Contacts of the strand formed by residues 42 - 49 (chain B) 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 GLY 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.6 15.0 - - - -
107A GLY 3.6 5.4 - - - -
108A SER 3.4 25.5 + - - -
36B ARG 3.7 1.0 - - - +
37B GLN* 3.2 6.6 - - - +
38B ASP 3.1 29.8 + - - -
40B GLY 4.7 0.4 - - - +
41B HIS* 1.3 78.5 - - - +
43B LEU* 1.3 63.0 + - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.2 42.8 - - + -
89A PHE* 4.4 6.7 - - + -
106A PHE* 3.6 42.6 + - + +
107A GLY 4.2 3.8 + - - -
35B TYR* 4.2 12.7 - - + -
36B ARG 3.4 2.5 - - - +
37B GLN* 3.0 51.6 - - + +
41B HIS 3.3 3.5 + - - +
42B GLY* 1.3 73.2 - - - -
44B ARG* 1.3 62.4 + - - +
45B LEU 4.3 0.2 + - - -
91B PHE* 4.2 13.5 - - + -
108B PHE* 4.3 16.4 - - + -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.4 4.7 - - - -
36B ARG* 2.9 45.4 + - - +
38B ASP* 3.2 25.7 + - - -
41B HIS* 3.4 63.5 + - + +
43B LEU* 1.3 76.3 - - - +
45B LEU* 1.3 64.0 + - - +
46B ILE* 3.5 4.3 + - - +
59B ASP* 5.6 3.4 - - + -
60B ILE* 3.5 41.4 - - + +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA* 3.3 32.5 - - + +
104A LEU 4.3 9.2 - - - +
105A THR* 6.1 0.9 - - - +
33B TYR* 3.8 18.8 - - + -
34B TRP 3.8 5.4 - - - +
35B TYR* 3.4 23.1 - - + +
44B ARG* 1.3 69.9 - - - +
46B ILE* 1.3 60.2 + - - +
47B HIS 3.3 28.0 - - - +
48B TYR* 4.1 11.4 - - + -
58B GLY* 3.8 13.7 - - - -
59B ASP* 2.9 41.8 + - - +
60B ILE* 3.3 11.1 + - - +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TRP 2.9 17.2 + - - +
35B TYR 4.2 2.2 - - - -
36B ARG* 3.7 32.3 - - + +
44B ARG 3.8 8.1 - - - +
45B LEU* 1.3 76.9 - - - +
47B HIS* 1.3 74.1 + - + +
58B GLY* 2.7 25.4 + - - -
60B ILE* 3.5 16.6 - - + +
61B PRO* 3.5 14.0 - - + +
65B TYR* 3.4 33.4 - - + -
77B LEU* 4.2 11.7 - - + -
90B TYR* 3.9 25.8 - - + -
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TRP* 3.1 24.0 + - + +
45B LEU* 3.3 6.3 - - - +
46B ILE* 1.3 99.3 + - + +
48B TYR* 1.3 68.8 + - - +
55B THR* 4.3 5.8 + - - +
56B GLU 3.5 6.8 + - - +
57B LYS* 3.7 25.3 + - + +
58B GLY 3.7 2.5 - - - +
61B PRO* 3.5 25.6 + - + +
65B TYR* 2.9 35.1 + - + -
66B LYS* 4.1 1.1 + - - -
67B ALA* 3.7 31.7 - - + +
75B PHE* 4.1 5.6 - - + -
77B LEU* 4.0 11.9 - - + -
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA 5.2 2.6 + - - -
102A SER* 6.0 0.2 - - - -
103A ALA* 4.4 11.6 + - + -
32B MET 3.2 15.5 - - - +
33B TYR* 3.3 26.5 - + + -
45B LEU* 4.1 17.9 - - + -
47B HIS* 1.3 79.4 - - - +
49B SER* 1.3 66.6 + - - +
50B TYR* 3.2 44.4 + + - -
55B THR* 3.8 2.6 + - - -
56B GLU* 2.8 53.6 + - + +
57B LYS 3.1 24.6 + - - -
58B GLY* 4.4 2.5 - - - -
75B PHE* 3.7 8.8 - - - -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 3.2 10.2 - - - +
32B MET 2.9 27.5 + - - +
48B TYR* 1.3 82.3 - - - +
50B TYR* 1.3 61.3 + - - +
51B GLY 3.0 9.1 + - - -
54B SER 2.4 29.5 + - - -
56B GLU* 4.7 2.5 - - - -
69B ARG* 2.7 39.4 + - - +
75B PHE* 4.3 7.0 - - - -
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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