Contacts of the helix formed by residues 42 - 53 (chain B) in PDB entry 3IO6
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 LYS 42 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASN* 5.6 2.0 + - - -
40B PRO 3.8 0.4 + - - -
41B ASP* 1.3 82.3 + - + +
43B LEU* 1.3 62.0 + - - +
44B GLU* 3.2 16.4 - - - +
45B GLU* 3.2 42.0 + - + +
46B LYS* 3.1 33.9 + - + +
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Residues in contact with LEU 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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10B TRP* 4.1 23.2 - - + -
11B ILE 3.6 33.2 - - - +
12B ASN* 3.8 15.4 + - + +
40B PRO* 3.4 40.8 + - + +
41B ASP 2.8 7.1 + - - -
42B LYS* 1.3 69.2 - - - +
44B GLU* 1.3 65.0 + - - +
45B GLU 3.0 5.2 - - - -
46B LYS* 4.1 7.6 - - - -
47B PHE* 2.9 34.5 + - - +
60B ILE* 4.2 19.1 - - + -
61B PHE 4.7 2.9 - - - +
62B TRP* 4.3 16.2 - - + -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 5.3 1.0 - - - +
42B LYS* 3.5 10.7 - - - +
43B LEU* 1.3 89.9 + - - +
45B GLU* 1.3 77.5 + - - +
48B PRO* 3.8 3.0 - - - +
60B ILE* 5.5 0.2 - - - -
62B TRP* 3.3 55.4 - - + +
66B ARG* 3.5 33.8 + - + +
70B TYR* 2.6 30.5 + - - +
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Residues in contact with GLU 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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42B LYS* 3.2 53.5 + - + +
43B LEU 3.0 0.2 - - - -
44B GLU* 1.3 90.4 - - + +
46B LYS* 1.3 67.0 + - + +
48B PRO* 3.4 12.1 - - - +
49B GLN* 3.6 20.6 + - - +
66B ARG* 4.5 12.1 - - - +
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Residues in contact with LYS 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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10B TRP* 4.5 10.1 - - + -
40B PRO* 5.2 9.4 - - + +
41B ASP* 3.5 34.7 + - - +
42B LYS* 3.1 28.3 + - + +
43B LEU* 3.1 6.9 + - - +
45B GLU* 1.3 80.7 - - + +
47B PHE* 1.3 65.1 + - - +
48B PRO 3.4 0.2 - - - -
49B GLN* 3.1 27.2 + - - +
50B VAL* 3.2 19.3 + - + +
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Residues in contact with PHE 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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10B TRP* 3.9 11.4 - + + -
43B LEU 2.9 16.8 + - - +
46B LYS* 1.3 76.2 - - - +
48B PRO* 1.4 64.0 - - + +
50B VAL* 3.3 2.3 + - - +
51B ALA* 2.9 46.1 + - + +
57B PRO* 3.6 34.1 - - + -
60B ILE* 3.6 27.8 - - + -
70B TYR* 3.8 26.9 - + - +
75B LEU* 4.1 9.4 - - + -
76B LEU* 3.9 30.1 - - + -
267B ASN* 3.6 33.0 - - + -
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Residues in contact with PRO 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 GLU 3.8 9.0 - - - +
45B GLU* 3.4 22.2 - - - +
47B PHE* 1.4 95.2 - - + +
49B GLN* 1.3 57.0 + - + -
51B ALA* 4.7 0.2 - - + -
52B ALA* 3.1 26.1 + - - +
66B ARG* 5.0 4.9 - - - +
70B TYR* 3.4 25.8 - - + -
75B LEU* 3.9 26.3 - - + +
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Residues in contact with GLN 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 GLU* 3.6 21.5 + - - +
46B LYS* 3.1 20.3 + - - +
47B PHE 3.1 1.0 - - - -
48B PRO* 1.3 81.9 - - + +
50B VAL* 1.3 63.6 + - + +
52B ALA* 4.0 3.5 - - - +
53B THR* 3.7 21.5 + - - +
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Residues in contact with VAL 50 (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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10B TRP* 4.0 18.4 - - + -
46B LYS* 3.2 17.2 + - + +
47B PHE* 3.6 5.4 - - - +
49B GLN* 1.3 78.0 - - + +
51B ALA* 1.3 61.9 + - - +
52B ALA 3.2 1.6 - - - -
53B THR* 3.0 16.7 + - - +
54B GLY 3.2 0.3 + - - -
55B ASP* 2.7 48.7 + - + +
56B GLY* 3.8 19.7 - - - -
57B PRO* 4.8 1.3 - - + -
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Residues in contact with ALA 51 (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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47B PHE* 2.9 33.5 + - + +
50B VAL* 1.3 75.6 - - - +
52B ALA* 1.3 60.4 + - - +
54B GLY* 3.0 18.1 + - - -
55B ASP 3.4 11.0 - - - +
75B LEU* 3.7 22.5 - - + +
267B ASN* 3.6 24.2 - - - +
269B ALA* 4.8 3.6 - - - +
356C THR* 4.4 6.2 + - - -
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Residues in contact with ALA 52 (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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48B PRO 3.1 22.4 + - - +
49B GLN* 4.0 7.2 - - - +
51B ALA* 1.3 79.0 - - - +
53B THR* 1.3 58.6 + - + +
54B GLY 3.3 1.6 + - - -
75B LEU* 3.6 12.8 - - + +
354C ARG 4.4 0.2 - - - -
355C GLN* 3.2 39.5 - - + +
356C THR* 3.3 10.6 + - - -
359C ALA* 4.1 8.1 - - + +
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Residues in contact with THR 53 (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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1B LYS* 6.1 0.2 - - - +
49B GLN 3.7 12.3 - - - +
50B VAL* 3.0 22.4 + - - +
52B ALA* 1.3 75.7 - - + +
54B GLY* 1.3 60.3 + - - +
55B ASP* 4.2 8.0 - - - +
353C GLY 4.4 10.2 - - - +
354C ARG* 3.4 27.4 - - - +
355C GLN* 4.5 0.9 - - - +
356C THR* 4.5 3.9 - - - +
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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