Contacts of the helix formed by residues 39 - 48 (chain A) in PDB entry 1E5E
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.2 7.2 - - - +
38A ASP* 1.3 90.7 - - - +
40A CYS* 1.3 64.0 + - - +
41A GLN* 3.2 11.5 + - - +
42A GLN* 2.9 36.1 + - - +
43A GLY 3.3 14.6 + - - -
328B ASP* 3.4 26.7 - - + +
335B LEU* 3.5 9.4 - - - -
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Residues in contact with CYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 1.3 69.4 - - - +
41A GLN* 1.3 66.6 + - - +
43A GLY* 3.2 1.6 + - - -
44A GLY* 2.9 21.7 + - - -
324B LYS* 3.6 35.9 - - + -
327B LEU* 3.4 43.5 - - - -
328B ASP* 2.8 17.7 + - - +
335B LEU* 4.2 6.5 - - - -
348B HIS* 5.3 3.8 - - + -
351B SER* 5.0 3.4 + - - +
352B MET* 3.8 18.1 - - + +
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 3.2 9.9 + - - +
40A CYS* 1.3 78.4 - - - +
42A GLN* 1.3 53.7 + - - +
44A GLY* 3.3 1.8 + - - -
45A ASN* 2.7 74.9 + - - +
320B PHE* 6.0 0.2 - - - -
324B LYS* 3.8 26.6 + - + +
328B ASP* 5.1 1.8 + - - +
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL 4.5 0.5 - - - +
37A PHE* 3.4 9.0 - - - -
38A ASP* 2.9 50.8 + - - +
39A ASN* 2.9 24.9 + - - +
41A GLN* 1.3 75.2 - - - +
43A GLY* 1.3 57.6 + - - +
45A ASN* 3.2 2.5 + - - +
46A ARG* 2.8 66.0 + - - +
51A GLU* 3.7 31.7 + - - +
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.5 39.2 - - - -
39A ASN 3.3 5.5 + - - -
40A CYS 3.2 6.9 + - - -
42A GLN* 1.3 79.5 - - - +
44A GLY* 1.3 60.3 + - - +
46A ARG* 3.2 2.1 + - - +
47A PHE* 3.0 32.0 + - - -
352B MET* 4.3 4.0 - - - -
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A CYS 2.9 17.2 + - - -
41A GLN* 3.7 4.3 - - - -
43A GLY* 1.3 70.8 - - - +
45A ASN* 1.3 58.0 + - - +
47A PHE* 3.4 3.8 + - - +
48A ALA* 2.9 29.7 + - - +
351B SER* 3.6 30.5 - - - +
352B MET* 4.5 1.8 - - - +
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Residues in contact with ASN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 2.7 52.7 + - - +
42A GLN* 3.4 4.7 - - - +
44A GLY* 1.3 74.4 - - - +
46A ARG* 1.3 64.1 + - - +
48A ALA* 3.3 5.4 + - - +
50A GLN* 2.9 47.7 + - + +
51A GLU* 3.1 31.4 + - + +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.3 1.6 - - - +
36A VAL 4.6 7.3 + - - -
37A PHE* 3.7 17.0 - - + -
38A ASP* 5.2 0.6 + - - -
42A GLN* 2.8 61.2 + - - +
43A GLY 3.8 4.0 - - - +
45A ASN* 1.3 71.6 - - - +
47A PHE* 1.3 63.7 + - - +
49A GLY* 3.0 14.6 + - - -
51A GLU* 3.6 17.9 + - + +
52A SER 2.9 27.2 + - - +
53A GLY* 3.7 19.5 - - - +
54A TYR 3.0 30.7 + - - +
55A ILE* 3.8 20.4 - - + +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.1 4.9 - + - -
43A GLY 3.0 22.8 + - - -
44A GLY 3.8 2.0 - - - +
46A ARG* 1.3 76.1 - - - +
48A ALA* 1.3 59.5 + - - +
49A GLY 3.5 0.7 + - - -
55A ILE* 3.5 40.4 - - + -
59A LEU* 4.3 13.7 - - + -
337B VAL* 3.8 18.4 - - + -
351B SER 3.6 15.3 - - - +
352B MET* 3.5 49.8 - - + +
353B THR* 4.2 5.6 - - - -
355B ALA* 4.7 10.2 - - + +
356B VAL* 6.1 0.9 - - + -
405B PPJ 4.7 6.7 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 2.9 18.1 + - - +
45A ASN* 3.3 2.4 + - - +
46A ARG 3.1 0.6 - - - -
47A PHE* 1.3 75.4 - - - +
49A GLY* 1.3 62.3 + - - +
50A GLN* 3.2 27.0 + - + +
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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