Contacts of the strand formed by residues 46 - 55 (chain A) in PDB entry 3TKL
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 VAL 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A THR* 4.2 5.8 - - - +
45A GLY* 1.3 85.1 - - - +
47A ASP* 1.3 60.9 + - - +
65A TRP* 4.0 28.0 - - + -
66A ASP 3.1 13.9 - - - +
67A THR* 4.1 8.5 - - + -
80A TYR* 3.2 47.6 - - + +
406B LEU* 4.6 0.7 - - + -
428B LEU* 3.7 23.2 - - + +
431B HIS* 4.1 9.6 - - + +
432B ASN* 3.2 21.5 - - - +
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Residues in contact with ASP 47 (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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28A LEU* 3.9 15.1 - - + +
29A LEU* 5.2 4.5 - - - +
43A THR* 4.5 4.2 - - + +
46A VAL* 1.3 74.9 - - - +
48A PHE* 1.3 75.5 + - - +
49A LYS* 4.0 16.3 + - - -
64A ILE 4.4 0.2 - - - -
65A TRP* 3.4 6.9 - - - -
66A ASP* 2.9 50.1 + - - +
428B LEU* 3.4 16.5 - - - +
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Residues in contact with PHE 48 (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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47A ASP* 1.3 85.4 + - - +
49A LYS* 1.3 70.8 + - - +
50A ILE* 3.2 22.0 - - + -
63A GLN* 3.4 29.2 - - + -
64A ILE 3.3 19.7 - - - -
65A TRP* 3.2 55.0 - + + -
409B ILE* 4.5 8.1 - - + -
410B ASN* 4.4 7.2 - - - -
413B ILE* 3.0 47.6 - - + +
428B LEU* 3.9 13.3 - - + +
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Residues in contact with LYS 49 (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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28A LEU* 3.6 33.6 - - + +
29A LEU* 3.7 27.2 - - - +
32A ALA* 3.6 20.9 - - + -
33A ASP* 3.9 23.7 + - - +
47A ASP* 4.0 15.8 + - - -
48A PHE* 1.3 80.0 + - - +
50A ILE* 1.3 66.5 + - - +
62A LEU 3.8 0.3 - - - +
64A ILE* 2.9 35.5 + - + +
413B ILE* 5.9 0.7 - - - -
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Residues in contact with ILE 50 (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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32A ALA* 4.7 6.5 - - - +
48A PHE* 3.2 30.3 - - + -
49A LYS* 1.3 77.1 - - - +
51A ARG* 1.3 70.6 + - - +
52A THR* 5.3 0.9 - - - +
61A LYS* 3.3 36.1 - - + -
62A LEU 3.4 4.7 - - - +
63A GLN* 3.5 25.4 - - + -
413B ILE* 3.8 34.8 - - + +
414B MET* 4.6 5.6 - - - -
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Residues in contact with ARG 51 (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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31A PHE* 2.7 67.4 + - + +
32A ALA* 4.0 17.7 - - + +
50A ILE* 1.3 80.8 - - - +
52A THR* 1.3 75.8 + - - +
53A ILE* 3.9 13.1 - - - +
62A LEU* 2.8 45.2 + - - +
64A ILE* 4.7 1.9 - - + +
162A GLU* 2.9 40.7 + - - -
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Residues in contact with THR 52 (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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6A PRO* 6.2 0.2 - - - +
7A GLU 5.1 2.0 + - - +
50A ILE* 5.3 0.9 - - - +
51A ARG* 1.3 97.0 + - - +
53A ILE* 1.3 66.5 + - - +
59A THR* 3.0 36.6 - - + -
60A ILE 3.2 12.3 - - - +
61A LYS* 4.1 18.1 - - + +
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Residues in contact with ILE 53 (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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31A PHE* 3.6 31.0 - - + -
51A ARG* 3.9 13.0 - - - +
52A THR* 1.3 85.1 - - - +
54A GLU* 1.3 63.4 + - - +
55A LEU* 4.8 2.0 - - + -
59A THR* 3.6 2.6 - - - -
60A ILE* 2.9 47.9 + - + +
62A LEU* 4.1 13.0 - - + -
162A GLU* 5.4 1.6 - - - +
166A MET* 3.6 36.6 - - + +
169A ALA* 3.8 28.7 - - + -
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Residues in contact with GLU 54 (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 ILE* 1.3 78.5 - - - +
55A LEU* 1.3 60.6 + - - +
56A ASP 4.3 0.2 - - - -
57A GLY* 3.6 30.2 + - - +
58A LYS 3.3 8.3 - - - +
59A THR* 4.2 14.7 + - + +
166A MET* 4.1 15.6 - - - +
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Residues in contact with LEU 55 (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 ILE* 4.2 4.0 - - + -
54A GLU* 1.3 73.7 + - - +
56A ASP* 1.3 87.4 + - - +
57A GLY 3.1 0.7 - - - -
58A LYS* 2.9 29.2 + - - +
60A ILE* 3.7 28.9 - - + +
166A MET* 3.6 40.4 - - + +
169A ALA* 3.9 4.3 - - + +
170A ALA* 3.5 40.8 - - + +
173A LYS* 4.1 9.4 - - + -
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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