Contacts of the helix formed by residues 52 - 62 (chain C) in PDB entry 1RX0
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 PRO 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C TRP* 3.5 40.2 - - + +
50C LEU* 3.0 14.1 - - + +
51C PHE* 1.3 77.9 - - + +
53C VAL* 1.3 64.5 + - - +
54C ASP 3.4 2.0 - - - -
55C VAL* 3.3 6.8 + - + +
56C MET* 3.0 33.9 + - + +
97C THR* 3.7 32.1 - - + +
218C SER* 3.8 12.3 - - - +
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Residues in contact with VAL 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 PHE* 2.7 38.8 + - + +
52C PRO* 1.3 71.8 - - - +
54C ASP* 1.3 70.6 + - - +
56C MET* 3.3 7.8 + - - +
57C ARG* 3.0 62.5 + - - +
133C PHE* 3.9 14.5 - - + -
175C GLU* 4.5 8.5 - - - +
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Residues in contact with ASP 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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52C PRO 3.4 0.6 - - - -
53C VAL* 1.3 85.7 - - - +
55C VAL* 1.3 65.6 + - + +
57C ARG* 3.3 12.8 + - - +
58C LYS* 3.1 33.1 + - - +
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Residues in contact with VAL 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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33C PHE* 3.4 23.6 - - + -
37C GLU* 4.0 26.9 - - + +
38C MET* 4.2 4.7 - - + -
41C ASN* 4.9 3.6 - - - +
45C TRP* 3.7 39.0 - - + +
52C PRO* 3.3 9.4 + - + +
53C VAL 3.3 0.4 - - - -
54C ASP* 1.3 76.2 - - + +
56C MET* 1.3 68.2 + - + +
58C LYS* 3.0 14.6 + - + +
59C ALA 3.0 17.7 + - - -
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Residues in contact with MET 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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51C PHE* 3.5 42.4 - - + -
52C PRO* 3.0 36.0 + - + +
53C VAL 3.8 3.6 - - - +
55C VAL* 1.3 77.4 - - + +
57C ARG* 1.3 58.9 + - - +
59C ALA* 3.1 10.5 + - - +
60C ALA 2.9 22.7 + - - -
97C THR* 4.1 27.1 - - + -
100C TYR* 3.7 26.2 - - - -
101C ILE* 4.3 13.2 - - + -
130C MET* 3.4 22.4 - - - +
133C PHE* 3.8 11.4 - - + -
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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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53C VAL* 3.0 42.2 + - - +
54C ASP* 3.7 12.3 + - - +
55C VAL 3.2 0.2 - - - -
56C MET* 1.3 73.8 - - - +
58C LYS* 1.3 64.5 + - - +
60C ALA* 3.3 8.6 + - - +
61C GLN* 3.0 32.4 + - - +
129C THR 4.1 6.5 - - - +
130C MET* 2.8 29.3 + - + +
131C GLU* 3.0 29.4 + - - +
133C PHE* 4.0 10.7 - - + -
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Residues in contact with LYS 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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33C PHE* 3.7 13.4 - - + -
37C GLU* 3.0 41.3 + - + +
54C ASP* 3.1 25.8 + - - +
55C VAL* 3.0 16.3 + - - +
57C ARG* 1.3 77.0 - - - +
59C ALA* 1.3 63.6 + - - +
61C GLN* 3.1 35.2 + - - +
62C LEU* 3.4 11.6 + - - +
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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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33C PHE* 3.6 28.0 - - + -
55C VAL 3.0 8.6 + - - +
56C MET* 3.1 13.4 + - - +
58C LYS* 1.3 77.2 - - - +
60C ALA* 1.3 61.7 - - - +
62C LEU* 3.0 14.9 + - - +
63C GLY 3.3 0.2 + - - -
64C PHE* 3.1 38.0 + - + +
90C LEU* 5.6 0.9 - - + -
101C ILE* 4.7 14.6 - - + -
130C MET* 5.7 0.9 - - - -
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Residues in contact with ALA 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 MET 2.9 12.3 + - - +
57C ARG 3.5 6.1 - - - +
58C LYS 3.2 0.2 - - - -
59C ALA* 1.3 76.6 - - - +
61C GLN* 1.3 59.3 + - - +
63C GLY* 2.9 18.4 + - - -
65C GLY* 3.7 12.3 - - - +
128C CYS 3.6 21.0 - - - +
129C THR* 3.4 29.9 - - - +
130C MET* 3.7 13.4 - - + -
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Residues in contact with GLN 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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54C ASP 5.2 0.2 + - - -
57C ARG* 3.0 28.2 + - - +
58C LYS* 3.2 32.0 - - - +
60C ALA* 1.3 76.9 - - + +
62C LEU* 1.3 62.4 + - + +
63C GLY* 3.2 0.6 + - - -
129C THR 6.0 0.4 - - - +
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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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29C VAL* 4.0 23.4 - - + +
33C PHE* 3.5 38.6 - - + -
36C ARG* 5.4 3.4 - - - +
58C LYS 3.7 9.2 - - - +
59C ALA 3.0 8.8 + - - +
61C GLN* 1.3 79.6 - - + +
63C GLY* 1.3 58.8 + - - +
64C PHE* 3.6 30.7 - - + -
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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