Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 1T84
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 ASP 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ALA* 2.7 24.5 - - - +
39A GLN 4.3 0.2 - - - +
40A LEU 3.2 4.0 + - - -
41A THR* 1.3 83.5 + - - +
43A ALA* 1.3 55.8 + - - +
44A GLU* 3.0 9.1 + - + +
45A THR* 3.4 24.7 - - - +
46A SER* 2.5 38.6 + - - -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLN 5.3 5.6 - - - +
15A ASN 5.0 10.3 + - - +
41A THR 4.3 0.2 - - - -
42A ASP* 1.3 71.1 + - - +
44A GLU* 1.3 60.1 + - - +
46A SER* 3.0 19.9 + - - -
47A LYS* 3.9 9.4 + - - +
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Residues in contact with GLU 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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42A ASP* 3.0 7.3 - - + +
43A ALA* 1.3 81.4 - - + +
45A THR* 1.3 63.8 + - - +
47A LYS* 4.0 7.8 + - - +
48A LEU* 3.6 17.7 + - - +
92A ARG* 5.3 2.6 + - - -
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Residues in contact with THR 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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39A GLN* 3.2 32.5 - - + +
42A ASP* 3.0 18.0 + - - +
44A GLU* 1.3 75.2 - - - +
46A SER* 1.3 66.6 + - - +
47A LYS 3.0 2.7 - - - -
48A LEU* 2.9 12.3 + - + -
49A ILE* 2.8 54.8 + - + +
89A MET* 4.4 5.2 - - + -
92A ARG* 5.2 10.4 - - + +
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Residues in contact with SER 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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11A TRP* 3.7 5.0 + - - -
16A GLY* 3.8 29.1 - - - -
17A PHE* 3.5 30.1 - - - -
39A GLN 3.9 1.9 + - - -
40A LEU 4.4 3.1 - - - -
42A ASP 2.5 21.5 + - - -
43A ALA* 3.0 20.5 + - - -
45A THR* 1.3 72.9 - - - +
47A LYS* 1.3 59.5 + - - +
50A TYR* 3.3 22.9 + - - +
108A WSK 3.7 2.4 - - - +
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Residues in contact with LYS 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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11A TRP* 3.7 29.2 - - + -
13A PRO* 6.1 1.1 - - + -
43A ALA 3.9 12.7 + - - +
44A GLU 4.3 6.3 + - - +
45A THR 3.0 0.2 - - - -
46A SER* 1.3 79.5 + - - +
48A LEU* 1.3 73.3 + - - +
49A ILE 3.1 1.8 - - - -
50A TYR* 3.0 41.7 + - + -
51A ASP* 3.7 1.0 + - - +
92A ARG* 6.0 2.0 - - - +
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Residues in contact with LEU 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 GLU 3.6 13.2 + - - +
45A THR* 2.9 13.3 + - + +
47A LYS* 1.3 85.4 - - - +
49A ILE* 1.3 72.5 + - + +
51A ASP* 3.8 14.7 - - + +
88A VAL* 4.0 25.5 - - + +
89A MET* 4.6 5.2 - - - -
91A LYS* 5.7 4.7 - - + -
92A ARG* 3.5 54.1 - - + +
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Residues in contact with ILE 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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17A PHE* 4.1 18.2 - - + -
30A PHE* 3.8 26.2 - - + -
35A ILE* 4.4 0.9 - - + -
39A GLN* 3.3 29.6 - - + +
40A LEU* 4.4 4.7 - - + -
45A THR* 2.8 36.9 + - + +
48A LEU* 1.3 77.2 - - + +
50A TYR* 1.3 53.0 + - - +
51A ASP 2.9 5.8 - - - -
52A PHE* 2.7 32.0 + - + +
53A ILE* 3.9 2.5 + - + +
85A LEU* 4.1 19.5 - - + -
88A VAL* 4.9 3.8 - - + -
89A MET* 3.8 22.2 - - + -
108A WSK 4.6 0.7 - - - -
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Residues in contact with TYR 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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3A PHE* 4.7 11.7 - + - +
9A VAL* 5.6 0.2 - - + -
11A TRP* 3.1 49.6 - + + -
46A SER 3.3 11.9 + - - +
47A LYS* 3.0 31.3 + - + +
49A ILE* 1.3 77.3 - - - +
51A ASP* 1.3 54.9 + - + +
52A PHE 2.9 0.7 - - - -
54A GLU* 2.7 79.9 + - + +
108A WSK 3.0 45.2 - + + -
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Residues in contact with ASP 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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3A PHE* 4.7 11.9 - - - -
47A LYS 3.7 1.3 + - - +
48A LEU* 3.8 15.7 - - + +
49A ILE 2.9 0.4 + - - -
50A TYR* 1.3 89.6 - - + +
52A PHE* 1.3 56.4 + - - +
54A GLU* 4.2 10.4 - - - +
55A ASP* 2.9 34.2 + - - +
88A VAL* 4.9 9.6 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 6.1 0.9 - - + -
29A LEU* 4.0 24.0 - - + -
30A PHE* 5.3 2.5 - + - -
49A ILE* 2.7 14.0 + - + +
51A ASP* 1.3 76.5 - - - +
53A ILE* 1.3 64.6 + - + +
54A GLU 3.0 3.4 - - - -
55A ASP* 4.1 1.1 - - - +
56A GLN* 2.7 73.9 + - + +
81A LEU* 3.1 28.0 - - + -
84A ALA* 3.8 5.4 - - + -
85A LEU* 3.5 62.1 - - + -
88A VAL* 4.4 16.1 - - + +
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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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17A PHE* 3.4 34.8 - - + -
22A LEU* 6.0 0.2 - - + -
26A LEU* 3.9 20.6 - - + -
29A LEU* 6.2 0.7 - - + -
30A PHE* 3.8 14.1 - - + -
49A ILE 4.5 3.6 - - - +
50A TYR 3.4 0.8 + - - -
52A PHE* 1.3 82.9 - - + +
54A GLU* 1.3 56.1 + - - +
56A GLN* 4.2 4.7 - - - -
58A GLY 3.3 17.8 + - - -
59A LEU* 3.3 44.9 - - + +
62A VAL* 5.0 2.7 - - + -
108A WSK 3.1 47.6 - - + -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.3 51.6 - - - +
50A TYR* 2.7 54.3 + - + +
51A ASP* 4.2 5.6 - - - +
53A ILE* 1.3 76.9 - - - +
55A ASP* 1.3 65.8 + - - +
57A GLY* 3.5 8.0 + - - -
108A WSK 2.9 58.3 + - + +
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Residues in contact with ASP 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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3A PHE* 4.2 16.8 - - + -
51A ASP* 2.9 29.1 + - - +
52A PHE* 4.1 0.9 - - - +
54A GLU* 1.3 80.5 - - - +
56A GLN* 1.3 70.7 + - - +
57A GLY* 2.9 8.3 + - - -
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Residues in contact with GLN 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 PHE* 2.7 66.9 + - + +
53A ILE* 4.4 3.8 - - - +
54A GLU 3.4 0.2 - - - -
55A ASP* 1.3 78.2 + - - +
57A GLY* 1.3 57.8 + - - +
58A GLY 3.5 0.4 - - - -
61A ALA* 5.8 0.7 - - - +
62A VAL* 3.8 24.5 - - + +
65A GLU* 4.4 9.7 - - - +
81A LEU* 3.0 27.2 - - + +
84A ALA* 4.6 8.7 - - - +
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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