Contacts of the helix formed by residues 34 - 48 (chain B) in PDB entry 3C33
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 GLY 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B PRO 3.3 13.5 - - - -
16B TYR 3.3 4.5 - - - -
18B MET* 4.2 1.1 - - - -
33B GLU* 1.3 79.2 - - - +
35B TYR* 1.3 68.1 + - - -
36B CYS 3.1 2.9 - - - -
37B LEU* 3.0 3.2 + - - +
38B ASP* 3.0 24.7 + - - -
250B TRP* 3.4 24.0 - - - -
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Residues in contact with TYR 35 (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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15B PRO 3.0 16.0 + - - +
16B TYR* 4.2 10.3 - + - -
34B GLY* 1.3 72.0 - - - -
36B CYS* 1.3 69.1 + - - +
38B ASP* 3.2 4.8 + - - +
39B LEU* 2.9 31.2 + - + +
105B PHE* 3.7 42.6 + + - -
106B MET* 3.4 24.9 - - + +
243B LEU* 4.0 19.9 + - + +
246B MET* 3.6 47.5 - - + +
247B LYS* 3.8 9.0 - - + -
250B TRP* 3.5 19.0 - - + +
251B TRP* 3.8 21.3 - + + -
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Residues in contact with CYS 36 (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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16B TYR* 2.8 44.4 + - - +
17B VAL* 3.8 13.0 - - + -
35B TYR* 1.3 89.0 - - - +
37B LEU* 1.3 57.8 + - + +
39B LEU* 3.6 5.6 - - - +
40B LEU* 2.9 29.9 + - - +
86B VAL* 3.8 18.8 - - + +
87B ALA* 3.8 28.9 - - - -
105B PHE* 4.6 7.2 - - - -
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Residues in contact with LEU 37 (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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10B THR* 6.2 0.2 - - + -
16B TYR 3.8 8.7 - - - +
17B VAL* 3.9 18.4 - - + -
29B ASN* 5.0 5.2 - - + +
32B PHE* 3.8 34.1 - - + +
33B GLU* 3.7 26.5 - - - +
34B GLY 3.0 11.8 + - - +
36B CYS* 1.3 75.6 - - + +
38B ASP* 1.3 61.1 + - - +
40B LEU* 3.4 10.1 + - + +
41B LYS* 2.9 44.6 + - - +
51B TYR* 4.6 5.1 + - + +
53B VAL* 4.2 25.6 - - + -
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Residues in contact with ASP 38 (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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34B GLY 3.0 9.9 + - - +
35B TYR 3.4 9.0 - - - +
37B LEU* 1.3 79.5 - - - +
39B LEU* 1.3 60.7 + - - +
41B LYS* 3.3 18.0 + - - +
42B GLU* 3.1 27.5 + - + +
246B MET* 3.9 19.6 - - + +
249B LYS* 2.9 26.8 + - - +
250B TRP* 2.9 31.5 + - - +
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Residues in contact with LEU 39 (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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35B TYR* 2.9 20.2 + - + +
36B CYS* 3.6 5.6 - - - +
37B LEU 3.3 0.2 - - - -
38B ASP* 1.3 75.2 - - - +
40B LEU* 1.3 59.5 + - - +
42B GLU* 3.2 3.7 + - - +
43B LEU* 2.9 46.4 + - + +
86B VAL* 4.1 19.3 - - + -
105B PHE* 3.9 43.3 - - + -
218B VAL* 4.4 7.6 - - + -
234B ILE* 4.9 3.8 - - + -
237B LEU* 4.1 14.8 - - + -
243B LEU* 4.0 26.9 - - + -
246B MET* 3.5 12.5 - - + +
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Residues in contact with LEU 40 (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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8B VAL* 3.9 31.4 - - + -
36B CYS 2.9 18.2 + - - +
37B LEU* 3.7 10.1 - - + +
39B LEU* 1.3 77.4 - - - +
41B LYS* 1.3 56.6 + - - +
43B LEU* 3.3 7.9 + - + +
44B SER* 2.9 31.5 + - - -
49B PHE* 4.0 23.1 - - + -
