Contacts of the helix formed by residues 44 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 3.0 19.1 + - - -
43A GLY* 1.3 77.9 - - - +
45A LEU* 1.3 62.2 + - - +
47A LEU* 3.1 27.2 + - - -
48A ASP* 3.1 16.3 + - - -
260A PHE* 3.3 24.0 - - - -
268A ILE* 4.0 13.2 - - - -
270A PHE* 4.8 0.4 - - - -
273A GLU* 2.8 23.8 + - - -
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Residues in contact with LEU 45 (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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44A SER* 1.3 69.9 + - - +
46A SER* 1.3 61.1 - - - +
48A ASP* 3.1 8.4 + - - +
49A ILE* 3.0 35.2 + - + +
270A PHE* 3.7 19.7 - - + -
273A GLU* 3.4 14.4 + - + +
274A LEU* 4.1 27.1 - - + +
277A LEU* 4.4 15.3 - - + -
320A GLU* 4.0 11.9 - - + +
323A VAL* 4.1 22.7 - - + -
324A ARG* 3.4 47.6 - - + +
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Residues in contact with SER 46 (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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44A SER* 3.4 1.4 + - - -
45A LEU* 1.3 79.7 - - - +
47A LEU* 1.3 57.8 + - - +
49A ILE* 3.5 13.2 + - - +
50A ALA* 2.9 27.7 + - - +
257A GLN 4.7 0.9 - - - +
258A ALA* 3.4 21.0 - - - +
259A GLU 3.5 15.5 + - - -
260A PHE* 4.1 0.9 - - - -
273A GLU* 2.9 21.1 + - - -
277A LEU* 4.4 18.6 - - - -
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Residues in contact with LEU 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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42A THR* 3.5 31.4 - - + +
44A SER* 3.1 20.2 + - - +
46A SER* 1.3 75.2 + - - +
48A ASP* 1.3 54.9 + - - +
49A ILE 3.1 1.6 - - - -
50A ALA* 3.0 4.4 + - + -
51A LEU* 2.7 51.5 + - + +
75A LEU* 4.0 25.4 - - + -
223A LEU* 4.5 16.2 - - + -
244A VAL* 4.3 23.3 - - + +
246A VAL* 4.3 13.7 - - + -
258A ALA* 3.6 12.3 - - + -
260A PHE* 4.8 0.2 - - + -
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Residues in contact with ASP 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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41A SER* 3.0 24.4 + - - -
42A THR* 2.9 32.6 + - - +
44A SER 3.1 16.5 + - - +
45A LEU* 3.1 9.5 + - + +
47A LEU* 1.3 75.7 - - - +
49A ILE* 1.3 62.6 + - - +
51A LEU* 3.6 2.6 + - - +
52A GLY 3.6 4.5 + - - -
54A GLY* 3.1 49.0 + - - +
55A GLY* 3.4 8.1 - - - +
270A PHE* 6.2 0.2 - - - -
324A ARG* 3.1 25.1 + - - +
328A LEU* 3.8 1.4 - - + +
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Residues in contact with ILE 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 LEU* 3.0 42.8 + - + +
46A SER* 3.6 11.2 - - - +
47A LEU 3.1 0.2 - - - -
48A ASP* 1.3 76.0 - - - +
50A ALA* 1.3 60.7 + - - +
52A GLY* 2.9 21.3 + - - -
256A LYS* 4.2 9.1 + - + +
277A LEU* 4.5 13.0 - - + -
323A VAL* 4.4 18.4 - - + -
324A ARG* 5.6 1.8 - - + -
327A LEU* 3.7 35.9 - - + +
328A LEU* 3.7 19.8 - - + +
329A SER* 5.2 0.7 + - - -
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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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46A SER 2.9 18.9 + - - +
47A LEU* 3.0 8.9 + - + +
49A ILE* 1.3 76.0 - - - +
51A LEU* 1.3 61.2 + - - +
52A GLY 3.1 1.4 + - - -
244A VAL 5.5 0.2 - - - +
246A VAL* 4.1 15.5 - - + +
253A ALA 4.3 6.1 - - - +
256A LYS* 3.4 38.5 - - + +
257A GLN 3.9 28.5 - - - +
258A ALA* 4.2 1.3 - - + -
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Residues in contact with LEU 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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42A THR* 3.5 32.1 - - + -
47A LEU* 2.7 31.4 + - + +
48A ASP* 3.7 8.3 - - - +
49A ILE 3.1 0.4 - - - -
50A ALA* 1.3 71.7 - - - +
52A GLY* 1.3 55.0 + - - +
53A ALA 2.9 10.0 + - - -
55A GLY* 3.7 30.1 - - - +
56A LEU* 4.0 7.2 - - + +
221A VAL* 3.6 38.6 - - + -
223A LEU* 4.3 9.0 - - + -
246A VAL* 4.4 8.5 - - + -
249A ASN* 3.2 23.7 + - - +
251A ILE* 4.1 6.4 - - + +
252A 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