Contacts of the strand formed by residues 96 - 102 (chain D) in PDB entry 4DQ0
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D LYS* 3.8 28.3 - - + +
34D THR 3.6 26.9 - - - -
35D LEU* 3.6 28.5 - - + -
56D ASP* 3.0 25.2 + - - +
58D TRP* 4.0 17.2 - - - -
92D PHE* 4.7 4.0 - + - -
93D ASP 4.2 18.0 + - - -
94D GLY* 4.3 8.0 - - - -
95D GLU* 1.3 76.4 - - - +
97D ASP* 1.3 61.9 + - - +
98D PHE 3.9 1.8 - - - +
99D ILE* 3.7 24.7 - - + -
123D CYS* 2.9 23.7 + - + +
124D THR* 3.7 4.3 - - - +
125D LYS* 2.9 30.4 + - - +
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Residues in contact with ASP 97 (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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29D VAL* 4.5 3.0 - - + +
30D LYS 5.5 2.7 - - - +
32D GLY* 3.7 12.3 - - - -
33D LYS* 2.8 37.7 + - - +
96D TYR* 1.3 72.4 - - - +
98D PHE* 1.3 62.0 + - + +
124D THR* 5.3 0.2 - - - -
125D LYS* 2.8 35.0 + - - +
128D GLY* 3.4 9.6 - - - -
129D TYR* 3.0 29.3 + - - -
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Residues in contact with PHE 98 (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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22D VAL* 5.7 2.9 - - + -
25D ALA* 4.3 18.2 - - + -
26D VAL* 5.3 3.1 - - + -
29D VAL* 3.9 29.6 - - + -
30D LYS 5.9 0.4 - - - +
32D GLY* 5.7 0.4 - - - -
33D LYS 3.2 2.5 + - - +
34D THR* 3.1 31.9 - - + +
35D LEU 2.8 31.5 + - - -
48D LEU* 4.3 16.4 - - + -
53D TYR* 4.4 9.9 - + + -
96D TYR* 3.2 1.9 - - - +
97D ASP* 1.3 83.3 - - + +
99D ILE* 1.3 72.4 + - - +
100D LEU* 3.9 17.9 - - + -
124D THR* 5.6 0.2 - - - +
129D TYR* 3.4 20.4 - - + -
131D LEU* 3.9 33.4 - - + -
193D LEU* 4.8 1.1 - - + -
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Residues in contact with ILE 99 (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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35D LEU* 3.2 29.6 - - + +
37D LEU* 4.8 3.1 - - + -
92D PHE* 4.8 0.2 - - + -
96D TYR* 3.7 21.5 - - + -
98D PHE* 1.3 82.9 - - - +
100D LEU* 1.3 66.4 + - - +
120D MET* 3.5 59.1 - - + +
123D CYS* 4.0 14.8 - - + +
124D THR* 3.5 10.1 - - - +
129D TYR 3.0 6.1 + - - -
130D ASN* 3.3 12.2 - - - +
131D LEU 2.9 25.1 + - - +
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Residues in contact with LEU 100 (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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22D VAL* 3.8 27.6 - - + -
34D THR* 3.5 24.5 - - + -
35D LEU 2.9 19.5 + - - +
36D ASP* 3.9 26.8 - - + +
37D LEU* 3.0 28.9 + - - +
44D ASN* 4.0 14.4 - - + +
48D LEU* 3.9 9.9 - - + -
98D PHE* 3.9 15.5 - - + -
99D ILE* 1.3 77.4 - - - +
101D SER* 1.3 62.1 - - - +
102D THR* 4.8 4.5 - - + +
120D MET* 5.1 0.2 - - - -
131D LEU* 3.3 22.9 - - + +
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Residues in contact with SER 101 (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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36D ASP* 5.4 0.4 - - - -
37D LEU* 4.0 13.6 + - - -
100D LEU* 1.3 76.6 - - - +
102D THR* 1.3 61.6 + - - +
104D VAL* 3.6 15.5 - - - +
105D LEU* 3.5 26.2 - - - +
120D MET* 4.4 13.5 - - - -
131D LEU 2.8 10.5 + - - -
132D ILE* 3.4 16.9 - - - +
133D VAL 3.1 24.1 + - - +
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Residues in contact with THR 102 (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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19D HIS* 4.2 21.3 - - + +
22D VAL* 4.2 12.8 - - + -
36D ASP* 5.2 2.7 + - - -
38D GLY 4.8 4.5 + - - +
43D ARG* 4.7 2.3 + - - -
44D ASN* 3.2 21.8 + - - -
100D LEU* 4.1 4.8 - - + +
101D SER* 1.3 75.9 - - - +
103D VAL* 1.3 77.5 + - - +
104D VAL* 3.2 11.5 + - - +
131D LEU* 3.9 27.4 - - + -
133D VAL* 4.0 18.4 - - + -
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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