Contacts of the helix formed by residues 41 - 48 (chain E) 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 GLY 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E VAL 2.9 17.0 + - - -
39E SER 3.2 1.2 + - - -
40E THR* 1.3 77.4 + - - +
42E LEU* 1.3 63.9 + - - +
43E ALA 3.2 2.7 - - - -
44E TYR* 3.2 29.2 + - - +
45E ASP* 3.6 1.0 - - - +
51E ARG* 3.3 17.3 + - - -
4R ARG* 3.3 12.8 + - - -
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D HTG 4.3 11.2 - - - +
37E PHE* 3.4 29.0 + - + +
40E THR* 3.2 16.2 - - - +
41E GLY* 1.3 78.3 - - - +
43E ALA* 1.3 62.8 + - - +
45E ASP* 3.1 2.6 + - + -
46E VAL* 2.9 35.2 + - + +
2R ASP* 4.3 13.0 - - - +
4R ARG* 3.3 35.4 - - + +
5R VAL* 3.9 36.1 - - + +
8R VAL* 4.3 5.4 - - + -
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 4.0 18.4 - - + -
68D LEU* 4.1 13.3 - - + +
37E PHE* 2.9 49.9 + - + +
38E VAL* 4.4 7.6 - - + +
41E GLY 3.2 0.8 - - - -
42E LEU* 1.3 76.5 - - - +
44E TYR* 1.3 62.7 + - + +
47E PHE* 3.3 28.6 + - - +
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Residues in contact with TYR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 3.8 39.0 + - + +
38E VAL 4.6 6.5 - - - -
41E GLY* 3.2 32.8 + - - +
43E ALA* 1.3 76.7 - - + +
45E ASP* 1.3 58.5 + - - +
48E GLY* 2.8 26.2 + - - -
49E THR* 3.0 34.1 + - + +
50E PRO 3.9 5.4 - - - -
51E ARG* 3.7 55.0 - - + +
52E PRO* 4.2 8.5 - - + +
43F ILE* 3.6 32.7 - - + +
36J LEU* 5.2 0.4 - - + +
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Residues in contact with ASP 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 3.5 13.0 + - - +
419D HTG 3.6 25.3 + - - +
42E LEU* 3.1 6.7 + - + +
44E TYR* 1.3 75.0 - - - +
46E VAL* 1.3 67.3 + - - +
48E GLY* 3.8 4.1 + - - +
51E ARG* 3.3 28.2 + - - -
4R ARG* 2.5 36.0 + - - +
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Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 3.8 12.7 - - + -
102D THR* 2.7 27.3 + - - -
419D HTG 4.0 44.2 - - + +
37E PHE* 4.0 12.3 - - + -
42E LEU* 2.9 41.9 + - + +
43E ALA 4.0 3.6 - - - +
45E ASP* 1.3 75.9 - - - +
47E PHE* 1.3 83.3 - - + +
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Residues in contact with PHE 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR* 3.6 31.2 - - + -
54D PHE* 3.4 36.3 - + + +
55D VAL* 3.7 25.3 - - + +
56D THR* 5.6 1.0 - - - +
101D PHE* 3.8 29.6 - + - -
102D THR* 3.8 6.7 - - - +
105D CYS* 3.6 23.4 - - - +
106D GLN* 4.0 4.0 - - - +
110D LEU* 5.8 0.2 - - + -
419D HTG 4.1 13.0 - - + -
37E PHE* 3.7 22.4 - + - -
43E ALA 3.3 23.9 + - - +
46E VAL* 1.3 86.2 - - + +
48E GLY* 1.3 63.5 + - - +
49E THR* 3.9 14.4 + - - +
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Residues in contact with GLY 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D THR* 4.1 1.7 - - - +
59D TYR* 3.8 5.7 + - - -
102D THR* 3.5 11.7 - - - +
106D GLN* 2.9 36.4 + - - +
44E TYR 2.8 10.1 + - - -
45E ASP* 3.8 1.8 + - - -
46E VAL 3.5 2.2 - - - -
47E PHE* 1.3 79.6 - - - +
49E THR* 1.3 63.1 + - - +
50E PRO* 3.7 6.6 - - - +
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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