Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 1T0H
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ARG* 1.3 68.4 - - - +
43A GLU* 1.3 62.0 + - - +
44A ALA* 3.0 4.7 - - - +
45A GLU* 3.5 31.9 + - + +
46A ARG* 3.5 19.0 + - - +
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Residues in contact with GLU 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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41A ARG* 3.0 13.3 - - + +
42A ARG* 1.3 78.4 - - - +
44A ALA* 1.3 61.3 + - - +
46A ARG* 2.9 43.5 + - - +
47A GLN* 3.0 27.5 + - + +
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Residues in contact with ALA 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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41A ARG 3.2 14.2 + - - +
42A ARG* 3.0 1.7 - - - -
43A GLU* 1.3 79.0 - - - +
45A GLU* 1.3 58.2 + - + +
47A GLN* 3.3 6.8 + - - +
48A ALA* 3.0 29.0 + - - +
79A PRO 4.9 0.9 - - - -
99A PHE* 5.5 0.7 - - - -
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Residues in contact with GLU 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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42A ARG* 3.5 25.3 + - + +
44A ALA* 1.3 78.0 - - + +
46A ARG* 1.3 58.3 + - - +
48A ALA* 3.3 2.3 + - - +
49A GLN* 2.9 31.5 + - - +
79A PRO 3.7 20.9 - - - +
80A VAL* 3.7 9.1 - - + +
81A PRO* 3.4 35.0 - - + +
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Residues in contact with ARG 46 (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 ARG 3.5 15.2 + - - +
43A GLU* 2.9 52.7 + - - +
45A GLU* 1.3 79.1 - - - +
47A GLN* 1.3 57.5 + - - +
49A GLN* 3.3 7.3 + - + +
50A ALA* 3.0 26.6 + - + +
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Residues in contact with GLN 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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43A GLU* 3.0 20.2 + - + +
44A ALA* 3.7 8.7 - - - +
46A ARG* 1.3 74.3 - - - +
48A ALA* 1.3 65.9 + - - +
50A ALA* 3.3 8.3 + - - +
51A GLN* 3.0 23.4 + - - +
99A PHE* 5.3 1.1 - - - -
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Residues in contact with ALA 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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44A ALA 3.0 16.9 + - - +
45A GLU 3.3 1.3 + - - +
47A GLN* 1.3 76.8 - - - +
49A GLN* 1.3 62.0 + - - +
51A GLN* 3.2 3.5 + - - +
52A LEU* 3.1 22.7 + - - +
79A PRO* 3.6 26.7 - - + +
80A VAL* 3.6 20.4 - - + -
99A PHE* 3.9 21.9 - - + -
117A PHE* 3.8 6.0 - - + -
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Residues in contact with GLN 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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45A GLU 2.9 18.0 + - - +
46A ARG* 3.7 7.0 - - - +
47A GLN 3.2 0.2 - - - -
48A ALA* 1.3 76.2 - - - +
50A ALA* 1.3 58.2 + - - +
52A LEU* 3.3 17.2 + - - +
53A GLU* 2.9 65.0 + - + +
80A VAL* 3.5 29.1 - - + +
83A MSE 4.5 10.1 - - - +
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Residues in contact with ALA 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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46A ARG* 3.0 14.2 + - + +
47A GLN* 3.6 11.2 - - - +
48A ALA 3.2 0.2 - - - -
49A GLN* 1.3 77.1 - - - +
51A GLN* 1.3 55.8 + - - +
53A GLU* 3.2 8.0 + - - +
54A LYS* 3.0 45.4 + - - +
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Residues in contact with GLN 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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47A GLN 3.0 14.1 + - - +
48A ALA 3.2 7.6 + - - +
50A ALA* 1.3 75.7 - - - +
52A LEU* 1.3 63.2 + - - +
54A LYS* 3.4 16.0 + - + +
55A ALA* 3.1 22.9 + - - +
58A LYS* 6.0 0.4 - - - +
97A GLU* 2.9 26.0 + - - +
98A LYS 3.5 19.4 + - - -
99A PHE* 3.5 31.9 + - + +
105A ILE* 3.9 9.4 - - + +
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Residues in contact with LEU 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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48A ALA 3.1 11.8 + - - +
49A GLN* 3.5 23.3 - - - +
51A GLN* 1.3 78.4 - - - +
53A GLU* 1.3 64.1 + - - +
55A ALA* 3.1 12.9 + - - +
56A LYS* 3.5 10.6 + - - +
80A VAL* 5.0 0.4 - - + -
83A MSE 3.7 34.5 - - + -
105A ILE* 3.8 16.5 - - + +
115A ILE* 3.6 41.2 - - + +
116A GLY* 3.8 18.2 - - - +
117A PHE* 3.8 23.6 - - + -
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Residues in contact with GLU 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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49A GLN* 2.9 48.6 + - + +
50A ALA* 3.2 6.7 + - - +
52A LEU* 1.3 74.8 - - - +
54A LYS* 1.3 64.8 + - + +
55A ALA 3.3 0.7 + - - -
56A LYS* 2.7 56.7 + - - +
57A THR* 4.8 0.3 + - - -
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Residues in contact with LYS 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 ALA* 3.0 34.0 + - + +
51A GLN* 3.7 13.6 - - + +
52A LEU 3.2 0.2 - - - -
53A GLU* 1.3 77.5 - - + +
55A ALA* 1.3 60.5 + - - +
56A LYS 3.4 0.5 + - - -
57A THR* 3.8 10.0 + - - -
58A LYS* 3.7 28.3 + - - +
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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 GLN 3.1 16.5 + - - +
52A LEU 3.1 1.7 + - - +
54A LYS* 1.3 72.4 - - - +
56A LYS* 1.3 60.9 + - - +
57A THR 2.9 5.1 + - - -
58A LYS* 3.0 18.4 + - + +
96A LYS* 2.8 28.2 + - + +
97A GLU* 4.4 16.4 - - + +
105A ILE* 3.8 15.0 - - + -
115A ILE* 3.5 20.4 - - + -
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Residues in contact with LYS 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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52A LEU* 3.5 9.1 + - - +
53A GLU* 2.7 46.5 + - - +
54A LYS 3.2 0.4 - - - -
55A ALA* 1.3 77.9 - - - +
57A THR* 1.3 60.5 + - - +
96A LYS* 3.1 13.6 + - - +
114A GLU* 4.4 16.3 + - - -
115A ILE* 3.9 29.2 - - + -
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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