Contacts of the helix formed by residues 42 - 57 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS 4.4 4.2 + - - -
38A PRO* 4.2 2.7 - - + +
40A LYS* 3.1 11.6 + - + +
41A CYS* 1.3 79.3 - - - +
43A ILE* 1.3 65.1 + - - +
44A ASN* 2.7 26.1 + - - +
45A ALA* 3.2 30.4 + - + +
46A GLN* 3.3 16.1 + - - +
66A SER* 4.5 3.3 + - - -
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Residues in contact with ILE 43 (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 CYS* 5.6 0.4 - - - -
42A ASP* 1.3 73.3 + - - +
44A ASN* 1.3 70.8 + - - +
46A GLN* 3.1 22.1 + - - +
47A LEU* 2.7 43.7 + - + +
66A SER* 4.5 8.4 - - - -
67A ASP* 3.3 50.5 - - + +
70A ALA* 4.1 13.2 - - + -
71A VAL* 3.9 14.8 - - + -
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Residues in contact with ASN 44 (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 ASP* 2.7 18.0 + - - +
43A ILE* 1.3 89.8 - - - +
45A ALA* 1.3 58.2 + - - +
47A LEU* 3.8 11.5 - - - +
48A GLN* 2.9 31.9 + - - +
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Residues in contact with ALA 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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36A PHE* 3.6 11.1 - - + -
38A PRO* 3.6 25.4 - - + -
42A ASP* 3.2 25.9 + - - +
44A ASN* 1.3 75.1 - - - +
46A GLN* 1.3 62.0 + - - +
48A GLN* 4.0 9.3 + - - +
49A MET* 3.0 24.9 + - - +
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Residues in contact with GLN 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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7A ILE* 3.7 26.8 - - + +
8A GLY 2.6 24.9 + - - +
9A LYS* 3.5 5.8 - - - +
36A PHE* 4.4 1.1 - - - -
38A PRO* 4.5 9.2 - - + -
42A ASP 3.3 8.7 + - - +
43A ILE* 3.1 19.7 + - + +
45A ALA* 1.3 77.1 - - - +
47A LEU* 1.3 54.6 + - - +
49A MET* 2.9 5.2 + - - +
50A LEU* 2.7 35.4 + - - +
63A ILE* 4.5 9.2 - - + +
64A ALA 3.0 19.0 + - - -
65A PRO* 3.8 4.0 - - - +
66A SER* 3.0 40.2 + - - -
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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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43A ILE* 2.7 34.1 + - + +
44A ASN* 3.5 13.0 + - - +
46A GLN* 1.3 74.0 - - - +
48A GLN* 1.3 60.3 + - - +
50A LEU* 3.5 13.1 - - + +
51A GLU* 3.3 25.0 + - - +
63A ILE* 5.6 0.2 - - + -
70A ALA* 3.8 19.3 - - + +
71A VAL* 3.7 38.4 - - + +
74A THR* 3.8 18.5 - - - +
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Residues in contact with GLN 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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44A ASN 2.9 18.1 + - - +
45A ALA* 4.1 7.7 + - - +
47A LEU* 1.3 75.1 - - - +
49A MET* 1.3 60.6 + - - +
50A LEU 3.1 0.2 - - - -
51A GLU* 3.0 14.5 + - + +
52A SER* 2.9 26.6 + - - -
80C GLU* 3.4 27.0 - - - +
81C MET* 4.3 10.8 - - - +
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Residues in contact with MET 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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7A ILE* 3.6 12.8 - - + -
36A PHE* 3.2 59.7 - - + -
45A ALA 3.0 19.1 + - - +
46A GLN 2.9 5.1 + - - +
48A GLN* 1.3 76.2 - - - +
50A LEU* 1.3 63.0 + - - +
52A SER* 3.2 14.0 + - - +
53A PHE* 3.1 38.8 + - + -
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Residues in contact with LEU 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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7A ILE* 3.5 22.6 - - + +
