Contacts of the helix formed by residues 50 - 63 (chain C) in PDB entry 2D28
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 SER 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C ARG 5.2 0.2 + - - -
49C VAL* 1.3 78.0 - - - +
51C GLU* 1.3 58.7 + - - +
52C ARG* 3.6 8.6 + - - +
53C ASP* 3.0 35.4 + - - +
54C HIS* 2.8 29.0 + - - +
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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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49C VAL 3.8 1.2 + - - +
50C SER* 1.3 72.3 - - - +
52C ARG* 1.3 63.1 + - - +
54C HIS* 3.4 8.2 + - + +
55C ALA* 3.0 25.5 + - - +
136C LEU* 3.9 19.3 - - + +
137C ARG* 3.5 28.6 + - + +
138C SER* 2.6 51.4 + - - -
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Residues in contact with ARG 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 SER* 3.2 8.5 + - - +
51C GLU* 1.3 78.6 - - - +
53C ASP* 1.3 62.4 + - - +
55C ALA* 3.4 2.1 + - - +
56C GLU* 2.8 39.5 + - + +
68C ASP* 6.0 3.2 - - - +
136C LEU* 3.8 43.7 - - + +
139C GLU* 4.4 6.9 + - - -
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Residues in contact with ASP 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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14C LEU* 3.8 2.9 - - + +
19C ARG* 3.6 48.8 + - + +
49C VAL* 4.3 7.9 - - + -
50C SER* 3.0 25.3 + - - +
52C ARG* 1.3 76.6 - - - +
54C HIS* 1.3 65.5 + - - +
56C GLU* 4.1 6.2 - - - +
57C THR* 2.7 31.9 + - - -
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Residues in contact with HIS 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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10C ILE* 5.1 2.4 - - - +
14C LEU* 4.9 3.6 - - - +
40C LEU* 4.6 21.2 - - + +
44C GLY* 6.5 0.4 - - - -
49C VAL* 3.8 15.1 - - + +
50C SER 2.8 17.1 + - - +
51C GLU* 3.6 8.3 - - - +
53C ASP* 1.3 77.4 - - - +
55C ALA* 1.3 63.9 + - - +
57C THR* 3.3 1.8 + - - -
58C CYS* 2.8 48.3 + - - -
111C ALA 3.6 7.0 + - - -
112C ASP* 2.8 22.1 + - - -
114C TYR* 3.5 19.1 + + - -
137C ARG* 3.2 22.8 + - + -
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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 3.0 16.7 + - - +
52C ARG 3.7 3.1 - - - +
54C HIS* 1.3 78.2 - - - +
56C GLU* 1.3 64.5 + - - +
57C THR 3.3 0.2 + - - -
58C CYS 3.4 0.3 + - - -
59C ALA* 2.9 24.9 + - - +
66C LEU* 4.0 8.3 - - + -
111C ALA 5.3 1.6 - - - -
134C VAL* 3.5 26.4 - - + +
135C GLY 4.2 10.1 - - - +
136C LEU* 3.8 23.6 - - + +
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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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19C ARG* 3.8 28.3 + - - +
52C ARG* 2.8 33.4 + - + +
53C ASP* 3.7 10.8 - - - +
55C ALA* 1.3 73.7 - - - +
57C THR* 1.3 57.6 + - - +
59C ALA* 3.3 4.7 + - - +
60C GLU* 2.9 35.3 + - - +
66C LEU* 3.8 24.2 - - - +
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Residues in contact with THR 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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10C ILE* 3.5 26.0 - - + +
13C ALA* 3.5 30.7 - - + -
14C LEU* 3.4 18.9 - - + +
19C ARG* 2.7 24.0 + - - +
53C ASP 2.7 19.1 + - - -
54C HIS 3.9 1.8 - - - -
56C GLU* 1.3 73.4 - - - +
58C CYS* 1.3 67.4 + - - +
60C GLU* 3.3 4.3 + - - +
61C VAL* 2.9 24.4 + - - +
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Residues in contact with CYS 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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10C ILE* 3.8 18.3 - - - +
54C HIS* 2.8 54.4 + - - +
55C ALA 3.6 4.5 - - - +
57C THR* 1.3 75.0 - - - +
59C ALA* 1.3 62.9 + - - +
61C VAL* 4.0 0.3 - - - -
62C LEU* 3.0 30.8 + - - +
111C ALA 4.4 0.4 - - - -
113C PRO* 3.7 24.0 - - + -
114C TYR* 3.8 20.4 - - - -
134C VAL* 4.3 6.3 - - + -
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Residues in contact with ALA 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 ALA 2.9 17.6 + - - +
56C GLU 3.5 5.4 - - - +
58C CYS* 1.3 77.6 - - - +
60C GLU* 1.3 56.5 + - - +
63C GLY* 2.8 27.2 + - - -
64C LEU 3.1 29.4 + - - +
66C LEU* 3.6 26.9 - - + -
134C VAL* 4.1 10.7 - - + +
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Residues in contact with GLU 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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13C ALA* 4.5 5.0 - - - +
17C ARG* 4.3 11.2 - - - +
19C ARG* 3.0 42.7 + - - -
56C GLU* 2.9 24.1 + - + +
57C THR* 3.3 12.4 + - - +
59C ALA* 1.3 77.3 - - - +
61C VAL* 1.3 66.1 + - + +
63C GLY* 3.6 6.1 + - - -
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Residues in contact with VAL 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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6C ALA* 4.5 2.2 - - - +
9C ARG* 3.4 74.6 + - + +
10C ILE* 3.8 22.2 - - + -
13C ALA* 4.1 13.5 - - + -
57C THR* 2.9 19.8 + - + +
58C CYS 4.2 0.7 - - - +
60C GLU* 1.3 81.0 - - + +
62C LEU* 1.3 66.4 + - + +
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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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6C ALA* 4.1 22.4 - - + -
9C ARG* 4.7 8.7 - - - +
10C ILE* 4.9 3.6 - - + -
58C CYS 3.0 16.1 + - - +
61C VAL* 1.3 87.2 - - + +
63C GLY* 1.3 61.5 + - - +
64C LEU* 3.4 20.6 + - + +
113C PRO* 3.5 51.8 - - + +
114C TYR* 3.8 8.1 - - + +
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Residues in contact with GLY 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 ALA 2.8 9.7 + - - -
60C GLU* 3.6 5.2 + - - -
61C VAL 3.4 3.0 - - - -
62C LEU* 1.3 78.1 - - - +
64C LEU* 1.3 62.0 + - - +
65C PRO* 4.2 2.1 - - - +
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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