Contacts of the helix formed by residues 47 - 57 (chain C) in PDB entry 4YLO
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 TYR 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LYS* 3.9 39.4 - - + +
38C PHE 4.9 0.3 - - - +
40C GLU* 4.1 23.3 - - + +
42C ASP* 5.5 3.1 - - + -
45C GLY* 3.0 37.8 + - - +
46C GLN* 1.3 80.1 - - + +
48C GLY* 1.3 68.6 + - - +
49C LEU 3.4 0.3 + - - -
50C GLU* 3.1 14.0 + - - +
51C ALA* 3.1 11.3 + - - +
461C GLU* 4.6 5.2 - - - -
583C GLU* 3.5 35.2 + - + +
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Residues in contact with GLY 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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37C LYS 4.3 0.8 + - - -
38C PHE* 3.5 39.7 - - - +
47C TYR* 1.3 71.5 - - - +
49C LEU* 1.3 65.1 + - - -
51C ALA* 3.0 11.1 + - - +
52C ALA* 3.0 15.5 + - - +
457C GLY 5.6 0.2 - - - -
461C GLU* 3.8 19.5 + - - +
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Residues in contact with LEU 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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38C PHE* 3.4 28.1 + - + +
39C ILE* 5.1 6.1 - - + +
47C TYR 3.4 1.0 + - - -
48C GLY* 1.3 70.0 - - - +
50C GLU* 1.3 65.4 + - + +
52C ALA* 3.3 4.4 + - - +
53C PHE* 2.9 54.7 + - + -
73C TYR* 3.6 50.5 - - + +
96C LEU* 4.5 18.4 - - + -
464C PHE* 4.1 21.5 - - + -
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Residues in contact with GLU 50 (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 GLU 3.8 16.3 - - - +
41C GLN* 4.4 7.6 - - - +
42C ASP 3.6 21.6 - - - +
43C PRO* 4.0 14.0 - - - +
45C GLY 3.6 14.6 - - - +
46C GLN* 4.9 1.1 - - - -
47C TYR* 3.1 8.9 + - + +
49C LEU* 1.3 79.5 - - - +
51C ALA* 1.3 64.3 + - - +
53C PHE* 3.8 4.0 - - - +
54C ARG* 3.0 32.1 + - - +
70C TYR* 3.3 24.9 + - - -
73C TYR* 3.2 25.6 + - - +
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Residues in contact with ALA 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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46C GLN* 3.4 37.5 - - + +
47C TYR 3.1 4.2 + - - +
48C GLY 3.0 4.9 + - - +
50C GLU* 1.3 79.8 - - - +
52C ALA* 1.3 61.8 + - - +
54C ARG* 3.6 2.3 + - - +
55C SER* 3.1 24.6 + - - -
461C GLU* 3.2 25.8 - - - +
465C ARG* 3.6 13.9 + - - +
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Residues in contact with ALA 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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48C GLY 3.0 12.4 + - - +
49C LEU 3.8 0.4 - - - +
51C ALA* 1.3 74.3 - - - +
53C PHE* 1.3 66.1 + - - +
55C SER* 2.8 23.4 + - - -
56C VAL* 3.0 14.4 + - - +
461C GLU* 5.4 2.0 - - + -
464C PHE* 3.5 37.7 - - + -
465C ARG* 3.7 21.0 - - + +
468C LEU* 3.7 7.9 - - + -
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Residues in contact with PHE 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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49C LEU* 2.9 50.5 + - + +
50C GLU 3.8 2.5 - - - +
52C ALA* 1.3 77.7 - - - +
54C ARG* 1.3 52.9 + - - +
56C VAL 3.1 1.4 + - - -
57C PHE* 2.6 60.7 + + - +
70C TYR* 3.4 42.8 - + + -
73C TYR* 4.0 8.3 - + - -
96C LEU* 4.8 1.6 - - + -
98C VAL* 3.4 33.9 - - + -
124C MET* 4.0 28.7 - - + -
464C PHE* 4.3 7.4 - + - -
468C LEU* 4.5 7.9 - - + -
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Residues in contact with ARG 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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43C PRO* 4.2 21.6 + - - +
44C GLU* 5.0 9.7 + - - +
50C GLU* 3.0 20.9 + - - +
51C ALA* 4.5 2.2 - - - +
53C PHE* 1.3 77.5 - - - +
55C SER* 1.3 57.5 + - - +
57C PHE* 2.8 24.5 - - - +
58C PRO* 5.5 6.1 - - + -
70C TYR* 4.7 21.4 - - + -
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Residues in contact with SER 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 ALA 3.1 17.0 + - - -
52C ALA* 2.8 17.3 + - - -
53C PHE 3.1 0.2 - - - -
54C ARG* 1.3 78.1 - - - +
56C VAL* 1.3 66.6 + - - +
57C PHE 4.4 0.9 - - - +
180C ARG* 5.4 4.6 + - - -
465C ARG* 4.0 28.0 + - - -
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Residues in contact with VAL 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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52C ALA 3.0 17.3 + - - +
55C SER* 1.3 90.1 + - - +
57C PHE* 1.3 71.8 + - + +
58C PRO 3.9 2.1 - - - +
59C ILE* 3.0 51.5 + - + +
465C ARG* 6.1 0.9 - - + -
468C LEU* 3.4 38.1 - - + +
469C VAL* 6.2 0.2 - - - -
471C VAL* 5.3 1.3 - - + -
472C GLU* 4.9 15.0 - - + +
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Residues in contact with PHE 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 PHE* 2.6 44.1 + + - +
54C ARG* 2.8 25.4 - - - +
55C SER 4.4 1.0 - - - +
56C VAL* 1.3 92.4 - - + +
58C PRO* 1.3 71.9 - - + +
59C ILE* 4.0 13.2 - - + -
68C LEU* 3.2 41.7 - - + -
70C TYR* 3.6 29.8 - - + -
100C LEU* 3.5 33.0 - - + -
124C MET* 6.2 3.6 - - + -
468C LEU* 5.3 5.8 - - + -
471C VAL* 6.2 1.3 - - + -
475C VAL* 6.4 0.2 - - + -
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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