Contacts of the helix formed by residues 39 - 49 (chain B) in PDB entry 2C95
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 4.1 0.4 + - - -
38B SER* 1.3 72.1 - - - +
40B GLY* 1.3 61.6 + - - +
42B LEU* 3.3 9.4 + - + +
43B LEU* 3.0 29.7 + - - +
72B VAL* 3.7 27.1 - - + +
76B LEU* 4.1 27.1 - - + -
92B ILE* 5.1 0.9 - - + -
93B ASP 3.2 10.3 + - - +
94B GLY* 3.2 13.2 + - - -
95B TYR* 4.0 21.8 - - + -
1196B B4P 2.8 25.2 + - - -
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.3 3.6 + - - -
39B THR* 1.3 80.4 + - - +
41B ASP* 1.3 56.2 + - - +
43B LEU* 3.4 4.3 + - - +
44B ARG* 2.9 41.6 + - - +
93B ASP 4.8 0.6 + - - -
1196B B4P 3.2 42.3 + - - -
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 5.4 5.2 - - - -
38B SER* 3.1 29.2 + - - +
40B GLY* 1.3 75.4 - - - +
42B LEU* 1.3 57.2 + - + +
44B ARG* 2.7 34.2 + - - +
45B SER* 3.0 32.3 + - - -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.1 6.5 - - + -
38B SER 3.1 20.1 + - - +
39B THR* 3.3 11.0 + - + +
41B ASP* 1.3 73.6 - - + +
43B LEU* 1.3 65.4 + - - +
45B SER* 3.3 9.0 + - - +
46B GLU* 3.2 20.6 + - - +
75B MET* 3.9 39.6 - - + +
76B LEU* 4.2 22.2 - - + +
79B ALA* 4.1 22.4 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR 3.0 20.8 + - - +
40B GLY 3.7 3.6 - - - +
42B LEU* 1.3 76.8 - - - +
44B ARG* 1.3 56.6 + - - +
46B GLU* 3.1 7.5 + - - +
47B VAL* 3.0 27.9 + - - +
57B LEU* 4.1 11.5 - - + +
61B MET* 3.9 15.9 - - + -
67B VAL* 4.0 30.7 - - + -
71B THR* 4.7 2.2 - - + -
72B VAL* 4.6 11.2 - - + -
75B MET* 3.9 27.4 - - + -
1196B B4P 3.4 48.0 - - + +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 4.7 1.0 + - - -
40B GLY 2.9 20.6 + - - +
41B ASP* 2.7 36.0 + - - +
43B LEU* 1.3 75.3 - - - +
45B SER* 1.3 61.3 + - - +
47B VAL* 3.3 9.5 + - - +
48B SER* 3.1 25.3 + - - -
61B MET* 4.2 15.0 - - + -
138B ARG* 3.4 53.0 - - - +
140B ASP* 5.0 0.8 + - - -
1196B B4P 3.0 42.6 + - - -
1197B MLI 3.9 20.0 - - + +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP 3.0 15.2 + - - -
42B LEU* 3.6 13.0 - - - +
43B LEU 3.3 0.4 - - - -
44B ARG* 1.3 73.7 - - - +
46B GLU* 1.3 63.4 + - - +
48B SER* 3.3 9.2 + - - -
49B SER* 3.2 19.1 + - - -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU 3.2 11.7 + - - +
43B LEU 3.1 8.9 + - - +
45B SER* 1.3 72.7 - - - +
47B VAL* 1.3 65.7 + - - +
49B SER* 2.6 31.8 + - - -
51B SER* 2.8 24.6 + - - -
53B ARG* 2.9 44.1 + - - +
54B GLY* 3.6 8.8 - - - -
57B LEU* 3.7 20.2 - - + -
75B MET* 4.0 8.3 - - + +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU 3.0 15.8 + - - +
44B ARG* 3.4 10.1 - - + +
46B GLU* 1.3 76.7 - - - +
48B SER* 1.3 63.8 + - - +
49B SER 3.3 0.7 + - - -
50B GLY* 3.3 11.6 + - - -
54B GLY* 3.5 25.8 - - - +
55B LYS* 5.7 0.2 - - - -
57B LEU* 4.3 3.1 - - + -
58B SER* 3.8 27.1 - - - +
61B MET* 3.5 24.7 - - + -
1197B MLI 4.3 12.6 - - - +
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG 3.1 11.2 + - - -
45B SER* 3.5 13.4 - - - -
46B GLU 3.1 0.2 - - - -
47B VAL* 1.3 76.5 - - - +
49B SER* 1.3 62.2 + - - +
50B GLY* 3.1 3.3 + - - -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER 3.2 9.6 + - - -
46B GLU* 2.6 31.3 + - - -
48B SER* 1.3 77.1 - - - +
50B GLY* 1.3 60.3 + - - +
51B SER* 3.2 20.5 + - - -
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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