Contacts of the helix formed by residues 49 - 58 (chain A) in PDB entry 1TW2
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 THR 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ALA 4.6 0.7 - - - -
48A ARG* 1.3 93.5 - - + +
50A VAL* 1.3 65.6 + - - +
51A LYS* 3.7 9.5 + - - +
52A ALA* 3.2 22.4 + - - +
53A LEU* 3.0 26.0 + - - +
83A GLY 4.3 6.3 - - - +
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Residues in contact with VAL 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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49A THR* 1.3 73.4 - - - +
51A LYS* 1.3 56.9 + - - +
53A LEU* 4.3 7.2 - - - -
54A ALA* 3.0 26.7 + - - +
61A PRO* 3.7 28.3 - - + +
64A LEU* 3.8 13.4 - - + +
65A LEU* 4.1 23.6 - - + +
68A ILE* 4.4 6.1 - - + -
83A GLY* 4.1 10.5 + - - +
85A PHE* 4.0 32.3 - - + -
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Residues in contact with LYS 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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49A THR* 3.1 9.4 + - - +
50A VAL* 1.3 76.9 - - - +
52A ALA* 1.3 59.8 + - - +
54A ALA* 3.3 6.1 + - - +
55A ALA* 3.0 27.3 + - + +
61A PRO* 5.1 12.8 - - + -
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Residues in contact with ALA 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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46A GLY 5.2 1.6 - - - +
47A ALA* 4.3 18.2 - - + -
48A ARG 4.7 0.7 - - - +
49A THR* 3.2 21.1 + - - +
51A LYS* 1.3 78.0 - - - +
53A LEU* 1.3 58.9 - - - +
55A ALA* 3.1 8.7 + - - +
56A ARG* 2.9 41.8 + - - +
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Residues in contact with LEU 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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39A LEU* 4.0 21.5 - - + +
42A HIS* 3.9 22.0 - - + -
43A ILE* 3.8 30.5 - - + -
47A ALA* 4.1 11.3 - - + +
49A THR 3.0 16.3 + - - +
50A VAL* 3.8 3.6 - - - +
52A ALA* 1.3 77.9 - - - +
54A ALA* 1.3 50.1 + - - +
56A ARG* 3.5 1.5 + - - +
57A THR* 2.5 59.8 + - + +
64A LEU* 3.7 11.4 - - + -
68A ILE* 4.1 24.7 - - + -
85A PHE* 5.7 2.5 - - + -
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Residues in contact with ALA 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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50A VAL 3.0 19.8 + - - +
51A LYS 3.6 4.9 - - - +
52A ALA 3.2 0.2 - - - -
53A LEU* 1.3 71.9 - - - +
55A ALA* 1.3 60.9 + - - +
58A ASP* 2.9 9.4 + - - -
59A THR* 2.8 56.3 + - - +
61A PRO* 3.8 27.1 - - + -
64A LEU* 3.6 4.0 - - + +
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Residues in contact with ALA 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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51A LYS 3.0 13.6 + - - +
52A ALA* 3.4 11.7 - - - +
54A ALA* 1.3 76.4 - - - +
56A ARG* 1.3 62.9 + - + +
58A ASP* 3.3 18.5 + - - +
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Residues in contact with ARG 56 (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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42A HIS* 3.4 49.8 + - + -
45A ALA* 3.8 30.9 + - - +
46A GLY* 2.9 33.7 + - - -
47A ALA* 3.7 9.5 - - - +
52A ALA* 2.9 26.3 + - - +
53A LEU* 3.9 4.0 - - - +
55A ALA* 1.3 78.5 - - + +
57A THR* 1.3 60.5 + - - +
58A ASP* 3.3 1.1 + - - +
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Residues in contact with THR 57 (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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37A LEU* 3.6 39.3 - - - +
39A LEU* 3.7 24.2 - - + -
42A HIS* 3.9 7.6 - - - +
53A LEU* 2.5 32.1 + - + +
54A ALA 3.4 1.0 + - - -
56A ARG* 1.3 75.9 - - - +
58A ASP* 1.3 71.3 + - - +
59A THR* 2.7 35.6 + - - +
64A LEU* 4.4 1.6 - - - +
127B ARG* 4.6 4.2 + - - -
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Residues in contact with ASP 58 (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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54A ALA 2.9 7.5 + - - -
55A ALA* 3.3 11.0 + - - +
56A ARG 3.3 4.1 - - - +
57A THR* 1.3 83.5 - - - +
59A THR* 1.3 61.1 + - - +
127B ARG* 4.0 22.5 - - - +
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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