Contacts of the helix formed by residues 45 - 60 (chain J) in PDB entry 1C17
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 LEU 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43J PRO* 3.2 11.1 - - + -
44J ASP* 1.3 79.2 - - - +
46J ILE* 1.3 85.1 + - + +
48J LEU* 4.1 1.1 - - - +
49J LEU* 3.7 18.4 + - - +
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Residues in contact with ILE 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J PRO* 5.5 6.7 - - + -
45J LEU* 1.3 98.6 - - + +
47J PRO* 1.3 78.8 - - + +
48J LEU 3.2 0.2 - - - -
49J LEU* 3.1 21.8 + - + +
50J ARG* 3.1 14.9 + - + +
44K ASP* 4.3 24.9 - - + +
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Residues in contact with PRO 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J PHE* 4.6 2.5 - - + -
36J LEU* 6.5 0.4 - - + -
39J ALA* 3.7 40.4 - - + +
42J GLN* 4.5 10.8 - - + +
43J PRO* 2.6 30.3 - - + +
44J ASP* 4.3 2.0 - - - -
46J ILE* 1.3 97.7 - - + +
48J LEU* 1.3 54.6 + - - +
50J ARG* 4.3 7.9 - - + -
51J THR* 2.4 48.0 + - - +
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Residues in contact with LEU 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ILE* 6.1 2.0 - - + -
50I ARG* 4.3 28.4 + - + +
44J ASP* 2.7 48.0 - - + +
45J LEU 4.1 2.7 - - - +
46J ILE 3.2 0.8 - - - -
47J PRO* 1.3 81.6 - - - +
49J LEU* 1.3 60.6 + - - +
51J THR* 3.8 6.4 - - - -
52J GLN* 3.2 33.8 + - + +
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J LEU 3.7 12.2 + - - +
46J ILE* 3.1 15.4 + - + +
48J LEU* 1.3 78.8 - - + +
50J ARG* 1.3 64.1 + - + +
52J GLN* 2.7 40.8 - - + +
53J PHE* 3.3 10.7 + - + +
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Residues in contact with ARG 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J PHE* 3.3 20.6 - - + -
46J ILE* 3.1 15.3 + - + +
47J PRO* 3.8 4.5 - - + +
49J LEU* 1.3 78.0 - - + +
51J THR* 1.3 65.5 + - - +
53J PHE* 3.1 37.5 + - - +
54J PHE* 3.0 48.8 + - - -
48K LEU* 4.4 26.6 + - + +
51K THR* 4.0 13.5 - - - +
52K GLN* 4.3 12.5 - - - +
55K ILE* 3.3 27.8 - - - +
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Residues in contact with THR 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I PHE* 5.9 1.1 - - + -
50I ARG* 3.9 17.3 - - - +
54I PHE* 4.3 15.7 - - + -
32J GLY* 4.9 8.0 - - - +
35J PHE* 3.0 28.1 - - + -
36J LEU* 5.1 15.7 - - + +
39J ALA* 5.7 0.2 - - - +
47J PRO* 2.4 33.1 + - - +
48J LEU* 3.8 7.4 - - - -
50J ARG* 1.3 73.0 - - - +
52J GLN* 1.3 62.6 + - - +
54J PHE* 3.1 4.5 + - - +
55J ILE* 3.0 27.5 + - + +
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Residues in contact with GLN 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ARG* 4.2 8.7 - - - +
53I PHE* 6.2 2.2 - - + -
48J LEU* 3.2 21.1 + - + +
49J LEU* 2.7 47.1 - - + +
51J THR* 1.3 76.0 - - - +
53J PHE* 1.3 60.6 + - + +
55J ILE* 3.4 12.8 - - + -
56J VAL* 2.7 52.0 + - + +
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Residues in contact with PHE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J LEU* 3.7 12.8 - - + +
50J ARG* 3.1 44.6 + - - +
52J GLN* 1.3 82.3 - - - +
54J PHE* 1.3 57.3 + + - +
