Contacts of the strand formed by residues 29 - 35 (chain A) in PDB entry 4J4D
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 TYR 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR 5.5 0.7 - - - -
9A TYR* 3.9 35.2 - + - +
21A THR* 3.9 14.6 - - + -
22A CYS 3.3 6.7 - - - +
23A GLU* 3.7 48.7 + - + -
24A ARG* 4.3 5.5 - - - +
28A GLY* 1.3 81.5 - - - -
30A ASN* 1.3 63.9 + - - +
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Residues in contact with ASN 30 (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 SER 3.7 1.2 - - - +
21A THR* 3.4 2.1 - - - -
22A CYS 2.8 29.9 + - - -
24A ARG* 4.1 17.7 - - - -
29A TYR* 1.3 77.3 - - - +
31A THR* 1.3 78.1 + - - +
32A SER* 4.2 3.0 - - - -
95B ASP 5.5 0.2 + - - -
96B GLY 3.1 29.5 + - - +
97B THR* 3.6 18.8 - - - +
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Residues in contact with THR 31 (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 THR* 3.7 25.6 - - + -
20A SER 3.3 7.2 - - - +
21A THR* 2.8 25.1 + - - +
30A ASN* 1.3 84.7 + - - +
32A SER* 1.3 65.6 + - - +
28C GLY* 5.2 4.2 - - - -
29C TYR* 5.0 6.4 + - - -
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Residues in contact with SER 32 (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 THR* 3.3 5.7 - - - +
20A SER 2.9 29.8 + - - +
22A CYS* 5.4 0.2 - - - -
30A ASN* 4.0 7.8 + - - -
31A THR* 1.3 76.2 - - - +
33A SER* 1.3 65.1 + - - +
96B GLY 4.1 1.0 + - - -
97B THR* 3.4 15.6 - - - -
98B LEU* 2.9 35.8 + - - +
29C TYR* 3.6 16.4 - - - +
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Residues in contact with SER 33 (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 VAL* 3.7 6.6 - - - +
18A LEU 2.9 16.4 - - - -
19A THR* 3.5 17.9 - - - -
32A SER* 1.3 79.2 + - - +
34A ILE* 1.3 61.2 + - - +
98B LEU* 4.2 6.3 - - - +
24C ARG* 3.7 14.1 - - - -
29C TYR 3.0 7.2 + - - +
30C ASN* 2.7 33.8 + - - +
31C THR* 3.0 22.9 + - - -
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Residues in contact with ILE 34 (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 VAL* 3.5 1.1 - - - -
18A LEU* 2.8 55.8 + - + +
33A SER* 1.3 75.8 - - - +
35A ASP* 1.3 70.5 + - - +
36A LEU* 3.7 11.9 + - + -
39A VAL* 6.1 1.8 - - + -
91B ILE* 4.2 13.9 - - + -
98B LEU* 3.9 23.8 - - + +
99B LYS* 3.8 12.6 - - - -
100B TYR* 3.5 33.7 - - + +
30C ASN* 3.4 5.2 - - - -
31C THR* 3.3 22.2 - - + +
32C SER* 5.5 0.2 - - - -
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Residues in contact with ASP 35 (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 SER* 2.7 29.8 + - - -
17A VAL* 4.0 12.7 - - + +
34A ILE* 1.3 78.0 - - - +
36A LEU* 1.3 56.5 + - - +
37A ASN* 2.9 18.6 + - - +
38A SER* 4.1 12.9 + - - -
39A VAL* 4.8 1.6 - - - +
30C ASN* 3.4 7.5 + - - +
31C THR 2.9 9.7 + - - +
32C SER* 4.0 13.5 - - - -
97D THR* 2.7 42.8 + - - +
99D LYS* 5.2 2.6 + - - -
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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