Contacts of the strand formed by residues 62 - 70 (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 SER 62 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X TYR* 3.9 0.3 - - - -
24X PHE* 2.8 35.1 + - - +
26X ASP 3.2 5.8 + - - -
27X LEU 3.4 26.0 - - - -
29X PHE* 3.2 31.0 + - - -
60X PHE* 3.6 4.2 - - - +
61X GLN* 1.3 80.3 - - - +
63X ALA* 1.3 56.4 + - - +
120X TYR* 2.9 23.1 - - - -
121X GLN* 4.1 2.2 - - - -
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Residues in contact with ALA 63 (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 3.0 14.6 - - - +
23X TYR* 4.2 13.7 - - + -
24X PHE* 4.0 2.5 - - - -
29X PHE* 4.0 1.6 - - - -
60X PHE* 6.1 0.4 - - + -
62X SER* 1.3 75.1 + - - +
64X ILE* 1.3 68.4 + - - +
65X TRP* 3.6 32.5 - - + -
118X ILE 4.0 0.2 - - - +
119X GLN 3.7 0.5 - - - -
120X TYR* 2.9 39.0 + - + +
130X LEU* 4.6 2.2 - - + -
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Residues in contact with ILE 64 (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* 3.4 1.9 - - - -
22X TYR* 2.8 55.1 + - + +
24X PHE* 4.1 8.9 - - + -
29X PHE* 3.3 48.2 - - + -
63X ALA* 1.3 79.2 - - - +
65X TRP* 1.3 78.0 + - - +
66X SER* 4.9 2.2 - - - +
117X LYS* 4.5 20.2 - - + -
118X ILE 3.4 9.4 - - - +
119X GLN* 4.7 5.2 - - + -
175X VAL* 5.3 19.1 - - + +
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Residues in contact with TRP 65 (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* 4.3 20.9 - - + -
20X LEU 3.2 6.7 - - - -
21X GLY* 3.4 21.5 - - - -
23X TYR* 3.2 42.2 + + - -
43X LEU* 3.5 42.8 - - + +
63X ALA* 3.6 24.2 - - + -
64X ILE* 1.3 78.7 - - - +
66X SER* 1.3 64.6 + - - +
116X ILE* 5.5 0.2 - - - -
117X LYS* 3.4 9.2 - - - +
118X ILE* 2.9 55.1 + - + +
120X TYR* 4.0 17.5 - - + -
130X LEU* 3.8 15.5 - - + -
132X PHE* 3.9 20.4 - + - -
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Residues in contact with SER 66 (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* 3.7 7.7 - - - +
20X LEU* 2.9 34.9 + - - -
22X TYR* 5.4 7.6 - - - -
64X ILE* 4.9 4.2 - - - +
65X TRP* 1.3 74.9 - - - +
67X GLY* 1.3 59.2 + - - +
116X ILE 3.6 6.0 + - - -
117X LYS* 3.1 28.9 + - - +
154X PRO* 3.3 20.6 - - - +
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Residues in contact with GLY 67 (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* 3.5 5.0 - - - +
66X SER* 1.3 75.7 + - - +
68X PHE* 1.3 70.7 + - - -
115X GLN* 3.6 6.1 - - - +
116X ILE* 2.9 30.2 + - - +
152X GLN 3.3 12.6 - - - -
154X PRO* 3.7 15.5 - - - +
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Residues in contact with PHE 68 (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* 3.9 2.0 - - - +
67X GLY* 1.3 75.6 - - - -
69X ILE* 1.3 59.5 + - - +
92X ASP* 5.7 0.2 - - - -
113X LEU* 4.0 27.4 - - + -
114X TYR 3.2 23.3 - - - +
115X GLN* 3.4 31.4 - - + -
116X ILE* 4.0 4.3 - - - -
151X LEU* 3.3 7.3 - - - +
152X GLN* 2.9 52.2 + - + +
153X LEU 3.4 24.2 - - - -
154X PRO* 4.0 12.3 - - + -
155X GLU* 4.1 15.7 - - + -
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Residues in contact with ILE 69 (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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68X PHE* 1.3 75.2 - - - +
70X LYS* 1.3 62.0 + - - +
71X VAL* 5.0 1.3 - - + +
79X PHE* 4.5 9.6 - - + -
91X VAL* 4.9 2.2 - - + -
108X LEU* 4.3 21.5 - - + -
113X LEU* 3.7 3.3 - - - -
114X TYR* 3.1 48.6 + - + -
116X ILE* 3.5 32.3 - - + -
136X TRP* 4.6 14.1 - - + -
146X ILE* 4.9 2.7 - - + -
150X ASN* 3.3 36.1 - - + +
151X LEU* 3.9 15.7 - - + -
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Residues in contact with LYS 70 (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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69X ILE* 1.3 75.0 - - - +
71X VAL* 1.3 64.5 + - - +
72X LYS* 5.2 16.4 - - + +
111X GLY* 5.1 7.0 - - - +
112X ARG 3.7 8.5 - - - +
113X LEU* 3.5 19.0 - - + +
149X ASP* 3.3 39.4 + - - +
150X ASN* 3.2 27.9 + - - +
152X GLN* 3.4 30.9 - - - +
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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