Contacts of the helix formed by residues 51 - 63 (chain C) in PDB entry 4CFQ
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 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C THR* 1.3 83.7 + - - +
52C GLU* 1.3 65.0 + - - +
53C ALA* 3.5 11.6 + - - +
54C ALA* 3.0 36.7 + - - +
55C PHE* 3.3 16.0 + - - -
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Residues in contact with GLU 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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31C LYS* 5.2 10.9 + - - +
35C LYS* 3.0 38.1 + - - +
51C ASP* 1.3 75.6 - - - +
53C ALA* 1.3 58.4 + - - +
55C PHE* 3.2 11.3 + - - +
56C GLN* 2.9 33.2 + - - +
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Residues in contact with ALA 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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51C ASP* 3.5 12.9 + - - +
52C GLU* 1.3 81.0 - - - +
54C ALA* 1.3 56.2 + - - +
56C GLN* 3.3 9.3 + - - +
57C LYS* 3.0 29.3 + - - +
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Residues in contact with ALA 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 THR* 3.7 24.0 - - + +
51C ASP* 3.0 23.0 + - - +
53C ALA* 1.3 73.5 - - - +
55C PHE* 1.3 61.5 + - - +
57C LYS* 3.4 7.2 + - - +
58C LEU* 3.0 27.7 + - - +
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Residues in contact with PHE 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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31C LYS* 5.3 9.1 - - + +
34C LEU* 4.5 8.7 - - + +
35C LYS* 3.5 59.9 - - + +
38C LEU* 5.0 12.3 - - + -
39C THR* 4.4 8.5 - - - -
46C LEU* 4.3 21.1 - - + -
50C THR* 3.1 49.1 - - + -
51C ASP 3.3 10.3 + - - -
52C GLU* 3.2 17.7 + - - +
54C ALA* 1.3 77.5 - - - +
56C GLN* 1.3 58.0 + - - +
58C LEU* 3.3 7.3 + - + +
59C MET* 2.9 29.5 + - - +
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Residues in contact with GLN 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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31C LYS* 6.0 9.1 - - + +
52C GLU* 2.9 20.0 + - - +
53C ALA* 3.6 8.6 - - - +
55C PHE* 1.3 78.0 - - - +
57C LYS* 1.3 62.4 + - - +
59C MET* 3.4 7.0 + - + +
60C SER* 3.0 23.4 + - - -
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Residues in contact with LYS 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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53C ALA 3.0 16.8 + - - +
54C ALA* 3.7 7.2 - - - +
56C GLN* 1.3 73.7 - - - +
58C LEU* 1.3 67.8 + - - +
60C SER* 3.2 8.5 + - - -
61C ASN* 2.7 53.9 + - - +
1904R THR* 4.7 4.8 - - - +
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Residues in contact with LEU 58 (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 LEU* 4.7 7.2 - - + -
38C LEU* 3.3 36.3 - - + -
54C ALA 3.0 17.0 + - - +
55C PHE* 3.7 9.4 - - + +
56C GLN 3.3 0.2 - - - -
57C LYS* 1.3 78.2 - - - +
59C MET* 1.3 63.0 + - - +
61C ASN* 3.2 6.3 + - + +
62C LEU* 2.9 38.7 + - + +
78C PHE* 3.9 15.9 - - + -
1902R ASP* 3.0 33.2 - - + +
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Residues in contact with MET 59 (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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29C LEU 3.5 12.3 - - - +
30C ASN* 3.7 3.4 - - - +
31C LYS* 3.6 40.6 - - + +
34C LEU* 4.1 20.3 - - + +
55C PHE 2.9 16.8 + - - +
56C GLN* 3.5 8.5 - - - +
58C LEU* 1.3 76.9 - - - +
60C SER* 1.3 63.9 + - - +
62C LEU* 3.2 3.3 + - - +
63C ASP* 3.1 27.7 + - + +
68C ASN* 3.0 39.7 - - - +
69C GLU* 3.5 17.7 - - - -
70C VAL* 4.2 8.8 - - + +
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Residues in contact with SER 60 (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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56C GLN* 3.0 15.1 + - - -
57C LYS* 3.5 13.8 - - - +
59C MET* 1.3 76.9 - - - +
61C ASN* 1.3 67.6 + - - +
63C ASP* 3.3 20.3 + - - +
66C ARG* 4.2 14.3 + - - +
1904R THR* 4.9 2.7 - - - +
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Residues in contact with ASN 61 (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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57C LYS* 2.7 53.5 + - - +
58C LEU* 3.2 8.7 + - + +
60C SER* 1.3 80.1 + - - +
62C LEU* 1.3 62.1 + - - +
63C ASP 3.4 0.3 + - - -
64C SER* 4.5 2.4 + - - -
1902R ASP* 4.2 32.4 + - + +
1903R ALA* 4.4 5.5 - - - +
1904R THR* 3.2 29.0 - - + +
1907R ALA* 3.6 18.0 - - - +
1908R ASP* 4.7 2.6 - - - +
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Residues in contact with LEU 62 (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 LEU* 4.7 8.7 - - + -
58C LEU* 2.9 33.2 + - + +
59C MET 3.8 3.6 - - - +
61C ASN* 1.3 76.1 - - - +
63C ASP* 1.3 57.9 + - - +
64C SER* 2.9 13.0 + - - -
70C VAL* 4.1 28.0 - - + -
74C GLU* 3.4 25.0 - - - +
77C VAL* 5.3 1.3 - - + -
78C PHE* 3.4 42.8 - - + +
1902R ASP* 3.1 39.5 - - + +
1907R ALA* 4.8 7.4 - - + -
1911R ASN* 4.4 2.4 + - - -
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Residues in contact with ASP 63 (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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59C MET* 3.1 18.0 + - + +
60C SER* 3.3 12.4 + - - +
61C ASN 3.3 0.9 - - - -
62C LEU* 1.3 73.1 - - - +
64C SER* 1.3 60.0 + - - +
65C ASN* 3.0 9.0 - - - +
66C ARG* 3.0 39.4 + - - +
67C ASP* 3.1 2.3 - - - +
68C ASN* 2.8 31.8 + - - -
69C GLU 3.7 8.1 - - - +
70C VAL* 5.3 0.9 - - + -
74C GLU* 3.7 5.6 - - - -
502C CA 2.3 30.2 - - - -
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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