Contacts of the helix formed by residues 50 - 65 (chain C) in PDB entry 5MR4
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 GLU 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU 3.9 6.4 + - - +
47C CYS 3.1 7.7 + - - +
48C ALA 3.3 0.8 - - - -
49C ALA* 1.3 79.7 - - - +
51C SER* 1.3 75.1 + - - +
52C ASN* 3.0 24.3 + - - +
53C CYS* 2.9 31.1 + - + +
54C SER* 3.0 22.0 + - - -
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Residues in contact with SER 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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48C ALA 5.5 0.4 - - - -
49C ALA 4.3 0.8 + - - -
50C GLU* 1.3 76.9 + - - +
52C ASN* 1.3 64.0 + - - +
54C SER* 3.8 6.6 - - - -
55C SER* 3.2 24.1 + - - -
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Residues in contact with ASN 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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50C GLU* 3.0 21.2 + - - +
51C SER* 1.3 77.7 + - - +
53C CYS* 1.3 57.7 + - - +
55C SER* 3.2 7.3 + - - -
56C ARG* 2.9 65.5 + - - +
84C VAL* 4.3 14.3 - - - +
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Residues in contact with CYS 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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47C CYS* 2.7 50.3 - - - +
50C GLU* 2.9 26.1 + - + +
52C ASN* 1.3 72.3 - - - +
54C SER* 1.3 53.9 + - - +
56C ARG* 3.1 9.5 + - - +
57C TYR* 2.7 35.3 + - - +
84C VAL* 5.0 7.2 - - + -
85C LEU* 3.9 16.1 - - - +
88C SER* 4.3 15.9 - - - -
89C PRO* 5.9 0.7 - - - -
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C CYS* 3.5 17.4 + - - -
48C ALA* 4.2 17.1 + - - +
50C GLU 3.0 16.5 + - - -
51C SER* 3.8 8.5 - - - -
53C CYS* 1.3 77.6 - - - +
55C SER* 1.3 57.5 + - - +
57C TYR* 3.5 6.1 + - - +
58C ARG* 3.0 29.4 + - - +
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER 3.2 17.1 + - - -
52C ASN* 3.6 6.1 - - - -
54C SER* 1.3 75.1 - - - +
56C ARG* 1.3 67.1 + - - +
58C ARG* 3.3 19.8 + - - +
59C THR* 3.0 28.5 + - - -
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASN* 2.9 40.3 + - - +
53C CYS 3.5 5.8 - - - +
55C SER* 1.3 78.0 - - - +
57C TYR* 1.3 57.2 + - - +
59C THR* 3.3 3.6 + - - -
60C LEU* 2.9 26.5 + - - +
77C GLU* 5.2 10.1 + - - +
80C ALA* 4.1 23.6 - - - +
81C ALA* 3.5 30.9 - - - +
84C VAL* 3.6 45.8 - - + +
85C LEU* 3.9 5.6 - - + -
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ASN* 3.9 20.5 + - - -
47C CYS* 3.8 13.9 - - - -
53C CYS 2.7 20.4 + - - +
54C SER* 3.6 7.2 - - - +
56C ARG* 1.3 71.1 - - - +
58C ARG* 1.3 65.7 + - - +
60C LEU* 3.3 1.6 + - - +
61C ARG* 3.0 66.3 + - - +
85C LEU* 3.7 12.7 - - + +
90C LEU* 3.5 27.6 - - + -
108C ILE* 4.1 16.0 - - + +
111C SER* 3.0 18.2 + - - -
112C ILE* 3.3 30.5 - - + -
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Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 3.0 18.3 + - - +
55C SER* 3.6 17.3 + - - +
57C TYR* 1.3 78.2 - - - +
59C THR* 1.3 61.1 + - - +
61C ARG* 3.5 33.6 - - - +
62C GLN* 3.1 23.6 + - + +
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Residues in contact with THR 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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55C SER* 3.0 18.2 + - - -
56C ARG* 3.6 9.1 - - - -
58C ARG* 1.3 73.3 - - - +
60C LEU* 1.3 59.4 + - - +
62C GLN* 3.2 8.0 + - + +
63C CYS* 2.9 43.4 + - - -
77C GLU* 4.4 33.0 + - + +
78C CYS 4.7 0.2 - - - +
81C ALA* 4.0 16.8 - - + -
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Residues in contact with LEU 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 ARG 2.9 16.2 + - - +
57C TYR 3.3 2.7 + - - +
59C THR* 1.3 75.4 - - - +
61C ARG* 1.3 55.5 + - - +
63C CYS* 3.1 11.0 + - + +
64C LEU* 2.9 52.2 + - + +
78C CYS* 4.4 6.5 - - + +
81C ALA* 4.2 4.7 - - + +
82C LEU* 4.2 41.7 - - + +
85C LEU* 3.4 28.9 - - + -
112C ILE* 3.8 26.2 - - + +
114C LEU* 5.3 1.1 - - + -
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER 5.4 0.2 + - - -
57C TYR* 3.0 63.0 + - + +
58C ARG* 3.5 39.0 + - - +
60C LEU* 1.3 78.1 - - - +
62C GLN* 1.3 57.7 + - - +
64C LEU* 3.4 1.7 + - - +
65C ALA* 3.0 31.1 + - - +
111C SER* 3.6 36.2 + - - +
112C ILE* 5.1 1.2 - - - +
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Residues in contact with GLN 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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58C ARG* 3.1 11.2 + - + +
59C THR* 3.2 11.2 + - - +
61C ARG* 1.3 76.0 - - - +
63C CYS* 1.3 67.4 + - - +
65C ALA* 3.4 20.5 + - - +
66C GLY* 4.2 0.7 + - - -
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Residues in contact with CYS 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 THR* 2.9 33.1 + - - -
60C LEU* 3.5 13.2 - - + +
62C GLN* 1.3 79.3 - - - +
64C LEU* 1.3 62.9 + - + +
66C GLY* 3.4 13.3 + - - -
78C CYS* 2.1 57.4 - - + -
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 2.9 37.2 + - + +
61C ARG 4.0 2.9 - - - +
63C CYS* 1.3 73.8 - - + +
65C ALA* 1.3 57.8 + - - +
66C GLY 3.0 15.3 + - - +
110C TRP 5.9 0.4 - - - +
111C SER 3.6 8.7 - - - +
112C ILE* 3.5 42.4 - - - +
113C HIS 3.9 14.6 - - - +
114C LEU* 4.3 21.8 - - + -
115C GLY 5.6 0.7 - - - +
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Residues in contact with ALA 65 (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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61C ARG 3.0 17.1 + - - +
62C GLN* 3.9 15.0 - - - +
63C CYS 3.4 1.4 - - - -
64C LEU* 1.3 73.3 - - - +
66C GLY* 1.3 55.9 + - - +
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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