Contacts of the helix formed by residues 46 - 61 (chain A) in PDB entry 3TR6
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 ALA 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLN 3.4 3.8 + - - -
45A THR* 1.3 75.2 - - - +
47A PRO* 1.3 72.6 - - + +
48A GLU* 3.7 23.3 - - - +
49A GLN* 3.0 8.0 + - + +
50A ALA* 2.9 21.4 + - - +
170A ASP* 5.6 0.4 + - - -
212A GLY* 4.0 22.4 - - - -
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Residues in contact with PRO 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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21A LEU* 3.7 27.8 - - + +
23A GLU* 4.0 4.0 - - - +
31A ARG* 3.5 35.2 - - - +
45A THR 3.4 5.1 - - - +
46A ALA* 1.3 83.0 - - + +
48A GLU* 1.3 66.2 + - - +
50A ALA* 3.5 2.8 + - - +
51A GLN* 3.0 27.9 + - - +
74A TYR* 3.5 25.3 + - + +
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Residues in contact with GLU 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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13A TYR* 2.8 35.9 + - + -
16A LEU* 5.4 5.6 - - + -
17A LEU* 4.1 23.5 - - + +
20A SER* 5.6 2.0 - - - +
21A LEU* 4.0 10.4 - - + +
46A ALA* 3.8 14.5 - - + +
47A PRO* 1.3 87.2 - - - +
49A GLN* 1.3 65.7 + - - +
51A GLN* 3.4 6.7 + - - +
52A LEU* 3.3 15.8 + - - +
211A ILE* 3.6 35.8 - - + +
212A GLY* 4.5 6.9 + - - +
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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 THR* 3.7 6.3 - - + +
46A ALA* 3.0 19.1 + - + +
48A GLU* 1.3 78.8 - - - +
50A ALA* 1.3 67.1 + - - +
52A LEU* 3.1 7.3 + - - +
53A LEU* 3.1 22.5 + - + +
142A TYR* 3.0 26.9 + - - -
170A ASP* 2.9 31.7 + - - +
211A ILE* 3.1 42.6 + - + -
212A GLY* 3.7 9.3 - - - -
214A GLY 3.7 7.3 + - - -
215A LEU* 3.8 22.2 - - + +
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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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45A THR* 3.8 11.3 - - + +
46A ALA 2.9 9.8 + - - +
47A PRO 3.7 1.8 - - - +
49A GLN* 1.3 77.0 - - - +
51A GLN* 1.3 57.9 + - - +
53A LEU* 3.0 13.9 + - - +
54A ALA* 2.9 27.2 + - - +
74A TYR* 3.5 35.7 - - + -
75A SER* 4.9 2.9 - - - -
78A ALA* 3.8 19.8 - - + +
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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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20A SER* 2.8 27.4 + - - +
21A LEU* 3.6 12.2 - - - +
22A ARG* 2.8 41.7 + - - +
47A PRO 3.0 16.5 + - - +
48A GLU* 3.6 9.2 - - - +
49A GLN 3.2 0.2 - - - -
50A ALA* 1.3 77.7 - - - +
52A LEU* 1.3 60.4 + - - +
54A ALA* 3.3 9.7 + - + +
55A LEU* 3.1 21.7 + - + +
78A ALA* 5.9 0.4 - - - -
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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 GLU 3.3 9.5 + - - +
49A GLN* 3.1 8.7 + - - +
51A GLN* 1.3 77.5 - - - +
53A LEU* 1.3 63.9 + - - +
55A LEU* 3.2 16.5 + - + +
56A LEU* 3.0 42.1 + - + +
209A ILE* 4.3 18.4 - - + -
211A ILE* 3.8 25.1 - - + -
215A LEU* 3.5 29.6 - - + -
217A LEU* 5.2 3.1 - - + -
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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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45A THR* 5.0 0.9 - - + -
49A GLN* 3.1 15.3 + - + +
50A ALA* 3.0 19.4 + - - +
52A LEU* 1.3 77.6 - - - +
54A ALA* 1.3 61.2 + - - +
56A LEU* 3.1 14.5 + - + +
57A VAL* 3.1 25.1 + - - +
