Contacts of the helix formed by residues 42 - 57 (chain B) in PDB entry 3C6Q
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 ASP 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LYS 4.4 4.2 + - - -
38B PRO* 4.2 2.7 - - + +
40B LYS* 3.1 11.6 + - + +
41B CYS* 1.3 79.9 - - - +
43B ILE* 1.3 65.3 + - - +
44B ASN* 2.7 26.0 + - - +
45B ALA* 3.2 30.4 + - + +
46B GLN* 3.3 15.9 + - - +
66B SER* 4.5 3.3 + - - -
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Residues in contact with ILE 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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41B CYS* 5.6 0.2 - - - -
42B ASP* 1.3 72.7 + - - +
44B ASN* 1.3 71.3 + - - +
46B GLN* 3.2 21.9 + - - +
47B LEU* 2.7 43.3 + - + +
66B SER* 4.5 8.6 - - - -
67B ASP* 3.4 50.5 - - + +
70B ALA* 4.1 12.6 - - + -
71B VAL* 3.9 14.8 - - + -
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Residues in contact with ASN 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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42B ASP* 2.7 18.0 + - - +
43B ILE* 1.3 89.6 - - - +
45B ALA* 1.3 58.2 + - - +
47B LEU* 3.9 11.3 - - - +
48B GLN* 3.0 31.8 + - - +
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Residues in contact with ALA 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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36B PHE* 3.6 10.7 - - + -
38B PRO* 3.6 26.2 - - + -
42B ASP* 3.2 26.2 + - - +
44B ASN* 1.3 75.3 - - - +
46B GLN* 1.3 63.0 + - - +
48B GLN* 4.0 9.3 + - - +
49B MET* 3.0 24.8 + - - +
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Residues in contact with GLN 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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7B ILE* 3.7 26.0 - - + +
8B GLY 2.6 25.1 + - - +
9B LYS* 3.5 6.0 - - - +
36B PHE* 4.3 1.1 - - - -
38B PRO* 4.5 9.2 - - + -
42B ASP 3.3 9.3 + - - +
43B ILE* 3.2 20.5 + - + +
45B ALA* 1.3 77.6 - - - +
47B LEU* 1.3 55.0 + - - +
49B MET* 2.9 5.1 + - - +
50B LEU* 2.7 35.4 + - - +
63B ILE* 4.5 9.2 - - + +
64B ALA 3.0 18.6 + - - -
65B PRO* 3.8 4.1 - - - +
66B SER* 3.0 39.5 + - - -
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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 ILE* 2.7 32.3 + - + +
44B ASN* 4.0 12.6 - - - +
45B ALA 3.4 0.4 - - - -
46B GLN* 1.3 74.5 - - + +
48B GLN* 1.3 60.1 + - - +
50B LEU* 3.5 12.3 - - + +
51B GLU* 3.3 24.8 + - - +
70B ALA* 3.8 21.1 - - + +
71B VAL* 3.7 39.0 - - + +
74B THR* 3.8 18.9 - - - +
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Residues in contact with GLN 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 ASN 3.0 18.4 + - - +
45B ALA* 4.0 7.7 + - - +
47B LEU* 1.3 75.8 - - - +
49B MET* 1.3 60.6 + - - +
50B LEU 3.2 0.2 - - - -
51B GLU* 3.0 13.6 + - + +
52B SER* 2.9 26.6 + - - -
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Residues in contact with MET 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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7B ILE* 3.6 12.6 - - + -
36B PHE* 3.2 59.2 - - + -
45B ALA 3.0 19.3 + - - +
46B GLN 2.9 5.1 + - - +
48B GLN* 1.3 74.7 - - - +
50B LEU* 1.3 64.5 + - - +
52B SER* 3.2 14.5 + - - +
53B PHE* 3.1 41.6 + - + -
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Residues in contact with LEU 50 (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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7B ILE* 3.5 22.1 - - + +
46B GLN 2.7 13.8 + - - +
47B LEU* 3.5 22.2 - - + +
49B MET* 1.3 73.7 - - - +
51B GLU* 1.3 60.9 + - - +
53B PHE* 3.3 6.5 + - - +
54B ILE* 3.1 31.1 + - + +
61B ILE* 3.8 29.8 - - + +
63B ILE* 3.8 25.4 - - + -
71B VAL* 4.7 2.2 - - + +
74B THR* 3.6 31.6 - - + -
75B ILE* 4.3 18.8 - - + +
78B ALA* 6.3 1.1 - - + -
85B VAL* 6.2 0.2 - - + -
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Residues in contact with GLU 51 (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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47B LEU 3.3 12.7 + - - +
48B GLN* 3.0 18.8 + - + +
50B LEU* 1.3 80.1 - - - +
52B SER* 1.3 54.1 + - - +
54B ILE* 3.4 17.1 + - - +
55B ALA* 2.9 29.7 + - - +
74B THR* 4.3 17.4 + - + +
77B LYS* 4.4 21.0 + - - +
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Residues in contact with SER 52 (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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48B GLN 2.9 11.6 + - - -
49B MET* 3.4 24.2 - - - +
50B LEU 3.2 0.2 - - - -
51B GLU* 1.3 74.9 - - - +
53B PHE* 1.3 56.7 + - - +
55B ALA* 3.2 6.2 + - - +
56B GLU* 2.6 51.6 + - - +
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Residues in contact with PHE 53 (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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5B GLY* 3.6 22.4 - - - -
6B VAL 4.1 2.0 - - - -
7B ILE* 3.3 34.1 - - + -
34B LYS* 3.6 37.9 - - + -
36B PHE* 4.6 4.5 - - + -
49B MET* 3.1 40.7 + - + -
50B LEU* 3.6 6.7 - - - +
52B SER* 1.3 76.2 - - - +
54B ILE* 1.3 63.6 + - - +
56B GLU* 3.7 11.3 - - - -
57B GLY 3.1 16.5 + - - -
58B VAL* 3.1 42.6 + - + +
61B ILE* 3.8 15.9 - - + -
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Residues in contact with ILE 54 (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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50B LEU* 3.1 17.8 + - + +
51B GLU* 3.5 17.7 - - - +
52B SER 3.1 0.2 - - - -
53B PHE* 1.3 72.7 - - - +
55B ALA* 1.3 69.3 + - - +
57B GLY* 2.9 15.1 + - - -
61B ILE* 4.3 7.0 - - + -
74B THR* 3.9 28.7 - - + +
77B LYS* 4.6 10.1 - - + +
78B ALA* 3.8 33.4 - - + +
81B MET* 4.4 24.7 - - + -
83B ILE* 4.0 12.7 - - + +
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Residues in contact with ALA 55 (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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51B GLU* 2.9 18.5 + - - +
52B SER* 3.5 7.0 - - - +
54B ILE* 1.3 78.6 - - - +
56B GLU* 1.3 59.3 + - - +
57B GLY* 2.8 8.0 + - - -
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Residues in contact with GLU 56 (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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3B THR* 5.0 3.3 - - - +
34B LYS* 3.4 37.6 + - - +
52B SER* 2.6 33.1 + - - +
53B PHE* 3.8 12.6 - - - +
55B ALA* 1.3 71.8 - - - +
57B GLY* 1.3 60.7 + - - +
58B VAL* 4.7 12.4 - - + +
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Residues in contact with GLY 57 (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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53B PHE 3.1 0.6 + - - -
54B ILE 2.9 14.1 + - - -
55B ALA 2.8 6.2 + - - -
56B GLU* 1.3 79.0 - - - +
58B VAL* 1.3 69.5 + - - +
59B ASN* 4.3 7.6 + - - +
83B ILE* 4.9 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