Contacts of the helix formed by residues 44 - 51 (chain D) in PDB entry 3CMT
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 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D THR* 3.0 19.3 + - - -
43D GLY* 1.3 78.0 - - - +
45D LEU* 1.3 61.4 + - - +
47D LEU* 3.1 27.0 + - - -
48D ASP* 3.1 16.7 + - - -
260D PHE* 3.3 24.2 - - - -
268D ILE* 4.0 12.1 - - - -
270D PHE* 4.4 0.9 - - - -
273D GLU* 2.5 28.2 + - - -
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Residues in contact with LEU 45 (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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44D SER* 1.3 70.2 - - - +
46D SER* 1.3 60.1 - - - +
48D ASP* 3.1 7.9 + - - +
49D ILE* 3.0 35.9 + - + +
270D PHE* 3.6 20.0 - - + +
273D GLU* 3.0 15.5 + - + +
274D LEU* 3.7 40.4 - - + +
277D LEU* 4.2 18.8 - - + -
320D GLU* 3.7 26.7 - - + +
323D VAL* 4.2 9.9 - - + -
324D ARG* 3.8 27.8 - - + +
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Residues in contact with SER 46 (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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44D SER* 3.4 0.9 + - - -
45D LEU* 1.3 78.1 - - - +
47D LEU* 1.3 57.6 + - - +
49D ILE* 3.5 12.5 + - - +
50D ALA* 2.9 28.2 + - - +
257D GLN 4.7 0.9 - - - +
258D ALA* 3.4 21.0 - - - +
259D GLU 3.5 16.0 + - - -
260D PHE* 4.1 0.9 - - - -
273D GLU* 2.6 25.5 + - - +
277D LEU* 4.2 18.4 - - - -
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Residues in contact with LEU 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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42D THR* 3.5 31.6 - - + +
44D SER* 3.1 20.1 + - - +
46D SER* 1.3 75.2 + - - +
48D ASP* 1.3 56.0 + - - +
50D ALA* 3.0 3.9 + - + -
51D LEU* 2.7 50.9 + - + +
75D LEU* 4.0 26.2 - - + -
223D LEU* 4.5 15.3 - - + -
244D VAL* 4.3 22.0 - - + +
246D VAL* 4.3 13.5 - - + -
258D ALA* 3.6 13.5 - - + -
260D PHE* 4.8 0.4 - - + -
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Residues in contact with ASP 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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41D SER* 3.0 19.6 + - - -
42D THR* 2.9 32.6 + - - +
44D SER 3.1 14.9 + - - +
45D LEU* 3.1 8.7 + - + +
47D LEU* 1.3 78.9 - - - +
49D ILE* 1.3 60.7 + - + +
51D LEU* 3.6 2.8 + - - +
52D GLY 3.6 4.3 + - - -
54D GLY* 3.1 49.5 + - - +
55D GLY* 3.4 7.3 - - - +
270D PHE* 5.6 0.2 - - - -
324D ARG* 2.8 30.3 + - - +
328D LEU* 3.4 3.2 - - + +
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Residues in contact with ILE 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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45D LEU* 3.0 37.9 + - + +
46D SER* 3.6 8.7 - - - +
47D LEU 3.1 0.2 - - - -
48D ASP* 1.3 74.9 - - + +
50D ALA* 1.3 66.0 + - - +
52D GLY* 2.9 16.1 + - - -
256D LYS* 4.2 9.1 + - + +
277D LEU* 4.0 27.6 - - + -
323D VAL* 4.0 13.0 - - + +
324D ARG* 5.5 2.7 - - + -
327D LEU* 3.9 37.5 - - + +
328D LEU* 3.8 15.7 - - + +
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Residues in contact with ALA 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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46D SER 2.9 17.9 + - - +
47D LEU* 3.0 9.4 + - + +
49D ILE* 1.3 75.4 - - - +
51D LEU* 1.3 61.5 + - - +
52D GLY* 3.2 1.2 + - - -
246D VAL* 4.1 15.8 - - + +
253D ALA 4.4 5.9 - - - +
256D LYS* 3.4 38.4 - - + +
257D GLN 3.9 28.0 - - - +
258D ALA* 4.2 1.6 - - + +
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Residues in contact with LEU 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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42D THR* 3.6 31.4 - - + -
47D LEU* 2.7 31.9 + - + +
48D ASP* 3.7 7.6 - - - +
49D ILE 3.1 0.2 - - - -
50D ALA* 1.3 72.7 - - - +
52D GLY* 1.3 55.8 + - - +
53D ALA 2.9 10.0 + - - -
55D GLY* 3.6 31.4 - - - +
56D LEU* 4.0 7.2 - - + +
221D VAL* 3.6 38.8 - - + -
223D LEU* 4.3 8.5 - - + -
246D VAL* 4.4 8.1 - - + -
249D ASN* 3.2 23.0 + - - +
251D ILE* 4.1 5.8 - - + +
252D ALA* 3.3 3.6 - - - +
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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