4.6 12.8 - - + -
90A GLU* 3.9 27.6 - - + +
91A LEU 3.6 2.2 - - - -
92A CYS* 4.1 11.9 - - - +
134A SER* 3.8 2.3 + - - +
135A VAL* 3.1 6.8 - - - +
136A CYS* 2.7 52.7 + - + +
138A CYS* 3.5 33.2 - - + -
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Residues in contact with ILE 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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20A VAL* 4.0 16.6 - - + -
21A ILE* 1.3 78.9 - - - +
23A LYS* 1.3 63.9 + - - +
36A LEU* 5.5 0.9 - - + -
38A VAL* 3.9 32.1 - - + -
89A PHE* 3.9 15.8 - - + +
90A GLU* 3.6 2.1 - - - -
91A LEU* 2.7 58.8 + - + +
93A ILE* 4.4 4.5 - - + -
124A VAL* 5.1 0.2 - - + -
126A VAL* 4.0 18.8 - - + -
130A ILE* 5.1 0.7 - - + -
132A LEU* 3.6 26.9 - - + -
134A SER 3.6 2.7 - - - -
135A VAL* 4.1 17.0 - - + -
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Residues in contact with LYS 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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21A ILE* 4.6 10.3 - - + -
22A ILE* 1.3 77.7 - - - +
24A GLY* 1.3 52.5 + - - +
88A GLN* 4.6 15.0 + - - +
89A PHE* 3.4 11.4 - - - +
90A GLU* 3.7 36.9 + - + -
132A LEU* 3.6 8.2 - - - +
133A THR* 2.7 36.7 + - + -
134A SER* 2.8 39.2 + - - +
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Residues in contact with GLY 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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23A LYS* 1.3 75.4 - - - +
25A THR* 1.3 62.0 + - - -
88A GLN* 3.2 5.2 - - - +
89A PHE* 2.8 52.9 + - - -
130A ILE* 5.5 0.2 - - - -
131A SER 2.9 14.1 - - - -
132A LEU* 4.2 1.6 - - - -
133A THR* 3.8 8.1 - - - -
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Residues in contact with THR 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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24A GLY* 1.3 76.3 + - - -
26A PRO* 1.3 83.5 - - + +
86A GLY* 4.2 11.4 - - - +
87A LYS 3.9 13.2 - - - -
88A GLN* 3.5 17.2 + - - +
89A PHE* 3.8 4.0 - - - -
130A ILE* 3.3 0.6 - - - -
131A SER* 2.6 49.4 + - - +
133A THR* 4.8 2.8 + - - -
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Residues in contact with PRO 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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25A THR* 1.3 97.0 - - + +
27A ILE* 1.3 63.8 + - - +
28A HIS 3.2 18.6 + - - +
30A PHE* 4.3 13.0 - - + -
34A PRO* 4.5 2.0 - - + -
58A PHE* 3.9 37.9 - - + -
83A PHE* 6.0 0.2 - - + -
84A GLU 4.8 4.0 - - - +
86A GLY* 4.9 7.8 - - - +
87A LYS 3.3 22.7 - - - +
89A PHE* 3.9 7.8 - - + -
129A ASP 3.3 10.1 - - - +
130A ILE* 4.2 2.7 - - + -
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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