Contacts of the helix formed by residues 37 - 46 (chain B) in PDB entry 2W7U
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 ASN 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 1.3 90.4 + - - +
38B LYS* 1.3 65.0 + - - +
39B HIS* 3.7 11.6 + - - +
40B ILE* 3.4 19.6 + - - +
41B ALA* 3.1 20.1 + - - +
78B ASP* 3.7 28.2 - - - +
80B ALA* 4.1 0.9 - - - -
154B SER* 3.0 39.8 + - - +
155B GLY* 3.1 18.2 - - - +
168B ILE* 4.0 5.2 - - + -
169B LEU 3.8 7.5 + - - +
170B TYR* 3.9 8.8 + - + +
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Residues in contact with LYS 38 (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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37B ASN* 1.3 69.4 - - - +
39B HIS* 1.3 50.9 + - - +
41B ALA* 2.9 10.0 + - - +
42B LYS* 2.9 40.1 + - + +
72B GLU* 3.4 33.0 - - + +
73B TYR* 2.9 27.5 + - - +
75B GLY 3.3 13.4 + - - -
76B LYS 5.0 2.7 - - - -
77B GLU 2.9 28.2 + - - -
78B ASP* 2.9 23.0 + - - +
79B LEU 3.4 23.5 + - - +
80B ALA* 3.8 10.8 - - + -
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Residues in contact with HIS 39 (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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37B ASN* 3.7 9.5 + - - +
38B LYS* 1.3 74.2 - - - +
40B ILE* 1.3 69.2 + - + +
42B LYS* 4.0 1.2 - - - +
43B SER* 2.6 48.3 + - - -
78B ASP* 3.8 7.9 + - - +
154B SER* 5.7 2.2 + - - -
122C ALA 3.1 27.8 + - - -
123C GLN* 4.4 10.9 + - - -
125C LYS* 4.0 30.8 - - + +
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Residues in contact with ILE 40 (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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21B PHE* 3.6 38.6 - - + -
23B GLY* 3.5 33.2 - - - +
24B GLY* 3.9 3.8 - - - +
25B THR 4.7 0.2 - - - +
36B THR* 3.7 17.7 - - - +
37B ASN* 3.4 27.0 + - - +
38B LYS 3.2 1.4 + - - -
39B HIS* 1.3 82.9 - - + +
41B ALA* 1.3 60.9 + - - +
43B SER* 3.5 4.4 + - - -
44B ASN* 3.0 29.9 + - - +
154B SER* 3.8 20.2 - - - +
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Residues in contact with ALA 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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21B PHE* 5.2 1.6 - - - -
36B THR* 4.3 2.4 - - + +
37B ASN 3.1 11.4 + - - +
38B LYS 2.9 9.3 + - - +
40B ILE* 1.3 78.7 - - - +
42B LYS* 1.3 57.6 + - + +
44B ASN* 3.7 5.7 + - - +
45B ASP* 3.2 25.3 + - - +
70B ILE* 3.4 26.9 - - + +
72B GLU* 6.2 0.2 - - + -
80B ALA* 3.8 19.5 - - + -
82B VAL* 4.0 18.4 - - + -
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Residues in contact with LYS 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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38B LYS* 2.9 23.1 + - + +
39B HIS 4.3 0.9 - - - +
41B ALA* 1.3 77.6 - - + +
43B SER* 1.3 65.4 + - - +
44B ASN 3.3 0.2 - - - -
45B ASP* 3.3 17.2 + - - +
46B ILE* 3.5 19.4 + - - +
70B ILE* 5.3 2.7 - - + -
72B GLU* 3.3 40.4 + - + +
125C LYS* 3.7 30.9 - - - +
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Residues in contact with SER 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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23B GLY* 6.4 1.6 - - - -
39B HIS* 2.6 38.3 + - - -
40B ILE* 3.9 6.5 - - - -
42B LYS* 1.3 76.5 - - - +
44B ASN* 1.3 60.8 + - - +
46B ILE* 3.3 21.2 - - - +
47B PHE* 4.0 11.8 + - - -
122C ALA* 4.2 5.3 + - - -
125C LYS* 3.3 23.1 - - - +
126C TYR* 4.9 10.8 - - - -
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Residues in contact with ASN 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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21B PHE* 3.9 24.3 - - + +
22B VAL* 4.1 17.9 + - - +
40B ILE 3.0 18.8 + - - +
41B ALA* 3.9 5.6 - - - +
43B SER* 1.3 76.3 - - - +
45B ASP* 1.3 58.5 + - - +
46B ILE 3.4 0.2 - - - -
47B PHE* 3.5 3.6 + - - -
48B LYS* 2.9 24.7 + - - +
49B ASN* 2.8 44.6 + - - +
50B ARG 4.4 4.0 + - - +
67B VAL* 4.0 17.2 - - - +
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Residues in contact with ASP 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 ALA 3.2 17.9 + - - +
42B LYS* 3.5 12.8 - - + +
43B SER 3.2 0.6 - - - -
44B ASN* 1.3 80.2 - - - +
46B ILE* 1.3 63.8 + - + +
48B LYS* 3.3 45.5 + - - +
67B VAL* 5.9 0.9 - - - +
70B ILE* 3.7 22.1 - - + +
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Residues in contact with ILE 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 LYS 3.7 8.7 - - - +
43B SER 3.3 16.2 - - - +
45B ASP* 1.3 79.2 - - + +
47B PHE* 1.3 63.4 + - + +
48B LYS* 5.5 0.2 - - - +
52C SER* 3.4 13.2 + - - -
55C HIS* 3.5 30.6 - - + +
64C ASN* 3.2 18.4 + - - +
125C LYS* 3.8 16.6 - - + -
126C TYR* 3.6 44.4 - - + +
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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