Contacts of the strand formed by residues 19 - 24 (chain X) in PDB entry 1T6B
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 LEU 19 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X GLY* 1.3 71.5 - - - -
20X LEU* 1.3 65.9 + - - +
21X GLY* 3.4 1.7 + - - -
37X SER* 3.2 21.9 - - - -
38X SER* 3.5 11.3 + - - -
40X THR 6.0 0.2 - - - +
43X LEU* 4.8 13.4 - - + +
65X TRP* 4.3 23.9 - - + -
66X SER 3.7 5.4 - - - +
67X GLY* 3.5 31.2 - - - +
68X PHE 3.9 14.1 - - - +
116X ILE* 4.1 20.9 - - + -
118X ILE* 4.4 10.3 - - + -
134X LEU* 4.6 5.2 - - + -
151X LEU* 3.9 29.5 - - + +
152X GLN 4.0 3.1 - - - +
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Residues in contact with LEU 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X GLY 3.7 3.4 + - - -
19X LEU* 1.3 69.7 - - - +
21X GLY* 1.3 59.0 + - - +
22X TYR* 3.0 39.3 - - + +
35X VAL* 4.2 8.1 - - + -
36X THR 3.8 16.4 - - - +
37X SER* 4.3 5.6 - - - -
64X ILE 3.9 0.9 - - - +
65X TRP* 3.2 5.3 - - - -
66X SER* 2.9 42.2 + - - +
153X LEU* 3.9 6.3 - - + +
154X PRO* 4.0 15.9 - - + -
156X LEU* 4.6 14.4 - - + -
182X GLY* 4.0 16.4 - - - +
236X PHE* 3.6 30.5 - - + -
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Residues in contact with GLY 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X LEU 3.4 1.6 + - - -
20X LEU* 1.3 74.1 - - - +
22X TYR* 1.3 62.7 + - - -
23X TYR* 3.8 8.6 - - - -
34X VAL 3.7 0.9 - - - +
35X VAL* 3.3 7.8 - - - +
36X THR 2.7 40.3 + - - -
64X ILE 3.4 0.7 - - - -
65X TRP* 3.4 24.9 - - - -
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Residues in contact with TYR 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X LEU* 3.0 29.5 - - + +
21X GLY* 1.3 72.7 - - - -
23X TYR* 1.3 63.5 + - - +
24X PHE* 3.5 24.1 - + + -
32X PRO* 5.4 2.5 - - + -
34X VAL 3.4 2.7 - - - -
35X VAL* 3.5 35.9 - - + -
63X ALA* 3.0 6.9 - - - +
64X ILE* 2.8 58.2 + - + +
65X TRP* 5.6 0.2 - - - -
66X SER* 5.4 6.3 - - - -
156X LEU* 5.3 0.9 - - - +
175X VAL* 4.7 20.4 - - + +
177X ASP* 4.7 5.7 + - - +
182X GLY* 2.9 23.3 + - - -
184X PRO* 3.7 24.3 - - + +
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Residues in contact with TYR 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X GLY* 3.8 20.6 - - - -
22X TYR* 1.3 76.7 - - - +
24X PHE* 1.3 55.1 + - - +
32X PRO* 3.5 2.5 - - - +
33X MET* 2.6 34.9 + - - -
34X VAL* 2.9 24.7 + - + +
36X THR* 4.0 11.7 - - + +
43X LEU* 2.7 26.1 + - - -
44X SER 4.7 0.2 + - - -
45X ILE* 3.6 36.4 - - + +
60X PHE* 4.0 34.1 - + + -
62X SER 3.9 3.6 - - - -
63X ALA* 4.2 9.9 - - + -
65X TRP* 3.2 32.8 + + - -
130X LEU* 4.0 10.8 - - + -
200X ARG* 5.9 0.9 - - - -
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Residues in contact with PHE 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X TYR* 3.5 37.2 - + + -
23X TYR* 1.3 74.5 - - - +
25X SER* 1.3 60.3 + - - +
26X ASP* 3.4 16.6 - - - +
29X PHE* 3.3 51.1 - + + -
31X ALA 3.2 24.7 - - - +
32X PRO* 3.5 22.0 - - + -
60X PHE* 3.1 11.3 - - - -
61X GLN 3.0 22.7 + - - -
62X SER* 2.8 33.7 + - - +
64X ILE* 4.1 11.4 - - + -
175X VAL* 6.3 2.5 - - - -
176X PRO* 6.3 1.3 - - + -
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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