Contacts of the helix formed by residues 39 - 49 (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 ASP 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C PRO 4.1 0.8 + - - -
38C VAL* 1.3 80.0 - - - +
40C CYS* 1.3 58.5 + - - +
41C VAL* 2.8 21.4 + - - +
42C ARG* 3.0 15.8 + - - +
43C ALA* 3.0 26.2 + - - +
93C CYS* 4.0 1.6 - - - -
94C ARG 3.3 18.4 - - - +
95C CYS* 5.1 1.1 - - - -
96C LYS* 6.5 1.3 - - + -
99C MET* 3.7 24.8 - - + +
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Residues in contact with CYS 40 (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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39C ASP* 1.3 72.8 - - - +
41C VAL* 1.3 65.0 + - - +
43C ALA* 3.8 1.8 - - - +
44C ASN* 3.0 25.6 + - - +
93C CYS* 2.1 60.8 - - - -
94C ARG* 3.5 3.3 + - - -
95C CYS* 4.1 5.4 - - - -
105C CYS* 3.4 23.9 - - - +
108C ILE* 3.5 13.0 - - + +
109C TYR* 3.9 23.8 - - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 2.8 13.8 + - - +
40C CYS* 1.3 72.3 - - - +
42C ARG* 1.3 63.6 + - - +
44C ASN* 3.4 5.9 + - - +
45C GLU* 3.2 29.7 + - + +
99C MET* 4.4 5.2 - - + -
100C LYS 5.8 0.2 - - - +
101C LYS* 3.7 43.7 - - + +
104C GLN* 4.1 10.3 - - + -
105C CYS* 3.5 34.3 - - + +
108C ILE* 3.9 7.6 - - + -
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Residues in contact with ARG 42 (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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38C VAL* 2.9 33.2 - - + -
39C ASP* 3.0 12.9 + - - +
41C VAL* 1.3 77.3 - - + +
43C ALA* 1.3 64.2 + - - +
45C GLU* 3.0 48.0 + - - +
46C LEU* 3.1 50.5 + - + +
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Residues in contact with ALA 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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38C VAL* 4.1 2.2 - - + +
39C ASP 3.0 19.0 + - - +
40C CYS* 3.8 7.2 - - - +
41C VAL 3.4 0.2 - - - -
42C ARG* 1.3 75.1 - - - +
44C ASN* 1.3 57.0 + - - +
46C LEU* 3.6 5.5 + - - +
47C CYS* 3.1 28.9 + - - +
89C PRO* 3.5 47.2 - - + +
90C LEU* 3.8 14.7 - - + +
93C CYS* 4.3 0.7 - - + -
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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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40C CYS 3.0 17.7 + - - +
41C VAL 3.5 5.3 + - - +
42C ARG 3.1 0.2 - - - -
43C ALA* 1.3 76.5 - - - +
45C GLU* 1.3 61.5 + - - +
47C CYS* 3.9 3.1 - - - +
48C ALA* 2.9 34.7 + - - +
57C TYR* 3.9 29.3 + - - -
90C LEU* 4.2 6.3 - - + +
108C ILE* 3.5 28.2 - - + +
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Residues in contact with GLU 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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41C VAL* 3.2 27.9 + - + +
42C ARG* 3.0 40.6 + - - +
44C ASN* 1.3 78.7 - - - +
46C LEU* 1.3 62.1 + - - +
48C ALA* 3.4 4.9 + - - +
49C ALA* 3.1 24.9 + - - +
101C LYS* 4.4 10.0 + - - -
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Residues in contact with LEU 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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38C VAL* 5.1 6.7 - - + -
42C ARG* 3.1 54.3 + - + +
43C ALA* 3.7 7.6 - - - +
45C GLU* 1.3 79.0 - - - +
47C CYS* 1.3 63.2 + - - +
49C ALA* 3.6 13.9 + - + +
50C GLU* 3.9 9.0 + - - +
89C PRO* 4.2 26.5 - - + -
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Residues in contact with CYS 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 ALA 3.1 18.1 + - - +
44C ASN* 3.9 4.7 - - - +
45C GLU 3.3 0.2 - - - -
46C LEU* 1.3 74.8 - - - +
48C ALA* 1.3 64.6 + - - +
50C GLU 3.1 24.1 + - - +
53C CYS* 2.7 57.1 - - - +
54C SER* 3.5 4.5 + - - -
57C TYR* 3.8 20.9 - - - -
88C SER* 5.8 1.1 - - - -
89C PRO* 5.8 1.5 - - + +
90C LEU* 3.8 15.3 - - + -
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Residues in contact with ALA 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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44C ASN* 2.9 26.2 + - - +
45C GLU* 3.8 6.1 - - - +
47C CYS* 1.3 76.8 - - - +
49C ALA* 1.3 60.6 + - - +
50C GLU* 3.4 1.6 + - - -
51C SER* 5.5 0.3 - - - -
54C SER* 4.2 18.9 + - - +
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Residues in contact with ALA 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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45C GLU 3.1 17.7 + - - +
46C LEU* 3.9 8.3 - - + +
47C CYS 3.2 1.0 - - - -
48C ALA* 1.3 76.5 - - - +
50C GLU* 1.3 57.9 + - - +
51C SER 4.3 0.4 + - - -
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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