Contacts of the strand formed by residues 16 - 23 (chain A) in PDB entry 4Y24
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.1 4.1 - - - +
14A GLY 3.7 1.9 + - - +
15A GLU* 1.3 75.0 - - - +
17A LEU* 1.3 62.1 + - - +
18A ARG* 3.7 27.1 + - - -
88A CYS* 4.0 20.2 - - - -
89A ILE 4.4 0.7 - - - -
90A THR* 3.6 18.2 - - + -
132A ALA 3.7 4.5 - - - +
133A PHE* 3.7 1.6 - - - -
134A ASP* 3.0 44.1 + - + +
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Residues in contact with LEU 17 (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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9A LEU* 4.5 11.0 - - + -
11A LEU* 3.8 20.2 - - + -
15A GLU 4.0 0.2 + - - -
16A CYS* 1.3 71.1 - - - +
18A ARG* 1.3 59.5 + - - +
19A VAL* 3.8 9.8 + - + -
34A LEU* 3.7 35.7 - - + -
87A VAL 3.5 6.1 - - - +
89A ILE* 2.9 46.2 + - + +
117A ILE* 5.2 1.3 - - + -
120A MET* 4.1 13.2 - - - -
131A VAL* 3.9 13.7 - - + -
132A ALA 3.6 5.2 - - - +
133A PHE* 3.5 35.7 - - + -
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Residues in contact with ARG 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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16A CYS* 3.7 22.5 - - + +
17A LEU* 1.3 71.9 - - - +
19A VAL* 1.3 62.2 + - - +
20A ARG* 4.3 4.8 - - - +
86A GLU* 2.6 35.1 + - - +
87A VAL 3.7 3.6 - - - -
88A CYS* 3.6 18.5 - - - +
130A CYS* 3.9 2.2 - - - +
131A VAL* 3.3 5.0 - - - +
132A ALA* 2.7 56.4 + - + +
134A ASP* 3.6 22.2 - - - +
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Residues in contact with VAL 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 LEU* 4.1 16.2 - - + +
18A ARG* 1.3 78.7 - - - +
20A ARG* 1.3 61.7 + - - +
32A LEU* 4.4 21.5 - - + -
85A ALA 3.9 0.9 - - - +
86A GLU* 3.3 4.3 - - - +
87A VAL* 2.8 41.2 + - - +
89A ILE* 5.3 2.7 - - + -
120A MET* 3.7 27.4 - - - -
126A PHE* 4.3 11.3 - - + -
128A ILE* 3.7 31.4 - - + -
130A CYS 3.5 5.4 - - - +
131A VAL* 4.5 5.6 - - + -
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Residues in contact with ARG 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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18A ARG* 4.3 4.6 - - - +
19A VAL* 1.3 76.6 - - - +
21A GLY* 1.3 60.9 + - - +
84A VAL* 3.6 26.9 - - + -
85A ALA 3.5 6.1 - - - +
86A GLU* 3.7 35.0 + - + +
126A PHE* 4.4 1.8 - - - -
128A ILE* 3.7 4.5 - - - +
129A LYS* 2.9 27.4 + - + -
130A CYS* 2.8 60.9 + - + +
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Residues in contact with GLY 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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20A ARG* 1.3 76.6 - - - +
22A GLU* 1.3 60.0 + - - -
84A VAL* 3.5 6.6 - - - +
85A ALA 2.8 33.6 + - - +
126A PHE* 3.4 21.6 - - - -
127A LYS 3.3 13.5 - - - -
128A ILE* 4.1 0.4 - - - -
129A LYS* 3.9 5.6 - - - -
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Residues in contact with GLU 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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21A GLY* 1.3 72.1 - - - -
23A VAL* 1.3 66.0 + - - +
24A ALA 3.6 1.9 + - - -
82A GLY 6.5 0.2 - - - -
83A SER 3.8 4.9 - - - +
84A VAL* 4.1 19.1 - - + +
126A PHE* 3.8 2.7 - - - -
127A LYS* 3.1 48.3 + - + +
129A LYS* 3.8 31.2 + - + +
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Residues in contact with VAL 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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22A GLU* 1.3 72.8 - - - +
24A ALA* 1.3 70.4 + - - +
25A PRO* 4.2 0.3 - - - +
27A ALA* 3.6 9.2 - - + -
30A PHE* 4.2 10.3 - - + -
49A PHE* 3.5 29.2 - - + -
79A PHE* 5.1 2.7 - - + -
80A GLN 3.8 7.6 - - - +
81A PRO* 3.9 8.1 - - + -
82A GLY* 2.9 26.2 + - - -
83A SER 2.8 21.6 + - - +
85A ALA* 4.1 13.5 - - + -
125A ASP 3.8 7.0 - - - +
126A PHE* 3.6 26.7 - - + -
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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