Contacts of the helix formed by residues 46 - 57 (chain D) in PDB entry 3T79
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 SER 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D LEU 3.9 5.2 - - - -
44D PHE 3.6 3.4 + - - -
45D LEU* 1.3 74.5 - - - +
47D GLN* 1.3 70.8 + - - +
48D LYS* 2.9 22.0 + - - +
49D TYR* 3.0 38.3 + - - -
50D ILE* 3.2 16.8 + - - +
88D LEU* 5.1 1.8 - - - -
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D SER* 1.3 72.8 + - - +
48D LYS* 1.3 65.5 + - + +
50D ILE* 4.7 7.2 - - - -
51D VAL* 2.9 34.5 + - + +
87D VAL* 3.7 27.9 - - - +
88D LEU* 4.1 21.1 - - + +
91D ARG* 3.9 37.4 - - + +
92D LEU* 5.9 1.3 - - - -
280D ASP 5.4 1.6 - - - +
281D PHE* 4.8 14.7 - - - -
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Residues in contact with LYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D SER* 2.9 20.4 + - - +
47D GLN* 1.3 75.6 - - + +
49D TYR* 1.3 90.8 + - + +
51D VAL* 3.8 3.5 - - - +
52D LYS* 2.9 30.6 + - - +
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 3.5 17.5 - - + +
29D TRP* 3.4 13.6 - + + -
30D LEU* 6.3 0.2 - - + -
33D MET* 5.6 15.5 - - + -
35D ASP 5.4 11.7 - - - -
43D LEU 4.3 8.5 - - - -
44D PHE* 3.9 27.1 - + + +
46D SER* 3.0 30.9 + - - +
48D LYS* 1.3 104.0 + - + +
50D ILE* 1.3 61.1 + - - +
52D LYS* 4.4 6.3 - - + -
53D TYR* 2.9 31.2 + - - +
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 3.5 25.1 - - + +
45D LEU* 4.5 8.5 - - + -
46D SER 3.2 21.9 + - - +
47D GLN* 4.0 3.6 - - - +
49D TYR* 1.3 77.4 - - - +
51D VAL* 1.3 57.2 + - - +
53D TYR* 3.3 3.1 + - + +
54D ILE* 2.9 51.6 + - + +
67D THR* 5.4 0.9 - - + -
71D MET* 3.9 39.9 - - + -
88D LEU* 3.9 29.4 - - + -
92D LEU* 4.2 14.8 - - + -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN* 2.9 33.5 + - + +
48D LYS* 3.8 3.1 - - - +
50D ILE* 1.3 73.3 - - - +
52D LYS* 1.3 66.2 + - - +
54D ILE* 3.4 1.5 + - - +
55D ALA* 3.0 24.9 + - - +
91D ARG* 3.4 49.8 - - + +
92D LEU* 4.5 12.1 - - + -
95D LEU* 4.1 13.0 - - + +
303D PRO* 4.4 8.5 - - + -
305D PHE* 4.0 21.5 - - + -
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TRP* 3.6 16.5 - - + -
33D MET* 4.0 26.2 - - + -
48D LYS 2.9 19.4 + - - +
49D TYR* 3.7 8.7 - - + +
51D VAL* 1.3 75.8 - - - +
53D TYR* 1.3 54.0 + - - +
55D ALA* 4.2 1.9 - - - +
56D SER* 2.7 49.6 + - - -
297D GLU* 3.1 31.6 + - - +
305D PHE* 6.0 1.8 - - - -
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Residues in contact with TYR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 4.7 5.6 + - + +
25D LYS* 3.3 27.6 - - + +
26D TYR* 3.5 37.2 - + + +
29D TRP* 3.4 40.5 - + + -
49D TYR 2.9 19.3 + - - +
50D ILE* 3.4 4.7 - - + +
52D LYS* 1.3 76.0 - - - +
54D ILE* 1.3 74.9 + - + +
56D SER* 3.1 6.3 + - - -
57D HIS* 2.9 47.3 + + - +
60D ILE* 3.9 31.3 - - + +
67D THR* 4.4 15.3 - - + -
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Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 2.9 41.3 + - + +
51D VAL 3.9 2.9 - - - +
53D TYR* 1.3 81.4 - - + +
55D ALA* 1.3 63.1 + - - +
57D HIS 3.2 18.7 - - - +
60D ILE* 3.9 11.3 - - + +
61D ALA* 3.5 8.3 + - - +
64D PRO* 4.0 22.7 - - + +
67D THR* 4.0 24.9 - - + -
68D CYS* 3.8 29.2 - - - +
92D LEU* 4.6 5.6 - - + -
95D LEU* 4.0 18.8 - - + -
99D LEU* 4.3 8.1 - - + -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL 3.0 13.0 + - - +
52D LYS 4.2 2.0 - - - +
54D ILE* 1.3 80.0 - - - +
56D SER* 1.3 61.1 + - - +
57D HIS 3.1 5.4 + - - +
58D ASP* 4.8 0.5 + - - -
61D ALA* 4.3 10.4 - - - +
95D LEU* 5.1 2.0 - - + -
99D LEU* 5.1 6.1 - - + -
305D PHE* 3.3 49.1 - - + -
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TRP* 4.0 5.7 + - - -
52D LYS* 2.7 37.3 + - - -
53D TYR* 3.1 3.5 + - - -
55D ALA* 1.3 76.0 - - - +
57D HIS* 1.3 87.3 + - - +
58D ASP 4.1 1.9 + - - -
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Residues in contact with HIS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TRP* 3.4 35.0 - + - +
53D TYR* 2.9 33.7 + + - +
54D ILE 3.2 1.2 - - - +
55D ALA 3.1 1.1 - - - -
56D SER* 1.3 110.0 + - - +
58D ASP* 1.3 51.5 + - - +
59D ASP* 2.9 22.2 - - - +
60D ILE* 3.4 18.8 - - + -
61D ALA* 2.7 37.1 + - - +
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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