75A SER* 4.4 5.6 - - - -
78A ALA* 5.8 0.2 - - + -
79A MSE 3.8 27.6 - - + -
140A LEU* 4.5 4.9 - - + +
142A TYR* 3.8 43.1 - - + +
168A ALA* 3.9 27.4 - - + -
215A LEU* 4.2 15.0 - - + -
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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 ALA 2.9 11.6 + - - +
51A GLN* 3.5 12.6 - - + +
52A LEU 3.3 0.2 - - - -
53A LEU* 1.3 75.1 - - - +
55A LEU* 1.3 63.2 + - - +
57A VAL* 3.4 3.7 + - - -
58A LYS* 3.2 22.7 + - + +
78A ALA* 3.7 23.6 - - + +
79A MSE 4.5 2.2 - - - +
82A ALA* 3.3 24.8 - - + +
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Residues in contact with LEU 55 (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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51A GLN* 3.1 13.4 + - + +
52A LEU* 3.5 21.1 - - + +
53A LEU 3.2 0.2 - - - -
54A ALA* 1.3 76.1 - - - +
56A LEU* 1.3 58.0 + - + +
58A LYS* 3.3 16.3 + - + +
59A LEU* 3.0 48.0 + - + +
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Residues in contact with LEU 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* 3.0 35.0 + - + +
53A LEU* 3.1 20.2 + - + +
55A LEU* 1.3 76.5 - - + +
57A VAL* 1.3 65.3 + - - +
59A LEU* 3.3 17.6 + - + +
60A MSE 3.0 35.3 + - + +
140A LEU* 4.6 7.9 - - + -
166A LEU* 3.7 31.6 - - + -
217A LEU* 4.1 28.7 - - + -
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Residues in contact with VAL 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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53A LEU 3.1 17.6 + - - +
54A ALA 3.6 7.9 - - - +
55A LEU 3.4 0.2 - - - -
56A LEU* 1.3 74.4 - - - +
58A LYS* 1.3 57.9 + - - +
61A GLN* 2.9 22.9 + - - -
62A ALA* 2.9 30.1 + - + +
65A VAL* 4.5 8.5 - - + -
79A MSE 3.9 25.6 - - + +
82A ALA* 3.6 29.8 - - + +
83A LEU* 3.8 13.0 - - + +
84A PRO* 4.4 1.0 - - + +
140A LEU* 3.6 22.0 - - + +
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Residues in contact with LYS 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* 3.2 16.7 + - - +
55A LEU* 3.6 17.7 - - + +
56A LEU 3.2 0.4 - - - -
57A VAL* 1.3 75.4 - - - +
59A LEU* 1.3 65.2 + - + +
61A GLN* 3.2 33.1 + - - +
81A LEU 4.5 4.0 + - - -
82A ALA* 3.8 35.6 - - + +
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Residues in contact with LEU 59 (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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55A LEU* 3.0 41.9 + - + +
56A LEU* 3.3 18.6 + - + +
58A LYS* 1.3 78.1 - - + +
60A MSE 1.3 64.2 + - + +
61A GLN* 4.9 2.1 - - - +
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Residues in contact with MSE 60 (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 LEU* 3.0 20.6 + - + +
59A LEU* 1.3 79.0 - - + +
61A GLN* 1.3 70.7 + - - +
62A ALA* 4.1 10.8 - - + +
139A ASP* 3.4 26.8 - - + +
140A LEU* 4.7 10.8 - - - -
162A ARG* 3.7 26.7 + - - +
164A GLY 3.4 24.2 - - - +
166A LEU* 3.8 33.9 - - + -
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Residues in contact with GLN 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 VAL 2.9 8.9 + - - -
58A LYS* 3.2 29.5 + - - +
59A LEU 3.2 2.3 - - - +
60A MSE 1.3 82.6 - - - +
62A ALA* 1.3 65.2 + - - +
63A LYS* 3.4 26.7 + - - +
82A ALA 5.4 1.2 + - - -
84A PRO* 4.3 27.5 - - + +
139A ASP* 4.7 1.2 - - - +
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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