51B TYR* 3.6 34.3 - - + -
53B VAL* 3.8 17.0 - - + -
84B LEU* 4.5 2.7 - - + -
86B VAL* 4.1 19.7 - - + +
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Residues in contact with LYS 41 (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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32B PHE 5.8 1.6 + - - -
37B LEU* 2.9 31.1 + - - +
38B ASP* 3.3 21.8 + - - +
40B LEU* 1.3 75.8 - - - +
42B GLU* 1.3 62.0 + - + +
44B SER* 3.6 4.7 - - - -
45B ASN* 3.0 26.0 + - - +
51B TYR* 3.5 20.3 + - - +
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Residues in contact with GLU 42 (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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38B ASP* 3.1 22.5 + - + +
39B LEU* 3.2 4.9 + - - +
41B LYS* 1.3 76.5 - - - +
43B LEU* 1.3 64.6 + - - +
45B ASN* 3.0 27.0 + - - +
46B ILE* 3.1 20.4 + - - +
237B LEU* 3.9 28.7 - - + +
240B GLU* 5.3 1.0 - - - +
242B LYS* 3.2 34.9 + - - +
246B MET* 4.4 10.1 - - - -
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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 LEU* 2.9 38.1 + - + +
40B LEU* 3.7 13.0 - - + +
42B GLU* 1.3 75.0 - - - +
44B SER* 1.3 58.0 + - - +
46B ILE* 3.4 4.1 + - - -
47B LEU* 2.9 37.7 + - + +
49B PHE* 3.9 14.4 - - + -
84B LEU* 5.7 1.1 - - + -
86B VAL* 5.2 3.1 - - + -
218B VAL* 4.3 12.3 - - + -
230B ILE* 4.2 27.1 - - + -
233B ALA* 3.6 28.0 - - + -
234B ILE* 4.2 14.4 - - + -
237B LEU* 4.1 13.9 - - + -
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Residues in contact with SER 44 (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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40B LEU 2.9 18.0 + - - -
41B LYS* 3.6 6.3 - - - -
43B LEU* 1.3 75.1 - - - +
45B ASN* 1.3 60.2 + - - +
48B GLY* 3.0 28.6 + - - -
49B PHE* 2.5 36.9 + - - -
50B LEU* 5.7 0.7 - - - +
51B TYR* 3.6 21.9 - - - -
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Residues in contact with ASN 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 LYS 3.0 15.2 + - - +
42B GLU* 3.0 24.1 + - - +
44B SER* 1.3 76.9 - - - +
46B ILE* 1.3 65.9 + - - +
48B GLY* 4.9 0.9 + - - -
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Residues in contact with ILE 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 GLU* 3.1 17.1 + - + +
43B LEU 3.9 2.9 - - - +
45B ASN* 1.3 88.7 - - - +
47B LEU* 1.3 70.0 + - + +
48B GLY 3.9 0.2 + - - -
233B ALA* 3.9 32.1 - - + +
236B GLN* 3.9 35.2 - - - +
237B LEU* 3.8 34.8 - - + -
240B GLU* 5.2 0.2 - - - +
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Residues in contact with LEU 47 (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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43B LEU* 2.9 17.2 + - + +
46B ILE* 1.3 95.2 - - + +
48B GLY* 1.3 63.6 + - - +
49B PHE* 3.8 19.1 - - + +
226B TYR* 5.2 6.5 - - + -
229B LYS* 3.9 42.6 - - + +
230B ILE* 3.8 30.5 - - + -
232B ILE* 6.6 0.2 - - + -
233B ALA* 4.3 5.2 - - + -
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Residues in contact with GLY 48 (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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44B SER 3.0 14.6 + - - -
45B ASN 4.6 1.5 - - - -
46B ILE 3.5 1.6 + - - -
47B LEU* 1.3 80.8 - - - +
49B PHE* 1.3 61.4 + - - +
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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