Contacts of the helix formed by residues 52 - 63 (chain C) in PDB entry 1YFJ
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 GLN 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C TYR* 3.7 14.5 + - - -
50C ASP* 3.0 11.3 + - - +
51C ILE* 1.3 75.1 - - - +
53C GLU* 1.3 59.8 + - - +
54C PRO* 3.3 8.4 - - + +
55C ILE* 2.9 40.5 + - + +
56C ILE* 3.2 11.4 + - - +
115C ILE 4.7 9.9 + - - +
117C ILE* 4.7 18.5 + - - +
180C ASP* 5.2 5.5 + - - +
181C TYR* 4.0 14.5 - - - +
183C LYS* 5.3 1.9 - - - -
184C PHE* 3.6 29.3 - - + -
403C SAH 2.9 25.0 + - - +
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Residues in contact with GLU 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 ILE 3.2 8.0 + - - +
52C GLN* 1.3 69.0 - - - +
54C PRO* 1.3 68.1 - - + +
56C ILE 3.1 1.5 + - - +
57C GLU* 2.7 52.7 + - + +
154C SER* 3.6 28.2 + - - +
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Residues in contact with PRO 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 GLN* 3.3 10.1 - - + +
53C GLU* 1.3 92.4 - - + +
55C ILE* 1.3 56.3 + - + +
57C GLU* 3.5 6.0 + - + +
58C MET* 2.9 27.7 + - - +
94C TYR* 3.8 21.5 - - - +
100C PRO* 5.3 0.7 - - - +
103C LEU* 3.5 14.8 - - + +
117C ILE* 4.1 35.2 - - + -
121C GLY* 5.5 2.9 - - - +
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Residues in contact with ILE 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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5C ILE* 4.9 2.5 - - + -
7C TYR* 3.9 21.5 - - + +
34C GLY* 4.5 4.9 - - - +
50C ASP* 5.5 5.4 - - + +
52C GLN* 2.9 44.1 + - + +
54C PRO* 1.3 75.4 - - + +
56C ILE* 1.3 67.0 + - + +
58C MET* 3.1 12.7 + - + +
59C TYR* 3.0 55.7 + - + +
103C LEU* 4.6 2.5 - - + -
115C ILE* 4.2 35.9 - - + +
117C ILE* 5.6 0.4 - - + -
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Residues in contact with ILE 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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33C CYS* 3.8 26.9 - - - -
48C ALA 4.2 4.5 - - - +
50C ASP* 3.5 22.4 - - + +
52C GLN 3.2 4.9 + - - +
53C GLU 3.1 6.1 + - - +
55C ILE* 1.3 76.2 - - + +
57C GLU* 1.3 66.8 + - - +
59C TYR* 3.1 19.0 + - + +
60C LYS* 3.0 30.7 + - + +
152C PHE* 3.8 21.1 - - + -
153C SER* 3.2 36.1 - - - +
154C SER* 3.8 11.0 - - - +
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Residues in contact with GLU 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 GLU* 2.7 47.1 + - + +
54C PRO* 3.8 6.7 - - + +
56C ILE* 1.3 75.5 - - - +
58C MET* 1.3 62.6 + - - +
60C LYS* 3.2 40.3 + - - +
61C ARG* 3.1 22.3 + - - +
100C PRO* 3.8 17.9 - - + +
154C SER* 5.1 1.6 + - - -
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Residues in contact with MET 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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5C ILE* 4.2 20.2 - - + -
54C PRO 2.9 14.9 + - - +
55C ILE* 3.1 16.5 + - + +
57C GLU* 1.3 76.8 - - - +
59C TYR* 1.3 92.1 + - + +
61C ARG* 3.2 4.2 + - - +
62C LEU* 2.9 25.8 + - + +
100C PRO* 3.5 28.4 - - + +
103C LEU* 4.0 15.9 - - + +
104C TYR* 3.5 47.1 - - + -
107C HIS* 5.5 1.1 - - - +
115C ILE* 4.9 7.2 - - + -
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Residues in contact with TYR 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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4C ALA* 3.9 19.7 - - + -
5C ILE* 3.7 9.1 - - + +
33C CYS* 5.2 0.7 - - - -
34C GLY 2.6 27.5 + - - -
35C GLY* 3.5 11.8 - - - -
36C LEU* 3.7 19.5 - - + -
55C ILE* 3.0 39.4 + - + +
56C ILE* 3.1 16.8 + - + +
58C MET* 1.3 96.4 - - + +
60C LYS* 1.3 64.0 + - - +
62C LEU* 3.0 18.9 + - + +
63C ILE* 3.2 15.8 + - - +
143C PHE* 3.7 13.7 - + + -
152C PHE* 3.7 39.3 - + + -
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Residues in contact with LYS 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 ILE* 3.0 27.3 + - + +
57C GLU* 3.2 40.6 + - - +
59C TYR* 1.3 75.3 - - - +
61C ARG* 1.3 59.5 + - - +
63C ILE* 3.3 26.9 - - + +
64C ASN* 3.8 8.7 - - - +
152C PHE* 3.9 26.5 + - + +
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Residues in contact with ARG 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 GLU 3.1 12.6 + - - +
58C MET 3.6 7.6 - - - +
59C TYR 3.0 1.0 - - - -
60C LYS* 1.3 74.1 - - - +
62C LEU* 1.3 60.9 + - + +
63C ILE 3.0 2.2 - - - -
64C ASN* 2.8 27.5 + - - +
65C VAL* 3.2 28.9 - - + +
99C ASP* 2.8 36.6 + - - -
100C PRO* 3.7 22.2 - - + +
101C LEU* 3.3 36.9 - - + +
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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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4C ALA* 5.3 3.1 - - + -
58C MET* 2.9 21.5 + - + +
59C TYR* 3.0 22.2 + - + +
61C ARG* 1.3 77.9 - - + +
63C ILE* 1.3 62.9 + - - +
64C ASN 2.9 1.6 + - - -
65C VAL* 3.1 32.7 + - + +
101C LEU* 4.8 5.8 - - + -
104C TYR* 3.6 60.8 - - + +
140C PHE* 4.3 7.9 - - + -
143C PHE* 3.6 27.6 - - + -
144C LYS* 3.4 13.7 - - - +
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Residues in contact with ILE 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 TYR 3.2 10.4 + - - +
60C LYS* 3.3 22.9 - - + +
61C ARG 3.0 0.2 - - - -
62C LEU* 1.3 77.3 - - - +
64C ASN* 1.3 73.3 + - - +
65C VAL 3.6 0.2 - - - -
143C PHE* 4.0 9.6 - - + -
144C LYS* 3.2 19.6 + - - +
147C CYS* 4.0 26.8 - - + +
150C ILE 5.5 2.5 - - - +
152C PHE* 3.7 27.1 - - + -
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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