Contacts of the helix formed by residues 41 - 49 (chain B) in PDB entry 4I6J
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 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LEU* 1.3 88.8 - - + +
42B ASP* 1.3 58.4 + - - +
43B ILE 2.9 5.4 - - - +
44B ILE* 3.3 13.4 + - - +
45B LEU* 3.0 26.2 + - - +
65B ASN* 2.8 36.1 + - - +
68B GLN* 2.8 40.2 + - - +
69B VAL* 3.7 23.4 - - + +
72B MET* 4.8 7.9 - - - +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 3.3 18.4 - - + +
41B GLN* 1.3 78.4 - - - +
43B ILE* 1.3 63.0 + - - +
45B LEU* 3.7 22.6 - - - +
46B GLN* 3.4 26.9 + - - +
72B MET* 5.1 5.4 - - - +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.7 32.5 - - + -
40B LEU* 3.5 34.7 - - + +
42B ASP* 1.3 76.4 - - - +
44B ILE* 1.3 60.7 + - - +
45B LEU 2.9 1.1 - - - -
46B GLN* 2.7 28.9 + - + +
47B VAL* 3.0 19.1 + - + +
104C ILE* 4.1 21.3 - - + +
105C LEU* 5.9 1.3 - - + -
108C ASN* 4.7 12.8 - - + +
116C LEU* 3.7 32.5 - - + -
120C CYS* 4.9 3.1 - - - -
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.9 20.9 - - + -
40B LEU 4.5 0.4 - - - -
41B GLN* 3.5 24.7 - - + +
43B ILE* 1.3 75.3 - - - +
45B LEU* 1.3 51.3 + - - +
47B VAL* 3.3 11.8 - - + +
48B PHE* 2.7 70.7 + - + -
65B ASN* 4.6 2.9 - - - +
66B TRP* 2.8 54.7 - - + +
69B VAL* 3.5 19.3 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN 3.0 14.8 + - - +
42B ASP* 3.7 20.9 - - - +
43B ILE 2.9 1.2 - - - -
44B ILE* 1.3 73.9 - - - +
46B GLN* 1.3 62.9 + - - +
48B PHE* 3.1 0.8 + - - +
49B LYS* 2.8 57.5 + - + +
69B VAL* 3.8 9.8 - - + +
72B MET* 3.3 33.4 - - + -
74B ASP* 4.3 19.7 - - + +
75B LEU* 3.8 33.9 - - + -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 3.4 21.0 + - - +
43B ILE* 2.7 17.0 + - + +
45B LEU* 1.3 79.1 - - - +
47B VAL* 1.3 62.6 + - - +
49B LYS* 3.3 44.6 + - - +
50B TYR* 3.7 15.6 - - + -
116C LEU* 3.9 20.3 - - + +
117C ASP* 5.7 3.9 - - - +
120C CYS* 3.5 20.0 - - + -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 6.2 1.3 - - + -
43B ILE* 3.0 19.2 + - + +
44B ILE* 3.3 13.9 - - + +
46B GLN* 1.3 75.9 - - - +
48B PHE* 1.3 62.4 + - + +
50B TYR* 2.8 30.4 + - - +
51B LEU* 3.8 7.3 - - + +
66B TRP* 5.7 2.2 - - + -
104C ILE* 5.5 1.1 - - + -
120C CYS* 3.9 24.6 - - + -
123C VAL* 4.0 22.7 - - + -
124C ALA* 4.1 12.3 - - + +
127C ILE* 3.9 27.4 - - + -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 2.7 54.9 + - + +
45B LEU* 3.1 7.6 + - - +
47B VAL* 1.3 73.0 - - + +
49B LYS* 1.3 55.2 + - - +
50B TYR 2.7 16.4 + - - -
51B LEU* 2.9 27.9 + - + +
56B ARG* 3.4 48.5 + - + -
59B ALA* 3.4 28.5 - - + -
60B SER* 3.8 12.1 - - - -
66B TRP* 4.2 15.7 - + - -
69B VAL* 3.8 8.1 - - + -
70B PHE* 4.3 12.1 - - - -
75B LEU* 3.8 26.5 - - + -
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 2.8 42.4 + - + +
46B GLN* 3.5 39.9 - - - +
47B VAL 3.2 0.6 - - - -
48B PHE* 1.3 75.7 - - - +
50B TYR* 1.3 65.2 + - + +
51B LEU 3.5 2.1 + - - +
56B ARG* 5.0 6.0 + - - +
74B ASP* 3.7 28.3 + - - +
75B LEU* 4.0 9.6 - - + +
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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