Contacts of the helix formed by residues 57 - 68 (chain A) in PDB entry 1TF6
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 LEU 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 3.1 35.0 - - + -
56A SER* 1.3 72.1 + - - +
58A HIS* 1.3 60.1 + - + +
60A LEU* 4.2 7.7 - - - +
61A THR* 3.0 19.4 + - - +
36C T 5.6 0.2 - - + -
37C C 3.5 39.9 - - + +
38C T 5.7 0.4 - - + -
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Residues in contact with HIS 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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56A SER* 2.8 9.5 + - - +
57A LEU* 1.3 80.9 - - + +
59A HIS* 1.3 74.7 + + - +
60A LEU 3.0 5.4 - - - -
61A THR* 2.8 18.5 + - - -
62A ARG* 3.2 33.8 + - + +
26B G 4.0 4.4 + - - -
38C T 3.8 23.1 - + + -
39C C 2.9 40.0 + + - -
40C C 4.4 5.5 + - - -
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 3.0 48.4 - + + -
55A THR* 4.8 10.5 + - - -
56A SER* 2.9 23.3 + - - +
58A HIS* 1.3 93.0 - + - +
60A LEU* 1.3 58.7 + - - +
62A ARG* 4.0 25.8 - - - +
63A HIS* 3.8 5.0 + - - +
23B T 6.1 0.2 - - + -
24B G 3.9 16.1 + + + -
25B G 2.9 49.7 + + - -
26B G 4.0 10.3 + - - -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.7 37.9 - - + +
44A PRO 3.0 37.9 - - - +
45A CYS* 3.7 13.7 - - + +
46A LYS* 4.1 18.8 - - + +
54A PHE* 4.1 11.2 - - + -
56A SER 3.5 1.6 + - - +
57A LEU* 4.2 10.1 - - - +
58A HIS 3.0 0.2 - - - -
59A HIS* 1.3 79.9 - - - +
61A THR* 1.3 66.9 + - - +
63A HIS* 2.9 17.6 + - + +
64A SER* 2.9 14.2 + - - +
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Residues in contact with THR 61 (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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57A LEU 3.0 17.1 + - - +
58A HIS* 2.8 21.7 + - - -
60A LEU* 1.3 76.6 - - - +
62A ARG* 1.3 54.1 + - - -
64A SER* 2.5 41.3 + - - +
65A LEU* 3.5 8.5 + - - +
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Residues in contact with ARG 62 (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 PHE* 5.4 4.0 - - + -
58A HIS* 3.2 27.4 + - + +
59A HIS* 4.0 34.5 - - - +
61A THR* 1.3 78.2 - - - +
63A HIS* 1.3 61.2 + - + +
65A LEU* 3.3 32.5 - - + +
66A THR* 3.3 9.2 - - - +
86A THR* 4.8 17.0 - - + +
22B A 5.8 1.6 - - + +
23B T 3.2 48.3 + - + +
24B G 2.9 43.8 + - - -
40C C 3.4 20.4 - - - +
41C C 3.8 4.8 - - - +
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Residues in contact with HIS 63 (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 CYS* 3.4 18.8 - - + +
50A CYS* 3.3 13.0 - - - -
52A LYS* 3.8 11.2 - - + -
54A PHE* 3.6 29.4 - + + -
59A HIS 3.8 0.9 - - - +
60A LEU* 2.9 16.3 + - + +
61A THR 2.8 0.8 - - - -
62A ARG* 1.3 79.5 - - + +
64A SER* 1.3 65.9 + - - +
66A THR* 2.8 34.7 + - - -
67A HIS* 3.0 10.7 + + - -
202A ZN 2.1 36.2 - - - -
23B T 3.4 24.7 + - - +
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Residues in contact with SER 64 (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 CYS* 5.6 2.5 - - - -
60A LEU* 2.9 14.7 + - - +
61A THR* 2.5 37.5 + - - +
63A HIS* 1.3 70.3 - - - +
65A LEU* 1.3 54.2 + - - -
66A THR 2.5 17.9 + - - -
67A HIS* 2.6 21.4 + - - +
68A THR* 3.4 10.2 - - - +
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Residues in contact with LEU 65 (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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61A THR 3.5 3.8 + - - +
62A ARG* 3.3 35.7 - - + +
64A SER* 1.3 74.1 - - - +
66A THR* 1.3 61.9 + - + +
68A THR* 3.8 1.8 - - - -
69A GLY* 2.9 21.5 + - - -
70A GLU* 2.9 46.7 + - + +
72A ASN* 5.6 10.3 - - - +
85A THR* 3.6 39.7 - - - +
86A THR* 6.3 0.9 - - + -
22B A 5.1 0.7 - - - +
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG 3.3 19.5 - - - +
63A HIS* 2.8 33.9 + - - +
64A SER 2.5 8.9 + - - -
65A LEU* 1.3 74.1 - - + +
67A HIS* 1.3 53.7 + - - -
68A THR 2.7 16.4 + - - -
69A GLY* 3.5 9.3 + - - +
22B A 3.6 39.7 + - + +
23B T 4.1 11.9 + - - +
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Residues in contact with HIS 67 (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 CYS* 3.2 12.0 - - - -
47A GLU* 3.8 30.6 + - + +
48A GLU 4.6 4.7 - - - -
49A GLY 5.7 0.2 - - - -
50A CYS* 3.0 19.1 - - + +
63A HIS* 3.0 16.0 + + - -
64A SER* 2.6 17.1 + - - +
66A THR* 1.3 74.1 + - - +
68A THR* 1.3 59.1 + - + +
202A ZN 2.1 38.3 - - - -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 3.4 19.7 - - - +
65A LEU* 3.8 0.7 - - - -
66A THR 2.7 3.2 + - - -
67A HIS* 1.3 84.5 - - + +
69A GLY* 1.3 58.8 + - - -
70A GLU* 2.6 50.4 + - + +
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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