Contacts of the helix formed by residues 56 - 69 (chain C) in PDB entry 1RJF
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 56 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C TYR* 5.0 1.2 + - - -
52C LEU* 2.9 24.9 + - - +
53C LYS 3.3 11.0 + - - +
54C LYS 3.5 0.2 - - - -
55C PHE* 1.3 83.2 - - - +
57C ARG* 1.3 61.8 + - - +
58C ARG* 3.8 9.0 + - - +
59C ALA* 3.4 32.1 + - - +
60C PHE* 3.5 13.3 + - - +
135C LEU* 5.3 6.1 - - - -
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Residues in contact with ARG 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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307A PHE* 3.3 62.1 - - + +
309A ASP* 3.3 30.7 + - - -
53C LYS 4.3 0.2 + - - -
56C SER* 1.3 72.7 + - - +
58C ARG* 1.3 60.1 + - - +
59C ALA 3.4 0.4 - - - -
60C PHE* 3.6 1.7 + - - +
61C GLY* 3.1 23.7 + - - -
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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
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10C TYR* 6.1 2.9 - - + -
56C SER* 3.5 7.4 + - - +
57C ARG* 1.3 77.8 - - - +
59C ALA* 1.3 63.4 + - - +
61C GLY* 3.4 2.1 + - - -
62C LYS* 3.3 41.6 + - + +
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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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10C TYR* 3.5 40.2 - - + +
52C LEU* 3.8 17.9 - - + -
56C SER* 3.4 25.9 + - - +
58C ARG* 1.3 78.2 - - - +
60C PHE* 1.3 60.6 + - - +
62C LYS* 3.6 2.3 + - - +
63C VAL* 3.2 30.0 + - - +
135C LEU* 5.1 0.2 - - + -
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Residues in contact with PHE 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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305A LEU 3.3 24.9 - - - -
306A GLN* 4.6 11.7 - - + -
307A PHE* 3.8 26.9 - + - -
49C LEU* 3.7 48.5 - - + -
50C ILE* 5.5 1.1 - - + -
52C LEU* 4.5 4.6 - - + +
53C LYS* 3.7 25.1 - - + +
56C SER 3.5 19.4 + - - +
57C ARG* 4.0 2.9 - - - +
58C ARG 3.4 0.2 - - - -
59C ALA* 1.3 77.1 - - - +
61C GLY* 1.3 60.7 + - - +
62C LYS 3.4 0.2 - - - -
63C VAL* 4.0 4.0 - - - +
64C ASP* 3.1 49.1 + - + +
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Residues in contact with GLY 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 ARG 3.1 16.5 + - - -
58C ARG* 3.4 3.5 + - - -
59C ALA 3.2 0.6 - - - -
60C PHE* 1.3 82.3 - - - +
62C LYS* 1.3 59.7 + - - +
64C ASP* 4.3 1.7 - - - +
65C LYS* 3.3 45.8 + - - +
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Residues in contact with LYS 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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7C GLN* 3.7 29.0 - - - +
10C TYR* 4.8 19.5 - - + -
14C SER* 3.9 1.2 + - - -
58C ARG* 3.3 33.3 + - + +
59C ALA 4.1 3.6 - - - +
60C PHE 3.4 0.2 - - - -
61C GLY* 1.3 76.4 - - - +
63C VAL* 1.3 64.3 + - - +
65C LYS* 4.7 1.6 - - - +
66C ALA* 3.3 25.1 + - - +
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Residues in contact with VAL 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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10C TYR* 3.8 28.7 - - + +
13C LEU* 4.1 10.1 - - + -
14C SER* 3.4 18.3 + - - +
17C LEU* 3.7 18.8 - - + -
49C LEU* 3.6 28.3 - - + -
52C LEU* 4.1 14.1 - - + -
59C ALA 3.2 18.4 + - - +
60C PHE 4.3 1.6 - - - +
62C LYS* 1.3 75.0 - - - +
64C ASP* 1.3 63.9 + - - +
67C MET* 3.2 24.3 + - - +
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Residues in contact with ASP 64 (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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306A GLN* 4.6 9.1 + - - -
49C LEU* 5.2 4.1 - - - +
60C PHE* 3.1 45.8 + - + +
61C GLY* 4.3 3.4 - - - +
62C LYS 3.4 0.2 - - - -
63C VAL* 1.3 77.1 - - - +
65C LYS* 1.3 68.4 + - + +
67C MET* 3.2 12.4 + - - +
68C ARG* 3.0 69.2 + - - -
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Residues in contact with LYS 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 GLY* 3.3 35.1 + - - +
62C LYS* 4.7 1.8 - - - +
64C ASP* 1.3 81.0 + - - +
66C ALA* 1.3 58.8 - - - +
68C ARG* 3.7 20.8 + - - +
69C SER* 3.1 26.6 + - - -
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Residues in contact with ALA 66 (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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11C ASP* 5.8 2.0 - - - +
14C SER* 3.5 22.2 - - - +
62C LYS 3.3 20.5 + - - +
64C ASP 3.3 0.6 - - - -
65C LYS* 1.3 76.6 - - - +
67C MET* 1.3 63.9 + - - +
68C ARG 3.4 0.2 - - - -
69C SER* 3.6 8.7 + - - -
70C SER 3.4 15.4 + - - -
336C BME 3.5 23.0 - - - +
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Residues in contact with MET 67 (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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68A ARG* 5.1 2.3 + - - +
14C SER* 3.7 18.4 - - - +
17C LEU* 3.5 49.1 - - + +
18C ALA* 4.0 17.3 - - + +
21C SER* 4.4 13.9 - - - +
49C LEU* 4.0 20.2 - - + -
63C VAL* 3.2 25.8 + - - +
64C ASP* 3.2 10.1 + - - +
66C ALA* 1.3 77.6 - - - +
68C ARG* 1.3 64.0 + - + +
69C SER 3.5 0.3 + - - -
70C SER* 3.5 15.6 + - - -
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Residues in contact with ARG 68 (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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22A VAL* 6.1 1.0 - - - +
67A MET 5.4 0.9 + - - +
68A ARG* 2.7 72.5 + - + +
69A SER* 5.8 1.0 - - - +
70A SER 2.7 28.5 + - - -
71A PHE* 4.4 11.5 - - - +
72A PRO* 4.6 4.8 - - - +
306A GLN* 3.8 18.2 - - - +
64C ASP* 3.0 53.6 + - - +
65C LYS* 3.7 18.4 + - - +
67C MET* 1.3 81.6 - - + +
69C SER* 1.3 53.6 + - - +
70C SER 3.4 1.1 - - - -
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Residues in contact with SER 69 (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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68A ARG* 4.2 4.0 - - - +
65C LYS 3.1 18.6 + - - -
66C ALA* 3.6 10.4 + - - -
67C MET 3.3 0.4 - - - -
68C ARG* 1.3 74.5 - - - +
70C SER* 1.3 62.2 + - - +
71C PHE* 3.4 22.4 - - - -
74C MET* 4.9 2.3 - - - +
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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