Contacts of the helix formed by residues 66 - 70 (chain D) in PDB entry 4IL6
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 SER 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D GLY 3.8 0.7 - - - -
52D THR 3.0 11.2 - - - -
53D THR 3.6 6.7 - - - -
54D PHE 3.8 6.2 + - - -
55D VAL 3.3 31.0 + - - -
65D SER* 1.3 79.4 - - - +
67D TYR* 1.3 63.6 + - - +
68D LEU* 3.7 2.4 + - - +
69D GLU* 2.9 39.5 + - - +
70D GLY 3.3 0.2 + - - -
71D CYS* 3.1 16.6 + - - +
76D VAL* 3.6 6.1 - - - -
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TRP* 5.4 2.4 - - - -
49D LEU* 6.4 1.6 - - + -
52D THR* 2.8 28.4 + - - -
53D THR* 3.5 24.0 + - - +
66D SER* 1.3 72.3 - - - +
68D LEU* 1.3 58.6 + - - +
70D GLY 3.0 4.3 + - - -
71D CYS 3.4 18.4 - - - +
73D PHE* 3.6 23.7 - - - -
76D VAL* 3.4 30.6 - - + +
406D BCR 5.6 1.1 - - + -
412D LMG 2.8 94.3 + - + +
37F ILE* 3.8 18.6 - - + -
40F MET* 3.5 17.0 - - - -
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Residues in contact with LEU 68 (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 THR 3.0 17.0 + - - +
54D PHE* 3.9 20.4 - - + +
66D SER* 3.1 6.9 - - - +
67D TYR* 1.3 76.5 - - - +
69D GLU* 1.3 57.0 + - - +
412D LMG 4.4 1.0 + - - -
38E VAL* 4.2 10.1 - - + -
43E ALA* 4.1 23.3 - - + -
44E TYR* 3.8 50.1 + - + +
49E THR* 4.1 9.9 - - + -
40F MET* 3.4 20.8 - - + -
43F ILE* 4.0 16.4 - - + +
36J LEU* 3.4 19.1 - - - +
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Residues in contact with GLU 69 (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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306A VAL* 3.5 20.6 - - - +
56D THR* 2.7 39.9 + - - -
64D ALA* 3.5 21.3 - - + -
65D SER 3.0 19.2 + - - -
66D SER* 2.9 25.9 + - - +
68D LEU* 1.3 77.2 - - - +
70D GLY* 1.3 56.2 + - - +
71D CYS 3.7 0.4 - - - -
44E TYR* 6.4 0.2 - - - -
49E THR* 3.6 17.2 - - + +
50E PRO* 4.4 1.7 - - - +
55E TYR* 2.6 33.4 + - - +
36J LEU* 3.7 15.6 - - - +
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Residues in contact with GLY 70 (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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306A VAL* 4.0 8.1 - - - +
67D TYR 3.0 6.5 + - - -
68D LEU 3.3 0.6 + - - -
69D GLU* 1.3 80.4 - - - +
71D CYS* 1.3 63.8 + - - +
72D ASN* 3.9 1.0 + - - -
412D LMG 3.3 27.2 + - - -
36J LEU* 3.8 12.8 - - - -
37J GLY* 3.2 22.8 - - - -
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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