46A GLN 2.7 9.8 + - - +
47A LEU* 3.5 21.5 - - + +
49A MET* 1.3 77.9 - - - +
51A GLU* 1.3 60.5 + - - +
53A PHE* 3.3 5.9 + - - +
54A ILE* 3.1 31.2 + - + +
61A ILE* 3.8 29.8 - - + +
63A ILE* 3.8 25.4 - - + -
71A VAL* 4.6 2.2 - - + +
74A THR* 3.6 31.6 - - + -
75A ILE* 4.3 18.8 - - + +
78A ALA* 6.3 1.1 - - + -
85A VAL* 6.2 0.2 - - + -
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Residues in contact with GLU 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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47A LEU 3.3 13.7 + - - +
48A GLN* 3.0 18.8 + - + +
50A LEU* 1.3 80.5 - - - +
52A SER* 1.3 54.1 + - - +
54A ILE* 3.4 16.2 + - - +
55A ALA* 2.9 29.6 + - - +
74A THR* 4.2 17.3 + - + +
77A LYS* 4.4 20.8 + - - +
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Residues in contact with SER 52 (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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48A GLN 2.9 11.2 + - - -
49A MET* 3.4 24.1 - - - +
50A LEU 3.2 0.2 - - - -
51A GLU* 1.3 74.5 - - - +
53A PHE* 1.3 57.1 + - - +
55A ALA* 3.2 6.0 + - - +
56A GLU* 2.6 51.7 + - - +
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY* 3.6 22.2 - - - -
6A VAL 4.1 2.0 - - - -
7A ILE* 3.3 33.4 - - + -
34A LYS* 3.6 38.1 - - + -
36A PHE* 4.6 4.5 - - + -
49A MET* 3.1 37.3 + - + -
50A LEU* 3.6 7.2 - - - +
52A SER* 1.3 78.8 - - - +
54A ILE* 1.3 62.7 + - - +
56A GLU* 3.7 11.7 - - - -
57A GLY 3.0 16.6 + - - -
58A VAL* 3.1 42.8 + - + +
61A ILE* 3.8 15.7 - - + -
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Residues in contact with ILE 54 (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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50A LEU* 3.1 17.8 + - + +
51A GLU* 3.5 17.3 - - - +
52A SER 3.1 0.2 - - - -
53A PHE* 1.3 75.6 - - - +
55A ALA* 1.3 66.7 + - - +
57A GLY* 2.9 15.4 + - - -
61A ILE* 4.3 6.7 - - + -
74A THR* 3.9 28.3 - - + +
77A LYS* 4.6 10.5 - - + +
78A ALA* 3.8 33.9 - - + +
81A MET* 4.4 24.5 - - + -
83A ILE* 4.0 12.6 - - + +
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Residues in contact with ALA 55 (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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51A GLU* 2.9 18.1 + - - +
52A SER* 3.5 7.0 - - - +
54A ILE* 1.3 79.3 - - - +
56A GLU* 1.3 59.6 + - - +
57A GLY* 2.9 7.6 + - - -
298B GLU* 5.8 0.3 - - - +
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Residues in contact with GLU 56 (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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3A THR* 5.0 2.9 - - - +
34A LYS* 3.4 37.8 + - - +
52A SER* 2.6 32.5 + - - +
53A PHE* 3.8 12.8 - - - +
55A ALA* 1.3 72.0 - - - +
57A GLY* 1.3 60.7 + - - +
58A VAL* 4.7 12.4 - - + +
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Residues in contact with GLY 57 (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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53A PHE 3.0 0.6 + - - -
54A ILE 2.9 14.1 + - - -
55A ALA 2.9 6.2 + - - -
56A GLU* 1.3 78.8 - - - +
58A VAL* 1.3 65.0 + - - +
59A ASN* 4.3 3.3 + - - +
83A ILE* 4.9 2.0 - - - -
291B GLU* 5.6 1.4 - - - +
294B LYS* 2.7 31.7 + - - +
298B GLU* 4.7 5.8 - - - -
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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