Contacts of the strand formed by residues 29 - 35 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR 5.0 5.2 + - - -
32A SER* 3.6 10.8 - - - +
33A SER* 3.0 25.4 + - - +
9C TYR* 3.4 36.0 + + - -
21C THR* 3.7 21.1 - - + -
22C CYS 3.4 2.9 - - - -
23C GLU* 3.8 43.0 + - + -
24C ARG* 4.4 1.1 - - - -
28C GLY* 1.3 80.8 - - - -
30C ASN* 1.3 60.5 + - - +
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Residues in contact with ASN 30 (chain C).
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* 3.6 8.7 - - - +
33A SER* 2.7 26.3 + - - +
34A ILE 3.2 21.3 + - - -
35A ASP* 3.4 5.3 + - - +
20C SER 3.7 0.9 - - - +
21C THR* 3.5 0.8 - - - -
22C CYS 2.8 32.3 + - - -
24C ARG* 3.9 17.0 - - + -
29C TYR* 1.3 74.2 - - - +
31C THR* 1.3 72.6 + - - +
32C SER* 3.9 0.6 - - - -
95D ASP 5.1 0.2 - - - -
96D GLY* 2.8 34.1 + - - +
97D THR* 3.1 20.0 + - - -
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Residues in contact with THR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER 3.0 9.3 + - - -
34A ILE* 3.3 16.1 - - + +
35A ASP 2.9 24.9 + - - -
97B THR* 5.9 0.3 - - - -
98B LEU 3.8 13.7 + - - -
99B LYS* 2.9 40.6 + - + +
100B TYR 6.0 0.2 - - - +
19C THR* 3.8 22.0 - - + -
20C SER 3.4 11.7 - - - +
21C THR* 3.2 11.7 + - - +
30C ASN* 1.3 73.2 + - - +
32C SER* 1.3 64.1 + - - +
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 5.5 0.4 - - - -
35A ASP* 4.0 19.1 - - - -
38A SER* 5.1 0.2 - - - -
19C THR* 3.3 6.4 - - - +
20C SER 3.0 30.3 + - - -
22C CYS* 5.2 0.2 - - - -
30C ASN* 3.9 13.2 + - - -
31C THR* 1.3 77.3 - - - +
33C SER* 1.3 64.1 + - - +
96D GLY 4.0 2.1 + - - -
97D THR* 3.5 13.5 - - - -
98D LEU* 3.0 32.6 + - - +
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Residues in contact with SER 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 2.7 44.5 + - - -
39A VAL* 4.8 4.2 - - - +
17C VAL* 3.8 14.2 - - - +
18C LEU 3.0 12.3 - - - -
19C THR* 3.6 16.4 - - - -
32C SER* 1.3 81.1 - - - +
34C ILE* 1.3 62.5 + - - +
97D THR* 5.7 1.0 - - - +
98D LEU* 4.4 7.0 - - - +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 5.1 1.3 - - - -
17C VAL* 3.5 3.8 - - - -
18C LEU* 2.8 61.6 + - + +
33C SER* 1.3 76.2 - - - +
35C ASP* 1.3 72.2 + - - +
36C LEU* 3.5 10.9 + - + -
39C VAL* 5.4 4.0 - - + -
91D ILE* 4.0 14.8 - - + -
98D LEU* 3.9 25.8 - - + +
99D LYS* 4.0 2.2 - - - -
100D TYR* 3.5 34.1 - - + +
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Residues in contact with ASP 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 5.8 1.4 - - - -
53A ASN* 5.2 6.2 + - - +
16C SER* 2.6 31.5 + - - -
17C VAL* 4.4 14.1 - - + +
34C ILE* 1.3 77.8 - - - +
36C LEU* 1.3 62.5 + - - +
37C ASN* 3.0 17.7 + - - +
38C SER* 3.5 25.2 + - - +
39C VAL* 4.3 2.3 - - - +
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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