56J VAL* 4.2 3.9 - - + +
57J MET* 2.9 51.9 + - + +
52K GLN* 6.4 0.9 - - + -
55K ILE* 5.5 1.8 - - + -
56K VAL* 6.5 1.1 - - + -
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Residues in contact with PHE 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ILE* 5.3 0.3 - - - -
31J LEU* 3.0 49.8 - - + +
32J GLY* 5.2 0.2 - - - -
35J PHE* 3.3 39.5 - + + -
50J ARG* 3.0 44.4 + - - -
51J THR* 3.1 7.2 + - - +
52J GLN 3.0 1.6 + - - -
53J PHE* 1.3 73.9 - + - +
55J ILE* 1.3 60.9 + - + +
56J VAL 2.9 1.1 - - - -
57J MET* 2.6 32.6 + - + +
58J GLY* 2.9 10.2 + - - -
32K GLY 5.3 2.5 - - - -
51K THR* 4.3 7.4 - - + -
55K ILE* 3.3 49.8 - - + -
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Residues in contact with ILE 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ARG* 3.3 26.9 - - - +
53I PHE* 5.4 2.2 - - + -
54I PHE* 3.2 39.3 - - + -
57I MET* 4.4 15.8 - - + +
28J ILE* 3.2 34.4 - - + +
32J GLY* 3.4 28.5 - - - -
51J THR* 3.0 11.2 + - + +
52J GLN* 3.2 16.2 - - + +
54J PHE* 1.3 76.6 - - - +
56J VAL* 1.3 63.8 + - + +
59J LEU* 2.9 22.7 + - - +
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Residues in contact with VAL 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I PHE* 6.3 2.0 - - + -
57I MET* 5.5 3.8 - - + -
52J GLN* 2.7 46.7 + - + +
53J PHE* 4.2 3.8 - - + +
55J ILE* 1.3 77.1 - - + +
57J MET* 1.3 51.0 + - - +
58J GLY 2.8 4.5 - - - -
59J LEU* 2.6 36.4 + - + -
60J VAL* 2.7 37.8 + - + +
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Residues in contact with MET 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J LEU* 5.0 2.2 - - + -
53J PHE* 2.9 59.3 + - + +
54J PHE* 2.6 22.6 + - + +
56J VAL* 1.3 72.9 - - - +
58J GLY* 1.3 56.1 + - - -
60J VAL* 3.6 8.5 + - - +
61J ASP* 3.4 17.8 + - - +
28K ILE* 4.2 26.0 - - + -
55K ILE* 4.4 20.0 - - + +
56K VAL* 5.7 3.4 - - + -
59K LEU* 4.1 39.3 - - + +
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Residues in contact with GLY 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ALA* 3.0 34.6 - - - +
27J GLY* 5.2 1.8 - - - -
28J ILE* 3.0 26.3 - - - +
31J LEU* 6.1 1.1 - - - +
54J PHE 2.9 9.0 + - - -
56J VAL 2.8 0.8 - - - -
57J MET* 1.3 76.6 - - - +
59J LEU* 1.3 55.2 + - - +
60J VAL 3.0 5.2 - - - -
61J ASP* 3.1 10.6 + - - -
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Residues in contact with LEU 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I MET* 4.0 38.1 - - + +
61I ASP* 5.3 9.9 - - + +
28J ILE* 2.9 14.6 - - + +
55J ILE 2.9 14.9 + - - +
56J VAL* 2.6 25.8 + - + +
58J GLY* 1.3 72.7 - - - +
60J VAL* 1.3 58.5 + - + +
61J ASP 3.5 0.4 - - - -
62J ALA* 4.6 5.8 - - + +
63J ILE* 3.7 20.3 + - + +
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Residues in contact with VAL 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J VAL* 2.7 35.2 + - + +
57J MET* 3.9 9.0 - - - +
58J GLY 3.0 0.2 - - - -
59J LEU* 1.3 83.6 - - + +
61J ASP* 1.3 50.8 + - - +
62J ALA 3.3 2.0 - - - -
63J ILE* 4.0 17.3 - - + -
64J PRO* 2.7 35.6 - - + +
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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