Contacts of the helix formed by residues 2044 - 2051 (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 SER2044 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2042D THR* 3.0 19.5 + - - -
2043D GLY* 1.3 77.7 - - - +
2045D LEU* 1.3 61.9 + - - +
2047D LEU* 3.1 26.1 + - - -
2048D ASP* 3.1 15.8 + - - -
2260D PHE* 3.3 23.7 - - - -
2268D ILE* 4.0 12.5 - - - +
2270D PHE* 4.3 1.1 - - - -
2273D GLU* 2.4 31.9 + - - -
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Residues in contact with LEU2045 (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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2044D SER* 1.3 69.8 - - - +
2046D SER* 1.3 61.6 + - - +
2048D ASP* 3.1 7.9 + - - +
2049D ILE* 3.0 35.3 + - + +
2270D PHE* 3.6 20.6 - - + +
2273D GLU* 2.9 15.3 + - + +
2274D LEU* 3.6 40.6 - - + +
2277D LEU* 4.2 19.3 - - + -
2320D GLU* 3.7 27.8 - - + +
2323D VAL* 4.2 9.9 - - + -
2324D ARG* 3.9 26.2 - - + +
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Residues in contact with SER2046 (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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2044D SER* 3.4 0.9 + - - -
2045D LEU* 1.3 78.3 - - - +
2047D LEU* 1.3 57.5 + - - +
2049D ILE* 3.4 12.7 + - - +
2050D ALA* 2.8 27.0 + - - +
2257D GLN 4.7 1.1 - - - +
2258D ALA* 3.4 20.7 - - - +
2259D GLU 3.5 16.2 + - - -
2260D PHE* 4.1 0.7 - - - -
2273D GLU* 2.6 24.4 + - - +
2277D LEU* 4.1 19.5 - - - -
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Residues in contact with LEU2047 (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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2042D THR* 3.5 30.5 - - + +
2044D SER* 3.1 20.2 + - - +
2046D SER* 1.3 74.4 + - - +
2048D ASP* 1.3 56.9 + - - +
2049D ILE 3.1 1.3 - - - -
2050D ALA* 3.0 3.6 + - + -
2051D LEU* 2.7 51.0 + - + +
2075D LEU* 4.0 25.8 - - + -
2223D LEU* 4.5 15.3 - - + -
2244D VAL* 4.3 22.7 - - + +
2246D VAL* 4.3 13.9 - - + -
2258D ALA* 3.5 12.5 - - + +
2260D PHE* 4.8 0.7 - - + -
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Residues in contact with ASP2048 (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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2041D SER* 3.0 20.4 + - - -
2042D THR* 2.9 32.3 + - - +
2044D SER 3.1 17.5 + - - +
2045D LEU* 3.1 8.1 + - + +
2047D LEU* 1.3 75.7 - - - +
2049D ILE* 1.3 61.0 + - + +
2051D LEU* 3.6 2.8 + - - +
2052D GLY 3.6 4.0 + - - -
2054D GLY* 3.1 46.7 + - - +
2055D GLY* 3.4 8.3 - - - +
2270D PHE* 5.4 0.5 - - - -
2324D ARG* 2.8 30.3 + - - +
2328D LEU* 3.5 2.7 - - - +
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Residues in contact with ILE2049 (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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2045D LEU* 3.0 40.8 + - + +
2046D SER* 3.6 8.5 - - - +
2047D LEU 3.1 0.2 - - - -
2048D ASP* 1.3 75.4 - - + +
2050D ALA* 1.3 66.0 + - - +
2052D GLY* 2.9 16.6 + - - -
2256D LYS* 4.2 8.9 + - + +
2277D LEU* 4.0 26.2 - - + -
2323D VAL* 4.0 14.1 - - + -
2324D ARG* 5.4 4.0 - - + -
2327D LEU* 3.8 38.2 - - + +
2328D LEU* 3.7 15.7 - - + +
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Residues in contact with ALA2050 (chain D).
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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2046D SER 2.8 20.9 + - - +
2047D LEU* 3.0 9.2 + - + +
2049D ILE* 1.3 73.0 - - - +
2051D LEU* 1.3 61.8 + - - +
2052D GLY* 3.1 1.4 + - - -
2246D VAL* 4.1 18.0 - - + +
2253D ALA 4.4 6.2 - - - +
2256D LYS* 3.4 35.9 - - + +
2257D GLN 3.9 27.8 - - - +
2258D ALA* 4.2 1.6 - - + +
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Residues in contact with LEU2051 (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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2042D THR* 3.6 31.4 - - + -
2047D LEU* 2.7 32.9 + - + +
2048D ASP* 3.8 7.6 - - - +
2049D ILE 3.1 0.4 - - - -
2050D ALA* 1.3 71.0 - - - +
2052D GLY* 1.3 55.8 + - - +
2053D ALA 2.9 9.4 + - - -
2055D GLY* 3.6 30.1 - - - +
2056D LEU* 4.0 8.1 - - + +
2221D VAL* 3.6 38.8 - - + -
2223D LEU* 4.3 8.1 - - + -
2246D VAL* 4.4 8.3 - - + -
2249D ASN* 3.2 23.1 + - - +
2251D ILE* 4.1 6.2 - - + +
2252D ALA* 3.3 3.5 - - - +
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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