Contacts of the helix formed by residues 28 - 37 (chain I) in PDB entry 2GLJ
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 GLY 28 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLU 3.4 5.1 + - - -
24I VAL* 3.6 8.7 - - - -
25I PHE* 2.7 20.5 + - - +
27I LEU* 1.3 86.2 - - - +
29I ASP* 1.3 59.6 + - - -
31I PHE* 3.5 0.7 - - - +
32I LYS* 2.9 34.6 - - - +
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Residues in contact with ASP 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL 4.5 1.3 + - - -
25I PHE* 3.1 11.2 + - + +
28I GLY* 1.3 69.0 - - - -
30I ARG* 1.3 55.5 + - - +
31I PHE 2.5 17.8 + - - -
32I LYS* 2.9 6.7 + - - +
33I ASN* 2.9 27.9 + - + +
34I PHE 3.5 1.4 + - - -
271I TYR* 4.6 5.0 - - - -
272I THR* 5.4 2.8 - - - +
275I GLU* 3.5 27.0 - - - +
449I LYS* 5.7 0.9 - - - +
452I ILE* 4.1 26.0 - - + +
453I TYR* 3.6 32.7 + - - +
456I LYS* 4.0 17.8 + - - +
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I PHE 3.3 3.6 + - - +
26I ALA 3.1 18.8 - - - +
27I LEU* 3.1 22.1 - - - +
29I ASP* 1.3 72.9 - - - +
31I PHE* 1.3 68.3 + - - +
33I ASN* 5.3 0.7 - - - -
34I PHE* 2.9 62.2 - - + +
250I ARG* 4.5 0.8 - - - +
251I ASP* 2.6 45.6 + - - +
259I VAL* 4.1 9.9 - - + -
449I LYS* 3.0 38.7 - - + +
452I ILE* 5.8 3.2 - - - +
167L ASP 5.8 1.4 + - - -
168L ASN* 5.8 3.2 + - - +
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Residues in contact with PHE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LEU* 3.0 21.1 - - + +
28I GLY 3.5 0.9 - - - +
29I ASP 2.5 4.6 + - - -
30I ARG* 1.3 81.8 - - - +
32I LYS* 1.3 74.2 + - + +
34I PHE* 3.0 18.7 - + - +
35I ILE* 2.7 46.8 + - + +
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Residues in contact with LYS 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I GLY* 2.9 30.6 + - - +
29I ASP* 2.9 10.7 + - - +
31I PHE* 1.3 96.8 - - + +
33I ASN* 1.3 51.2 + - - +
35I ILE* 2.9 9.2 - - - +
36I SER* 2.8 32.2 + - - -
271I TYR* 2.9 24.3 + - + +
275I GLU* 3.1 35.7 + - - +
456I LYS* 4.7 2.8 - - - +
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Residues in contact with ASN 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ASP* 2.9 19.7 + - + +
30I ARG* 5.3 0.6 - - - -
32I LYS* 1.3 69.6 - - - +
34I PHE* 1.3 58.1 + - - +
35I ILE 2.5 18.2 + - - -
36I SER* 2.5 20.3 + - - -
37I ASN* 2.7 28.7 + - - +
259I VAL* 5.2 7.1 - - - +
264I GLN* 5.1 4.0 + - - -
267I ARG* 4.9 1.8 + - - +
268I ILE* 4.0 24.4 - - - +
271I TYR* 3.5 34.7 - - + +
452I ILE* 3.9 25.2 - - + +
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Residues in contact with PHE 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ASP 3.5 1.2 + - - -
30I ARG* 2.9 60.1 - - + +
31I PHE* 3.0 32.3 - + - +
33I ASN* 1.3 81.1 + - - +
35I ILE* 1.3 53.8 + - + +
37I ASN* 3.6 6.2 - - - +
38I CYS* 2.7 30.9 - - - -
248I LYS* 5.8 5.4 - - + -
249I ALA* 2.9 30.4 - - - +
250I ARG* 3.3 17.9 - - - -
259I VAL* 4.0 21.8 - - + -
167L ASP 5.8 2.0 - - - -
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Residues in contact with ILE 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I PHE* 2.7 27.8 + - + +
32I LYS* 2.9 19.5 - - - +
33I ASN 2.5 7.8 + - - -
34I PHE* 1.3 78.8 - - + +
36I SER* 1.3 67.5 + - - +
37I ASN 3.4 0.9 - - - -
38I CYS* 3.1 23.0 + - + +
39I LYS* 3.3 49.0 + - + +
248I LYS* 5.7 5.8 - - - +
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Residues in contact with SER 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LYS 2.8 12.8 + - - -
33I ASN* 2.5 24.3 + - - -
35I ILE* 1.3 76.8 - - - +
37I ASN* 1.3 52.4 + - - -
38I CYS 2.7 12.5 + - - -
39I LYS* 5.6 0.2 - - - -
40I THR* 2.6 33.5 + - - -
45I VAL* 5.1 10.0 - - - +
48I LEU* 5.8 7.4 - - - +
49I ILE* 5.8 1.9 - - - +
267I ARG* 5.7 5.0 - - - +
271I TYR* 3.7 26.3 - - - +
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Residues in contact with ASN 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ASN* 2.7 43.2 + - - +
34I PHE* 3.6 6.4 - - - +
36I SER* 1.3 72.5 - - - +
38I CYS* 1.3 57.3 + - - +
40I THR 3.7 14.1 - - - +
41I GLU* 3.9 12.6 - - - +
249I ALA* 3.4 24.4 + - - +
259I VAL* 5.4 2.3 - - - +
261I GLY* 4.0 9.5 - - - -
262I TYR 3.6 27.5 + - - +
264I GLN* 4.9 13.8 + - - +
267I ARG* 4.6 17.9 - - + +
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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