Contacts of the helix formed by residues 38 - 45 (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 ARG 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.1 11.6 + - - +
36A THR 4.4 4.7 + - - +
37A LEU* 1.3 78.7 - - - +
39A LEU* 1.3 64.9 + - - +
40A VAL 3.4 2.0 - - - -
41A ASP* 3.0 28.8 + - + +
42A HIS* 3.0 29.8 + - + -
96A ASP* 4.1 15.6 + - - +
103A ARG* 3.4 43.8 - - - +
107A ASP* 4.8 2.2 + - - -
110A GLN* 5.5 4.2 - - - +
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Residues in contact with LEU 39 (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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34A ALA* 3.1 24.7 + - + +
37A LEU* 3.1 18.7 - - + -
38A ARG* 1.3 77.7 - - - +
40A VAL* 1.3 64.6 + - + +
42A HIS* 3.3 3.9 + - - +
43A ILE* 3.2 25.7 + - + +
53A LEU* 4.0 16.2 - - + +
57A THR* 3.7 24.0 - - + -
64A LEU* 3.8 20.0 - - + -
67A LEU* 4.4 4.9 - - + -
68A ILE* 4.7 8.5 - - + -
71A LEU* 3.4 33.0 - - + -
77A LEU* 4.4 13.7 - - + -
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Residues in contact with VAL 40 (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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34A ALA* 4.7 2.6 + - + +
38A ARG 3.4 0.4 - - - -
39A LEU* 1.3 80.5 - - + +
41A ASP* 1.3 62.0 + - - +
43A ILE* 3.4 9.8 + - - +
44A LEU* 3.2 35.0 + - + +
76A LEU* 5.2 1.1 - - + +
77A LEU* 4.3 15.0 - - + -
87A PRO* 4.1 20.6 - - + -
91A GLY* 3.4 32.1 - - - +
92A GLU* 4.4 2.2 - - - -
94A LEU* 4.2 25.6 - - + +
95A ALA* 4.1 14.6 - - - +
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Residues in contact with ASP 41 (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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38A ARG* 3.0 25.5 + - + +
40A VAL* 1.3 78.0 - - - +
42A HIS* 1.3 57.9 + - + +
44A LEU* 3.3 9.2 + - - +
45A ALA* 3.0 29.1 + - - +
94A LEU 4.2 1.1 - - - +
95A ALA* 3.6 9.2 - - - +
96A ASP* 3.0 44.0 + - - +
97A ASP* 4.9 0.7 + - - +
103A ARG* 3.7 14.2 - - - -
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Residues in contact with HIS 42 (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 3.4 20.2 + - - -
38A ARG* 3.0 37.5 + - + -
39A LEU 3.3 6.0 + - - +
41A ASP* 1.3 74.4 - - + +
43A ILE* 1.3 65.6 + - - +
45A ALA* 3.2 14.3 + - + +
46A GLY 3.4 1.0 + - - -
47A ALA* 3.0 22.6 + - - +
53A LEU* 3.9 14.6 - - + -
56A ARG* 3.4 57.3 + - + -
57A THR* 3.9 6.4 - - - +
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Residues in contact with ILE 43 (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* 3.2 18.3 + - + +
40A VAL* 3.7 7.9 - - - +
41A ASP 3.3 0.2 - - - -
42A HIS* 1.3 76.2 - - - +
44A LEU* 1.3 64.8 + - + +
45A ALA 3.3 0.7 + - - -
46A GLY* 3.4 8.3 + - - -
47A ALA* 3.5 20.9 + - - +
53A LEU* 3.8 29.6 - - + -
77A LEU* 4.1 29.6 - - + -
85A PHE* 3.4 29.2 - - + +
86A VAL* 4.3 6.7 - - + -
87A PRO* 3.6 20.2 - - + -
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Residues in contact with LEU 44 (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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40A VAL* 3.2 30.7 + - + +
41A ASP* 3.3 9.6 + - - +
43A ILE* 1.3 78.6 - - + +
45A ALA* 1.3 59.3 + - - +
46A GLY 3.3 1.2 + - - -
87A PRO* 4.0 20.9 - - + -
92A GLU* 4.3 20.9 - - + +
95A ALA* 4.4 16.8 - - + -
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Residues in contact with ALA 45 (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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41A ASP 3.0 16.4 + - - +
42A HIS* 3.7 11.2 - - + +
43A ILE 3.2 0.8 - - - -
44A LEU* 1.3 76.2 - - - +
46A GLY* 1.3 56.7 - - - +
56A ARG* 3.8 18.6 + - - +
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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