Contacts of the helix formed by residues 52 - 63 (chain D) in PDB entry 1YFL
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D TYR* 4.8 2.4 + - - -
50D ASP* 2.9 11.0 + - - +
51D ILE* 1.3 76.1 - - - +
53D GLU* 1.3 65.5 + - - +
54D PRO* 3.3 4.6 - - - +
55D ILE* 3.2 36.6 + - + +
56D ILE* 3.3 13.9 + - - +
115D ILE 3.9 19.2 + - - -
117D ILE* 3.6 27.3 - - - +
180D ASP* 4.8 1.4 + - - -
181D TYR* 4.6 7.9 - - - +
183D LYS* 4.1 13.2 + - - +
184D PHE* 3.9 29.4 - - + -
302D SFG 3.1 24.2 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE 2.7 9.7 + - - +
52D GLN* 1.3 69.4 - - - +
54D PRO* 1.3 73.9 - - + +
56D ILE* 3.8 1.6 - - + +
57D GLU* 2.9 40.0 + - + +
154D SER* 3.1 35.8 + - - +
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Residues in contact with PRO 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLN* 3.4 7.9 - - - +
53D GLU* 1.3 96.0 - - + +
55D ILE* 1.3 58.0 + - - +
57D GLU* 3.6 7.6 + - + +
58D MET 3.2 14.6 + - - -
94D TYR* 4.0 18.0 + - - +
98D ARG* 6.3 1.1 - - - +
100D PRO* 5.2 1.6 - - - +
103D LEU* 3.4 15.9 - - + +
117D ILE* 3.2 42.4 - - + -
121D GLY* 5.2 6.3 - - - +
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.7 4.9 - - + -
7D TYR* 3.7 28.9 - - + +
34D GLY* 4.7 2.7 - - - +
50D ASP* 5.4 3.6 - - - +
52D GLN* 3.2 36.3 + - + +
54D PRO* 1.3 77.3 - - + +
56D ILE* 1.3 63.5 + - + +
58D MET* 2.8 38.1 + - + +
59D TYR* 3.0 42.2 + - + +
103D LEU* 4.5 2.7 - - + -
115D ILE* 4.1 29.2 - - + -
117D ILE* 5.1 0.2 - - + -
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Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D CYS* 4.3 11.0 - - - -
48D ALA 4.6 3.1 - - - +
49D ASN 4.6 0.2 - - - -
50D ASP* 3.3 36.3 - - + +
52D GLN 3.3 8.7 + - - +
53D GLU* 3.8 5.2 - - + +
55D ILE* 1.3 76.4 - - + +
57D GLU* 1.3 64.2 + - + +
59D TYR* 3.1 27.7 + - + +
60D LYS* 3.2 25.1 + - - +
152D PHE* 3.7 23.1 - - + -
153D SER* 3.1 33.7 - - - +
154D SER* 3.9 9.9 - - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 2.9 37.6 + - + +
54D PRO* 3.7 7.9 - - + +
56D ILE* 1.3 77.2 - - - +
58D MET* 1.3 60.7 + - - +
60D LYS* 2.6 40.3 + - - +
61D ARG* 3.2 14.9 + - - +
100D PRO* 3.5 25.5 - - + +
154D SER* 5.5 0.5 + - - -
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Residues in contact with MET 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.0 22.4 - - + -
54D PRO 3.2 12.6 + - - +
55D ILE* 2.8 36.4 + - + +
57D GLU* 1.3 76.9 - - - +
59D TYR* 1.3 75.0 + - + +
61D ARG* 3.1 2.4 + - - +
62D LEU* 2.9 24.6 + - + +
100D PRO* 3.6 14.6 - - + +
101D LEU* 5.7 0.2 - - - -
103D LEU* 3.8 17.0 - - + +
104D TYR* 3.3 60.6 - - + +
107D HIS* 5.3 1.6 - - - +
115D ILE* 4.4 7.2 - - + -
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Residues in contact with TYR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ALA* 4.2 12.6 - - + -
5D ILE* 4.2 6.6 - - + +
34D GLY 2.2 36.7 + - - -
35D GLY* 3.5 7.8 - - - -
36D LEU* 3.7 28.9 - - + -
55D ILE* 3.0 41.6 + - + +
56D ILE* 3.1 21.7 + - + +
58D MET* 1.3 88.2 - - + +
60D LYS* 1.3 65.1 + - - +
62D LEU* 2.9 25.2 + - + +
63D ILE* 3.1 15.4 + - - +
143D PHE* 3.8 13.7 - + + -
152D PHE* 3.7 33.9 - + + -
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 5.8 0.2 + - - -
56D ILE* 3.2 28.3 + - - +
57D GLU* 2.6 42.4 + - - +
59D TYR* 1.3 78.2 - - - +
61D ARG* 1.3 62.5 + - - +
63D ILE* 3.6 22.8 - - + +
64D ASN* 3.8 9.7 - - - +
152D PHE* 4.3 29.0 + - + +
154D SER* 5.5 3.2 + - - -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU 3.2 6.6 + - - +
58D MET 3.1 8.6 + - - +
59D TYR 3.0 0.8 - - - -
60D LYS* 1.3 75.2 - - - +
62D LEU* 1.3 68.6 + - + +
63D ILE 3.0 1.3 - - - -
64D ASN* 2.8 22.6 + - - +
65D VAL* 3.2 27.7 - - + +
69D ASP* 6.3 0.4 - - - +
99D ASP* 2.6 33.5 + - - -
100D PRO* 3.6 23.5 - - + +
101D LEU* 3.3 32.2 - - + +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ALA* 5.8 2.5 - - + +
5D ILE* 5.6 1.6 - - + -
58D MET* 2.9 20.4 + - + +
59D TYR* 2.9 24.4 + - + +
61D ARG* 1.3 77.6 - - + +
63D ILE* 1.3 57.8 + - - +
64D ASN 2.8 6.9 + - - -
65D VAL* 3.0 27.9 + - + +
101D LEU* 5.2 3.6 - - + -
104D TYR* 3.6 57.7 - - + -
140D PHE* 4.0 19.4 - - + -
143D PHE* 3.7 24.2 - - + -
144D LYS* 3.0 13.6 + - - -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR 3.1 12.6 + - - +
60D LYS* 3.6 17.3 - - + +
61D ARG 2.8 1.0 + - - -
62D LEU* 1.3 75.2 - - - +
64D ASN* 1.3 70.4 + - - +
65D VAL 3.7 0.2 - - - -
143D PHE* 3.9 17.0 - - + -
144D LYS* 3.6 14.7 + - - +
147D CYS* 4.2 21.1 - - + +
150D ILE 5.9 1.8 - - - +
152D PHE* 4.0 26.0 - - + -
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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