Contacts of the helix formed by residues 40 - 55 (chain B) in PDB entry 3S1K
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 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER 5.4 0.4 - - - +
37B ASP* 2.8 33.1 + - + +
39B SER* 1.3 85.4 + - - +
41B SER* 1.3 63.4 + - - +
42B ALA 3.3 2.7 - - - -
43B ASN* 3.2 41.2 + - - +
44B LEU* 2.8 39.3 + - + +
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Residues in contact with SER 41 (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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9B HIS* 3.5 8.5 + - - -
12B TYR* 3.4 33.8 - - - +
34B LEU* 2.8 33.8 - - - +
38B PRO* 2.2 30.4 + - - +
39B SER 3.4 1.0 - - - -
40B GLN* 1.3 76.6 - - - +
42B ALA* 1.3 57.3 + - - +
44B LEU* 3.3 2.9 + - - +
45B LEU* 2.9 29.3 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 4.0 30.2 - - + +
39B SER 5.2 1.5 + - - +
40B GLN 3.3 0.8 - - - -
41B SER* 1.3 78.5 - - - +
43B ASN* 1.3 69.5 + - - +
45B LEU* 3.1 4.5 + - - +
46B ALA* 3.0 23.7 + - - +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER 5.4 1.6 + - - -
40B GLN* 3.2 40.0 + - - +
42B ALA* 1.3 80.0 - - - +
44B LEU* 1.3 57.3 + - - +
46B ALA* 3.3 6.8 + - - +
47B GLU* 2.9 33.6 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.0 13.0 - - + -
30B PHE* 3.6 28.7 - - + +
33B SER* 3.8 21.3 - - - +
34B LEU* 3.5 39.3 - - + +
40B GLN* 2.8 39.5 + - + +
41B SER* 3.5 5.4 - - - +
43B ASN* 1.3 76.1 - - - +
45B LEU* 1.3 56.2 + - - +
47B GLU* 3.5 10.7 + - - +
48B ALA* 2.9 30.5 + - - +
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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
----------------------------------------------------------
12B TYR* 3.4 32.5 - - + +
15B GLU* 3.7 39.0 - - + +
16B ILE* 3.7 30.9 - - + +
19B LEU* 4.9 1.6 - - + -
41B SER 2.9 13.6 + - - +
42B ALA 3.1 7.2 + - - +
44B LEU* 1.3 73.9 - - - +
46B ALA* 1.3 56.1 + - - +
48B ALA 3.2 1.0 + - - -
49B LYS* 2.7 65.8 + - + +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA 3.0 16.0 + - - +
43B ASN* 3.8 6.3 - - - +
45B LEU* 1.3 76.7 - - - +
47B GLU* 1.3 58.2 + - - +
49B LYS* 3.8 8.3 - - - +
50B LYS* 2.9 51.8 + - - +
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Residues in contact with GLU 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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30B PHE* 3.6 24.0 - - + -
43B ASN* 2.9 18.6 + - - +
44B LEU* 3.6 15.6 - - - +
46B ALA* 1.3 77.8 - - - +
48B ALA* 1.3 56.1 + - - +
50B LYS* 3.4 8.3 + - - +
51B LEU* 2.9 30.5 + - + +
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Residues in contact with ALA 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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16B ILE* 4.1 16.8 - - + -
19B LEU* 3.5 16.5 - - + +
22B LEU* 4.3 4.1 - - + +
30B PHE* 3.7 30.2 - - + -
44B LEU 2.9 19.5 + - - +
45B LEU 3.2 4.0 + - - +
47B GLU* 1.3 77.4 - - - +
49B LYS* 1.3 56.5 + - - +
51B LEU* 3.6 2.1 - - - +
52B ASN* 2.8 30.0 + - - +
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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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15B GLU* 5.0 7.4 + - - +
19B LEU* 4.0 22.0 - - + +
45B LEU* 2.7 54.2 + - + +
46B ALA* 3.8 7.2 - - - +
48B ALA* 1.3 70.6 - - - +
50B LYS* 1.3 65.3 + - - +
52B ASN* 3.3 2.9 + - - +
53B ASP* 3.1 33.8 + - - +
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Residues in contact with LYS 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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46B ALA* 2.9 38.6 + - - +
47B GLU* 3.6 7.4 - - - +
49B LYS* 1.3 75.1 - - - +
51B LEU* 1.3 60.9 + - - +
53B ASP* 3.7 6.4 + - - +
54B ALA* 3.2 21.7 + - - +
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Residues in contact with LEU 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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22B LEU* 3.7 20.9 - - + -
26B GLN* 3.8 20.2 - - + +
30B PHE* 3.8 20.9 - - + -
47B GLU* 2.9 18.0 + - + +
48B ALA* 3.6 4.5 - - - +
50B LYS* 1.3 74.7 - - - +
52B ASN* 1.3 65.6 - - - +
54B ALA* 3.0 18.8 + - + +
55B GLN* 3.0 41.6 + - + +
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Residues in contact with ASN 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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19B LEU* 3.5 32.9 - - + +
20B PRO* 3.3 14.3 - - - +
21B ASN* 2.7 68.2 + - - +
22B LEU* 3.8 9.4 + - + +
48B ALA 2.8 21.1 + - - +
49B LYS 3.3 3.6 + - - +
51B LEU* 1.3 72.7 - - - +
53B ASP* 1.3 74.5 + - - +
55B GLN* 3.3 8.2 + - - -
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Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN* 5.0 0.2 - - - +
49B LYS* 3.1 19.0 + - - +
50B LYS* 4.0 6.0 - - - +
52B ASN* 1.3 87.4 + - - +
54B ALA* 1.3 65.2 + - - +
55B GLN 3.4 0.2 + - - -
56B ALA* 3.4 19.0 + - - +
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Residues in contact with ALA 54 (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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50B LYS 3.2 12.9 + - - +
51B LEU* 3.0 15.7 + - + +
53B ASP* 1.3 79.4 - - - +
55B GLN* 1.3 61.4 + - + +
56B ALA 3.2 6.3 + - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN* 3.0 37.3 + - - +
22B LEU* 4.4 1.4 - - - +
23B ASN* 4.8 2.2 - - - +
26B GLN* 2.7 39.6 + - - +
51B LEU* 3.0 35.1 + - + +
52B ASN 3.7 8.3 - - - +
53B ASP 3.2 0.8 - - - -
54B ALA* 1.3 78.7 - - + +
56B ALA* 1.3 61.9 + - - +
57B PRO* 3.8 2.8 - - - +
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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