Contacts of the strand formed by residues 31 - 38 (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 ASN 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B HIS* 3.2 2.6 - - - +
30B ASN* 1.3 86.5 - - - +
32B MET* 1.3 72.1 + - - +
33B TYR* 3.5 24.5 + - + +
48B TYR* 5.6 0.2 - - - -
49B SER 3.2 5.4 - - - +
50B TYR* 2.7 45.3 - - - -
94B SER* 3.2 2.6 - - - -
95B GLY 2.9 42.6 + - - +
96B GLY* 4.7 0.4 - - - -
97B GLY* 3.7 19.0 - - - +
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Residues in contact with MET 32 (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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23B CYS* 3.7 31.2 - - - +
25B GLN* 3.5 44.4 - - + +
30B ASN 4.2 0.6 + - - -
31B ASN* 1.3 80.1 - - - +
33B TYR* 1.3 64.3 + - - +
48B TYR* 3.2 5.4 - - - +
49B SER 2.9 30.0 + - - +
69B ARG* 3.7 18.4 - - - +
72B GLN 3.6 11.9 - - - +
73B GLU 3.7 13.9 - - - +
75B PHE* 3.6 32.5 - - + -
92B CYS* 4.4 1.6 - - - -
93B ALA 3.2 8.3 - - - +
94B SER* 4.3 5.2 - - - -
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Residues in contact with TYR 33 (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* 3.8 29.1 - - + -
104A LEU 4.9 1.7 + - - -
31B ASN* 3.5 35.3 + - + +
32B MET* 1.3 74.6 - - - +
34B TRP* 1.3 61.6 + - - +
35B TYR* 3.9 16.1 - + + -
45B LEU* 3.8 15.7 - - + -
47B HIS 3.6 5.2 - - - -
48B TYR* 3.3 26.9 - + + -
50B TYR* 5.9 2.0 - + - -
75B PHE* 3.7 6.9 - - - -
91B PHE 3.9 0.7 - - - +
92B CYS* 3.4 7.8 - - - -
93B ALA* 2.8 43.6 + - + +
94B SER 4.3 0.2 - - - -
95B GLY* 4.0 10.8 - - - -
97B GLY* 5.4 3.5 + - - -
98B GLY 5.4 0.2 + - - -
106B LEU* 3.3 44.0 - - + +
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Residues in contact with TRP 34 (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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6B GLN* 3.5 34.5 - - + -
21B LEU* 3.9 21.8 - - + -
22B SER 3.7 13.5 - - - -
23B CYS* 3.7 19.4 - - + +
33B TYR* 1.3 73.1 - - - +
35B TYR* 1.3 62.3 + - - +
45B LEU* 3.8 2.6 - - - +
46B ILE* 2.9 29.3 + - + +
47B HIS* 3.1 12.6 + - + +
75B PHE* 3.0 51.8 + + + -
76B SER 4.3 0.7 - - - -
77B LEU* 3.9 47.3 - - + +
90B TYR* 3.7 24.0 - - + -
91B PHE 3.5 22.2 - - - -
92B CYS* 3.8 10.1 - - + -
112B THR* 4.8 0.9 - - - -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.8 40.0 + - - +
106A PHE* 3.5 21.9 - + - -
33B TYR* 3.9 23.5 - - + -
34B TRP* 1.3 75.7 - - - +
36B ARG* 1.3 61.0 + - - +
43B LEU* 4.2 23.1 - - + -
44B ARG 3.4 8.5 - - - +
45B LEU* 3.4 45.4 - - + +
46B ILE* 4.2 3.8 - - - -
90B TYR* 3.4 9.4 - - - +
91B PHE* 2.9 41.4 + - + +
93B ALA* 4.9 1.3 - - + -
106B LEU* 3.7 17.5 - - + +
108B PHE* 4.1 15.7 - + - -
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Residues in contact with ARG 36 (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* 1.3 75.2 - - - +
37B GLN* 1.3 60.7 + - - +
38B ASP* 2.7 36.6 + - - +
42B GLY 3.7 1.0 - - - +
43B LEU* 3.4 3.2 - - - -
44B ARG* 2.9 38.3 + - + +
46B ILE* 3.7 16.2 - - + -
60B ILE* 3.8 29.1 - - + +
65B TYR* 2.8 38.6 + - - -
85B SER* 3.2 27.9 + - - -
86B GLN* 3.9 4.6 - - - +
87B THR 3.8 2.4 + - - -
88B SER* 3.6 21.4 + - - +
89B VAL 3.5 4.5 - - - -
90B TYR* 3.9 9.6 - - + -
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Residues in contact with GLN 37 (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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37A GLN* 3.1 31.6 + - - +
87A VAL* 5.4 1.8 - - - +
89A PHE* 3.5 19.6 - - - -
36B ARG* 1.3 72.2 - - - +
38B ASP* 1.3 66.5 + - - +
42B GLY* 3.2 11.4 - - - +
43B LEU* 3.0 23.2 - - + +
88B SER* 2.9 16.6 + - - -
89B VAL* 2.9 29.8 + - + +
91B PHE* 3.3 21.4 - - + -
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Residues in contact with ASP 38 (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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36B ARG* 2.7 42.6 + - - +
37B GLN* 1.3 79.5 - - - +
39B THR* 1.3 71.8 + - + +
40B GLY 3.1 0.7 + - - -
41B HIS* 2.9 32.6 + - + +
42B GLY* 3.1 13.8 + - - +
44B ARG* 3.2 12.9 + - - +
87B THR 4.3 2.1 - - - +
88B SER* 2.9 21.6 + - - -
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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