Contacts of the strand formed by residues 86 - 93 (chain A) in PDB entry 1TCR
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 ALA 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.4 29.2 - - + -
37A GLN 3.4 13.5 - - - +
38A TYR* 4.2 11.0 - - + +
39A PRO* 5.7 1.8 - - - -
84A ASP 3.1 9.6 + - - +
85A SER* 1.3 76.1 - - - +
87A VAL* 1.3 62.0 + - - +
88A TYR* 4.0 4.2 - - + -
110A THR 3.8 0.2 - - - +
111A LYS* 3.5 3.5 - - - +
112A VAL* 2.7 34.4 + - - +
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Residues in contact with VAL 87 (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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36A VAL* 3.3 3.6 - - - +
37A GLN* 2.8 43.7 + - + +
86A ALA* 1.3 77.7 - - - +
88A TYR* 1.3 63.0 + - - +
89A PHE* 3.3 37.2 + - + -
108A SER 5.5 0.2 - - - +
109A GLY* 4.4 1.3 - - - -
110A THR 3.3 19.1 - - - +
111A LYS* 4.2 25.4 - - + +
37B GLN* 5.4 1.3 - - - +
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Residues in contact with TYR 88 (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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5A GLN* 3.3 8.1 + - - -
18A LEU* 5.2 2.5 - - + -
20A LEU* 3.4 21.8 - - + -
34A TRP* 3.8 7.9 - - + -
35A TYR 3.5 2.2 - - - -
36A VAL* 3.5 27.1 - - + +
38A TYR* 4.9 3.8 + - - -
46A LEU* 3.6 33.9 - - + +
62A PHE* 3.8 24.0 - + - -
75A LEU* 3.9 5.8 - - + -
84A ASP* 2.7 35.3 + - + +
86A ALA* 3.9 9.1 - - + +
87A VAL* 1.3 74.9 - - - +
89A PHE* 1.3 61.6 + - - +
109A GLY* 3.4 0.2 - - - -
110A THR 2.8 32.7 + - - +
112A VAL* 3.5 32.8 - - + -
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Residues in contact with PHE 89 (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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5A GLN* 3.7 1.1 - - - -
34A TRP* 3.2 8.4 - - - -
35A TYR* 2.7 45.9 + - + +
37A GLN* 3.4 19.1 - - + -
43A LEU* 3.9 23.1 - - + -
87A VAL* 3.3 34.1 - - + -
88A TYR* 1.3 72.9 - - - +
90A CYS* 1.3 60.7 + - - +
106A PHE* 4.0 20.9 - + + -
107A GLY 3.8 10.1 - - - -
108A SER 3.6 10.3 - - - -
109A GLY* 3.5 25.8 - - - -
37B GLN* 3.5 22.4 - - - -
42B GLY* 3.6 16.2 - - - -
43B LEU* 4.4 5.2 - - + -
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Residues in contact with CYS 90 (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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3A VAL* 3.8 8.7 - - + +
5A GLN* 3.1 17.0 + - - +
22A CYS* 2.2 50.9 - - + -
32A LEU* 5.6 2.5 - - - -
33A PHE 3.5 12.8 - - - -
34A TRP* 4.1 14.1 - - + -
73A PHE* 4.4 9.6 - - - -
89A PHE* 1.3 74.5 - - - +
91A ALA* 1.3 66.2 + - - +
106A PHE* 3.4 4.0 - - - +
107A GLY 2.7 28.9 + - - -
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Residues in contact with ALA 91 (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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3A VAL* 4.1 5.2 - - - -
32A LEU* 3.6 8.1 - - - +
33A PHE* 3.0 39.4 + - + +
35A TYR* 4.7 1.3 - - + -
90A CYS* 1.3 78.2 - - - +
92A VAL* 1.3 59.2 + - - +
104A LEU* 3.3 24.0 - - + -
105A THR 2.9 15.9 - - - +
106A PHE* 3.8 20.9 - - + -
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Residues in contact with VAL 92 (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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1A GLN 3.5 22.9 + - - +
2A SER 3.9 7.0 - - - +
3A VAL* 3.4 23.5 - - + +
24A TYR* 4.6 5.2 - - + -
26A TYR* 3.9 14.1 - - + -
30A PRO* 3.6 29.2 - - + -
31A TYR 3.4 3.1 - - - -
32A LEU* 3.7 11.9 - - + -
91A ALA* 1.3 75.3 - - - +
93A SER* 1.3 65.0 + - - +
103A ALA 4.0 0.7 - - - +
104A LEU* 3.7 2.4 - - - -
105A THR* 2.8 47.4 + - - -
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Residues in contact with SER 93 (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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1A GLN 5.9 0.2 - - - +
26A TYR* 3.3 24.7 - - - -
30A PRO* 3.4 1.6 - - - +
31A TYR* 3.2 31.8 + - - +
33A PHE* 3.1 28.2 - - - -
92A VAL* 1.3 74.7 - - - +
99A GLY* 1.3 60.6 + - - +
102A SER* 3.3 21.3 - - - -
103A ALA 4.5 2.5 - - - -
104A LEU* 4.0 14.1 - - - +
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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