Contacts of the helix formed by residues 42 - 57 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C PRO* 4.6 4.3 - - - +
40C LYS* 2.9 25.0 + - + +
41C CYS* 1.3 74.5 - - - +
43C ILE* 1.3 82.4 + - - +
44C ASN* 2.9 34.2 + - - +
45C ALA* 3.0 23.3 + - + +
46C GLN* 3.3 14.6 + - - +
66C SER* 5.1 1.3 + - - -
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C CYS 4.3 0.6 - - - -
42C ASP* 1.3 78.0 - - - +
44C ASN* 1.3 67.0 + - - +
46C GLN* 3.4 15.7 + - - +
47C LEU* 3.0 56.1 + - + +
66C SER* 4.4 7.1 - - - -
67C ASP* 3.7 28.7 - - + +
70C ALA* 3.4 26.2 - - + -
71C VAL* 3.5 22.9 - - + -
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Residues in contact with ASN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP* 2.9 25.8 + - - +
43C ILE* 1.3 82.8 - - - +
45C ALA* 1.3 64.4 + - - -
46C GLN 3.1 1.3 - - - -
47C LEU* 3.3 16.2 + - - +
48C GLN* 2.9 25.6 + - - +
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 4.2 10.0 - - + -
38C PRO* 3.9 25.4 - - + -
40C LYS 5.0 1.1 - - - +
42C ASP* 3.0 21.0 + - + +
44C ASN* 1.3 75.4 - - - +
46C GLN* 1.3 58.1 + - - +
48C GLN* 3.1 12.4 + - - +
49C MET* 2.9 29.5 + - - +
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Residues in contact with GLN 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.5 28.9 - - + +
8C GLY 2.6 24.8 + - - +
9C LYS* 3.5 5.7 + - - +
36C PHE* 4.7 1.1 - - - -
38C PRO* 4.5 9.4 - - + -
42C ASP 3.3 7.3 + - - +
43C ILE* 3.5 16.4 - - - +
44C ASN 3.1 0.6 - - - -
45C ALA* 1.3 75.9 - - - +
47C LEU* 1.3 62.8 + - + +
49C MET* 3.3 6.2 + - - +
50C LEU* 2.9 28.6 + - - +
63C ILE* 4.3 11.1 - - + +
64C ALA 3.4 14.6 + - - -
65C PRO* 4.2 1.6 - - - +
66C SER* 3.0 44.8 + - - -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 3.0 41.8 + - + +
44C ASN* 3.3 19.0 + - - +
46C GLN* 1.3 73.5 - - + +
48C GLN* 1.3 71.4 + - - +
50C LEU* 2.9 20.0 + - + +
51C GLU* 2.9 21.2 + - + +
63C ILE* 5.5 0.7 - - + -
70C ALA* 4.1 18.2 - - + +
71C VAL* 4.2 15.3 - - + -
74C THR* 3.8 21.5 - - + +
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Residues in contact with GLN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 6.3 0.6 - - - -
44C ASN 2.9 13.5 + - - +
45C ALA* 3.1 15.3 + - - +
47C LEU* 1.3 78.5 - - - +
49C MET* 1.3 66.1 + - - +
50C LEU 2.7 11.1 + - - -
51C GLU* 3.0 7.7 + - - +
52C SER* 3.0 20.8 + - - -
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Residues in contact with MET 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.1 3.8 - - + -
36C PHE* 3.1 61.5 - - + -
45C ALA 2.9 7.7 + - - +
46C GLN 3.7 4.3 - - - +
48C GLN* 1.3 84.8 - - - +
50C LEU* 1.3 55.6 + - - +
52C SER* 3.8 16.2 - - - -
53C PHE* 2.9 59.0 + - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.6 18.2 - - + -
46C GLN 2.9 10.3 + - - +
47C LEU* 3.1 16.2 - - + +
48C GLN 2.7 2.2 + - - -
49C MET* 1.3 75.1 - - - +
51C GLU* 1.3 54.4 + - - +
53C PHE* 2.9 6.2 + - + +
54C ILE* 2.6 44.5 + - + +
61C ILE* 3.7 36.8 - - + -
63C ILE* 4.0 22.4 - - + -
71C VAL* 5.4 1.3 - - + +
74C THR* 3.7 29.2 - - + +
75C ILE* 4.5 16.2 - - + -
78C ALA* 5.9 0.4 - - + -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 2.9 18.5 + - + +
48C GLN* 3.5 7.9 - - - +
50C LEU* 1.3 71.1 - - - +
52C SER* 1.3 56.1 + - - +
54C ILE* 3.5 9.3 - - - +
55C ALA* 2.8 37.2 + - - +
74C THR* 3.5 24.5 + - + +
77C LYS* 3.3 30.3 + - - +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLN* 3.0 13.5 + - - -
49C MET* 3.4 25.2 - - - -
51C GLU* 1.3 75.5 - - - +
53C PHE* 1.3 63.7 + - - +
55C ALA* 3.0 16.5 + - - +
56C GLU* 3.0 30.9 + - - +
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Residues in contact with PHE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLY* 4.1 13.2 - - - -
6C VAL 4.1 2.5 - - - -
7C ILE* 3.6 35.0 - - + -
34C LYS* 3.4 55.4 - - + -
36C PHE* 4.7 5.4 - - + -
49C MET* 2.9 39.5 + - + +
50C LEU* 2.9 13.2 + - + +
52C SER* 1.3 71.6 - - - +
54C ILE* 1.3 70.7 + - - +
55C ALA 3.2 0.3 + - - -
56C GLU* 3.3 17.3 + - - -
58C VAL* 3.1 47.7 + - + +
61C ILE* 4.6 2.9 - - + -
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 2.6 27.6 + - + +
51C GLU* 3.5 20.0 - - - +
53C PHE* 1.3 72.8 - - - +
55C ALA* 1.3 65.3 + - - +
57C GLY* 3.0 16.1 + - - -
58C VAL* 4.5 1.1 - - - +
61C ILE* 4.6 6.3 - - + -
74C THR* 3.7 20.2 - - + +
77C LYS* 4.4 15.3 - - + -
78C ALA* 3.7 33.4 - - + +
81C MET* 4.1 31.4 - - + +
83C ILE* 4.2 16.1 - - + +
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLU 2.8 13.3 + - - +
52C SER* 3.2 12.3 - - - +
54C ILE* 1.3 74.9 - - - +
56C GLU* 1.3 60.2 + - + +
57C GLY* 2.8 12.3 + - - -
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.3 24.2 + - - +
52C SER* 3.0 37.7 + - - +
53C PHE* 3.3 18.2 + - - +
55C ALA* 1.3 75.3 - - + +
57C GLY* 1.3 62.5 + - - +
58C VAL* 4.4 7.4 - - + -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE 3.0 11.4 + - - -
55C ALA 2.8 8.8 + - - -
56C GLU* 1.3 81.0 - - - +
58C VAL* 1.3 68.5 + - - +
59C ASN* 3.6 11.6 + - - +
83C 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