Contacts of the strand formed by residues 138 - 143 (chain A) in PDB entry 3TR6
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 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LYS* 3.7 36.4 + - + +
65A VAL 4.6 3.8 - - - -
66A ILE* 3.5 33.4 - - + -
90A ILE* 3.9 11.6 - - + +
129A LEU* 3.5 23.7 - - + +
134A GLN* 3.9 31.7 + - + -
137A GLN* 1.3 84.2 - - + +
139A ASP* 1.3 62.6 + - - +
140A LEU 5.1 0.2 - - - +
141A ILE* 4.4 9.2 - - + -
160A LEU* 2.9 38.6 + - + +
161A LEU* 3.4 14.0 - - + +
162A ARG* 2.8 31.1 + - - +
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Residues in contact with ASP 139 (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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60A MSE 3.4 13.5 - - + +
61A GLN 4.7 1.5 - - - +
62A ALA* 3.8 18.8 - - + -
63A LYS* 2.8 30.0 + - - +
64A LYS* 3.0 19.0 + - - +
137A GLN 4.7 3.8 - - - +
138A TYR* 1.3 75.1 - - - +
140A LEU* 1.3 57.7 + - - +
161A LEU* 3.8 2.9 - - - -
162A ARG* 2.8 39.6 + - - +
165A GLY* 3.3 4.0 - - - -
166A LEU 2.8 29.3 + - - -
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Residues in contact with LEU 140 (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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53A LEU* 4.5 7.6 - - + +
56A LEU* 4.6 7.6 - - + -
57A VAL* 3.6 40.4 - - + +
60A MSE 4.7 4.7 - - - -
62A ALA* 4.4 6.1 - - + -
64A LYS 3.5 2.3 + - - +
65A VAL* 3.3 19.5 - - + +
66A ILE 3.0 22.9 + - - -
79A MSE 4.1 15.9 - - - -
138A TYR 3.7 0.4 - - - -
139A ASP* 1.3 81.9 - - - +
141A ILE* 1.3 74.3 + - - +
142A TYR 5.0 0.2 - - - +
166A LEU* 3.3 40.6 - - + +
168A ALA* 4.6 10.5 - - + -
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Residues in contact with ILE 141 (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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66A ILE* 3.5 37.7 - - + +
68A ILE* 4.0 19.5 - - + -
126A LEU* 5.8 0.2 - - + -
138A TYR* 4.4 4.3 - - + -
140A LEU* 1.3 83.5 - - - +
142A TYR* 1.3 61.8 + - - +
143A ILE* 3.9 4.0 + - + -
157A SER* 3.2 54.7 - - - +
160A LEU* 4.1 11.2 - - + -
161A LEU* 3.8 13.7 - - + -
166A LEU 2.8 11.9 + - - +
167A ILE* 3.4 5.4 - - + +
168A ALA* 2.8 27.7 + - - +
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Residues in contact with TYR 142 (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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45A THR* 3.2 8.7 + - - +
49A GLN* 3.0 18.5 + - - -
53A LEU* 3.8 21.8 - - + -
66A ILE 2.9 11.4 + - - +
67A ASP* 3.4 18.8 - - - +
68A ILE* 2.8 31.2 + - - +
75A SER* 3.5 26.5 - - - -
79A MSE 3.8 23.8 - - + -
140A LEU* 4.3 1.3 - - + +
141A ILE* 1.3 72.3 - - - +
143A ILE* 1.3 60.5 + - - +
144A ASP* 3.1 32.6 + - + -
168A ALA* 3.4 22.4 - - + -
170A ASP* 3.4 18.9 + - + -
215A LEU* 4.1 12.3 - - + -
224A SAH 3.8 2.9 - - - -
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Residues in contact with ILE 143 (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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68A ILE* 4.1 17.3 - - + -
141A ILE* 4.3 3.8 - - + -
142A TYR* 1.3 72.8 - - - +
144A ASP* 1.3 62.5 + - - +
145A ALA 4.8 2.7 - - - +
150A THR* 4.6 18.8 - - + +
153A TYR* 3.8 31.0 - - + -
154A TYR* 3.7 34.3 - - + +
157A SER* 3.9 8.5 - - - +
167A ILE* 3.8 21.8 - - + -
168A ALA 2.8 14.3 + - - +
169A VAL* 3.8 15.4 - - + +
170A ASP 3.3 24.3 + - - +
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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