Contacts of the helix formed by residues 47 - 56 (chain H) in PDB entry 3L3T
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 THR 47 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TRP* 3.2 14.4 - - - +
45H PHE* 4.1 0.7 - - - +
46H ASP* 1.3 92.9 + - + +
48H GLU* 1.3 58.3 + - - +
49H GLU* 2.4 45.4 + - - +
50H TYR* 3.3 9.7 - - - +
51H CYS* 3.3 15.8 + - - +
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Residues in contact with GLU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TRP* 3.4 53.6 - - + +
29H LYS* 5.5 5.5 + - - +
30H CYS* 4.2 14.9 + - + +
47H THR* 1.3 70.1 - - - +
49H GLU* 1.3 63.0 + - - +
51H CYS* 3.6 3.0 - - - +
52H MET* 3.1 33.8 + - + +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H THR* 2.4 45.7 + - - +
48H GLU* 1.3 72.7 - - - +
50H TYR* 1.3 64.1 + - - +
51H CYS 2.5 11.0 + - - -
52H MET* 4.0 13.1 - - - +
53H ALA* 3.1 25.1 + - - +
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Residues in contact with TYR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H PHE* 3.6 28.0 - + + -
46H ASP* 3.2 23.6 - - - +
47H THR* 3.3 10.3 - - - +
49H GLU* 1.3 83.4 + - - +
51H CYS* 1.3 53.3 + - - +
52H MET 3.2 0.7 - - - -
53H ALA* 3.3 12.9 - - + +
54H VAL* 2.7 61.6 + - + +
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Residues in contact with CYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TRP* 4.1 2.2 - - + -
22H TYR* 3.6 20.0 - - - -
23H PHE* 3.6 4.7 - - - -
30H CYS* 2.0 44.6 - - + -
45H PHE* 3.6 37.3 - - + +
47H THR 3.3 17.9 + - - +
48H GLU 3.6 2.0 - - - +
49H GLU 2.5 9.7 + - - -
50H TYR* 1.3 73.1 - - - +
52H MET* 1.3 55.5 + - - +
54H VAL 3.3 0.2 + - - -
55H CYS* 2.8 36.0 + - - +
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Residues in contact with MET 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 3.1 43.1 - - + -
28H GLY 4.5 3.1 - - - +
29H LYS* 4.1 9.2 - - - -
30H CYS* 3.2 25.8 - - + +
48H GLU* 3.1 27.3 + - + +
49H GLU* 3.7 15.9 - - - +
50H TYR 3.2 0.2 - - - -
51H CYS* 1.3 73.2 - - - +
53H ALA* 1.3 61.5 + - - +
56H GLY* 2.9 41.3 + - - +
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H GLU* 3.1 19.3 + - - +
50H TYR* 2.9 22.3 + - + +
52H MET* 1.3 79.5 - - - +
54H VAL* 1.3 61.3 + - + +
57H SER* 4.2 8.7 + - - -
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Residues in contact with VAL 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 5.6 6.1 - - + -
5H CYS* 4.0 6.6 - - - -
45H PHE* 4.0 28.3 - - + -
50H TYR* 2.7 57.7 + - + +
51H CYS 4.0 0.9 - - - +
53H ALA* 1.3 77.0 - - + +
55H CYS* 1.3 61.2 + - - +
56H GLY 3.7 0.2 - - - -
57H SER* 3.5 13.2 + - - -
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Residues in contact with CYS 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H CYS* 2.0 48.3 - - - +
23H PHE* 3.5 41.7 - - + -
45H PHE* 3.6 35.0 - - - -
51H CYS 2.8 11.8 + - - +
54H VAL* 1.3 76.8 - - - +
56H GLY* 1.3 59.0 + - - +
57H SER* 3.0 11.3 + - - -
58H ALA 4.8 0.5 + - - -
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Residues in contact with GLY 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 4.2 4.7 - - - -
28H GLY 5.6 0.4 - - - -
52H MET* 2.9 41.6 + - - +
55H CYS* 1.3 77.3 - - - +
57H SER* 1.3 50.9 + - - +
58H ALA* 2.4 36.1 + - - +
59H ILE 4.1 2.4 - - - +
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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