Contacts of the helix formed by residues 37 - 48 (chain B) in PDB entry 4L5L
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 ASP 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B SER 4.1 4.9 - - - +
33B TYR* 3.6 16.2 - - + -
34B GLY* 3.0 35.0 + - - +
36B CYS* 1.3 79.3 - - - +
38B GLY* 1.3 60.4 + - - +
39B GLU 3.4 2.5 - - - -
40B LYS* 3.2 35.0 + - + +
41B TRP 3.2 9.7 + - - -
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Residues in contact with GLY 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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8B TRP* 4.4 20.2 - - - -
34B GLY 4.3 1.8 + - - -
35B ARG 4.9 1.9 + - - -
36B CYS* 3.2 6.7 - - - +
37B ASP* 1.3 73.1 - - - +
39B GLU* 1.3 65.4 + - - +
40B LYS 3.1 1.3 - - - -
41B TRP* 3.3 6.3 + - - +
42B GLN* 3.2 25.8 + - - +
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Residues in contact with GLU 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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36B CYS 4.8 3.2 + - - +
37B ASP 3.4 0.2 - - - -
38B GLY* 1.3 75.7 - - - +
40B LYS* 1.3 57.9 + - - +
42B GLN* 3.2 11.0 + - + +
43B ASN* 2.7 48.4 + - - +
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 5.2 10.9 - - - +
32B SER 4.2 9.2 + - - -
33B TYR* 3.5 26.9 - - - -
37B ASP* 3.2 35.5 + - + +
38B GLY 3.1 0.6 - - - -
39B GLU* 1.3 78.2 - - - +
41B TRP* 1.3 63.8 + - - +
43B ASN* 2.9 13.6 + - + +
44B ASP* 2.9 37.3 + - - +
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Residues in contact with TRP 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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8B TRP* 4.5 11.9 - + + -
33B TYR* 3.5 36.0 - + + -
37B ASP 3.2 6.0 + - - +
38B GLY* 3.5 10.5 - - - +
40B LYS* 1.3 77.1 - - - +
42B GLN* 1.3 67.8 + - - +
44B ASP 3.1 0.7 + - - -
45B LYS* 2.7 74.1 + - + +
48B LEU* 4.1 7.2 - - + -
50B LEU* 4.2 8.7 - - + -
54B ASN 3.2 33.9 - - - -
55B LEU* 3.6 29.2 - - + -
57B TYR* 3.6 26.0 - + - -
301B GSH 2.9 26.0 + - - -
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Residues in contact with GLN 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 GLY 3.2 15.5 + - - +
39B GLU* 3.2 12.5 + - + +
41B TRP* 1.3 96.7 - - - +
43B ASN* 1.3 61.0 + - - +
45B LYS* 3.5 29.5 - - - +
46B HIS* 3.1 25.5 + - - +
301B GSH 4.6 2.2 + - - -
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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
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39B GLU* 2.7 44.4 + - - +
40B LYS* 2.9 10.2 + - + +
42B GLN* 1.3 76.9 - - - +
44B ASP* 1.3 67.0 + - - +
46B HIS* 3.2 15.4 + - - +
47B ASN* 3.2 21.5 - - - +
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Residues in contact with ASP 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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31B HIS* 5.1 5.9 - - - -
33B TYR* 2.3 43.0 + - - +
40B LYS* 2.9 28.4 + - - +
41B TRP* 3.6 4.3 - - + +
43B ASN* 1.3 73.2 - - - +
45B LYS* 1.3 59.7 + - - +
47B ASN* 2.7 28.2 + - - +
48B LEU* 2.9 33.7 + - + +
57B TYR* 4.8 1.2 + - - -
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Residues in contact with LYS 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 TRP* 2.7 61.7 + - + +
42B GLN* 3.5 28.8 + - - +
44B ASP* 1.3 71.8 - - - +
46B HIS* 1.3 65.8 + - - +
47B ASN 3.2 0.7 + - - -
48B LEU* 3.6 12.9 + - - +
49B GLY 4.6 2.6 + - - -
50B LEU* 5.2 5.2 + - - +
53B PRO* 4.1 33.9 + - + +
301B GSH 3.0 22.4 + - - -
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Residues in contact with HIS 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 GLN 3.1 15.6 + - - +
43B ASN* 3.2 16.4 - - - +
44B ASP 3.0 0.8 - - - -
45B LYS* 1.3 79.9 - - - +
47B ASN* 1.3 70.4 + - - +
48B LEU 4.0 0.2 + - - -
49B GLY* 4.8 2.1 + - - -
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Residues in contact with ASN 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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43B ASN* 3.2 16.6 - - - +
44B ASP* 2.7 15.8 + - - +
46B HIS* 1.3 92.8 + - - +
48B LEU* 1.3 65.2 + - + +
49B GLY* 3.1 4.5 + - - -
59B LYS* 4.7 2.4 + - - -
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Residues in contact with LEU 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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31B HIS* 6.2 1.8 - - + -
41B TRP* 4.1 5.4 - - + -
44B ASP* 2.9 39.1 + - + +
45B LYS* 3.6 7.6 + - - +
47B ASN* 1.3 81.3 - - + +
49B GLY* 1.3 63.0 + - - +
50B LEU* 3.5 20.8 + - + +
57B TYR* 3.5 49.1 - - + +
59B LYS* 2.8 41.2 + - + +
64B SER* 5.0 0.5 + - - -
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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