Contacts of the helix formed by residues 28 - 37 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23W GLU 3.4 5.3 + - - -
24W VAL 3.6 7.9 - - - -
25W PHE* 2.7 21.1 + - - +
27W LEU* 1.3 85.1 - - - +
29W ASP* 1.3 59.9 + - - -
31W PHE* 3.5 0.7 - - - +
32W LYS* 3.0 33.3 - - - +
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Residues in contact with ASP 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24W VAL 4.5 1.1 + - - -
25W PHE* 3.1 10.8 + - + +
28W GLY* 1.3 68.5 - - - -
30W ARG* 1.3 56.4 + - - +
31W PHE 2.4 17.5 + - - -
32W LYS* 2.9 7.5 + - - +
33W ASN* 2.9 26.8 + - + +
34W PHE 3.5 1.4 + - - -
271W TYR* 4.6 5.3 - - - -
272W THR* 5.4 2.9 - - - +
275W GLU* 3.5 26.9 - - - +
449W LYS 5.7 0.7 - - - +
452W ILE* 4.1 25.5 - - + +
453W TYR* 3.6 33.8 + - - +
456W LYS* 4.1 17.1 + - - +
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Residues in contact with ARG 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N ASP 5.8 2.0 + - - -
168N ASN* 5.7 3.4 + - - +
25W PHE 3.3 4.0 + - - +
26W ALA 3.1 18.2 - - - +
27W LEU* 3.1 22.0 - - - +
29W ASP* 1.3 72.8 - - - +
31W PHE* 1.3 68.2 + - - +
33W ASN* 5.3 0.4 - - - -
34W PHE* 2.9 60.2 - - + +
250W ARG* 5.8 1.0 - - - +
251W ASP* 2.6 44.3 + - - +
259W VAL* 4.1 10.5 - - + -
449W LYS* 3.0 40.3 - - + +
452W ILE* 5.8 3.7 - - + +
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Residues in contact with PHE 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27W LEU* 3.0 22.2 - - + +
28W GLY 3.5 0.9 - - - +
29W ASP 2.4 5.5 + - - -
30W ARG* 1.3 82.1 - - - +
32W LYS* 1.3 76.1 + - + +
34W PHE* 3.0 19.3 - + - +
35W ILE* 2.8 43.2 + - + +
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Residues in contact with LYS 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W GLY* 3.0 31.0 + - - +
29W ASP* 2.9 10.6 + - - +
31W PHE* 1.3 97.0 - - + +
33W ASN* 1.3 52.0 + - - +
35W ILE* 2.9 9.1 - - - +
36W SER* 2.8 32.7 + - - -
271W TYR* 2.9 23.6 + - + +
275W GLU* 3.1 34.8 + - - +
456W LYS* 4.7 3.0 - - - +
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Residues in contact with ASN 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ASP* 2.9 20.6 + - + +
30W ARG* 5.3 0.2 - - - -
32W LYS* 1.3 69.5 - - - +
34W PHE* 1.3 57.8 + - - +
35W ILE 2.5 18.0 + - - -
36W SER* 2.5 20.2 + - - -
37W ASN* 2.7 26.3 + - - +
259W VAL* 5.2 6.1 - - - +
264W GLN* 5.1 3.6 + - - -
267W ARG 4.9 2.0 + - - -
268W ILE* 3.9 24.4 - - - +
271W TYR* 3.5 33.4 - - + +
272W THR* 6.3 0.2 - - - -
447W SER* 5.1 0.3 + - - -
452W ILE* 3.9 25.4 - - + +
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Residues in contact with PHE 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N ASP 5.8 2.7 - - - -
29W ASP 3.5 2.0 + - - -
30W ARG* 2.9 61.0 - - + +
31W PHE* 3.0 32.1 - + - +
33W ASN* 1.3 81.3 + - - +
35W ILE* 1.3 54.3 + - + +
37W ASN* 3.6 6.1 - - - +
38W CYS* 2.7 29.6 - - - -
248W LYS* 5.8 5.4 - - + -
249W ALA* 2.8 36.7 - - - +
250W ARG* 3.3 12.1 - - - -
259W VAL* 4.0 21.8 - - + -
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Residues in contact with ILE 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31W PHE* 2.8 27.4 + - + +
32W LYS* 2.9 20.2 - - - +
33W ASN 2.5 7.6 + - - -
34W PHE* 1.3 78.7 - - + +
36W SER* 1.3 66.7 + - - +
37W ASN 3.4 0.7 - - - -
38W CYS* 3.1 23.9 + - + +
39W LYS* 3.3 48.9 + - + +
248W LYS* 5.7 5.8 - - - +
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Residues in contact with SER 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W LYS 2.8 12.2 + - - -
33W ASN* 2.5 19.4 + - - -
35W ILE* 1.3 75.0 - - - +
37W ASN* 1.3 58.2 + - - -
38W CYS 2.8 7.1 + - - -
39W LYS* 5.6 0.7 - - - -
40W THR* 2.6 33.4 + - - -
45W VAL* 5.0 10.6 - - - +
48W LEU* 5.7 7.1 - - - +
49W ILE* 5.8 2.1 - - - +
267W ARG* 5.6 4.7 - - - +
271W TYR* 3.7 31.4 - - - +
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Residues in contact with ASN 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W ASN* 2.7 43.1 + - - +
34W PHE* 3.6 6.8 - - - +
36W SER* 1.3 72.9 + - - +
38W CYS* 1.3 57.8 + - - +
40W THR 3.7 13.9 - - - +
41W GLU* 3.9 12.3 - - - +
249W ALA* 3.4 24.7 + - - +
259W VAL* 5.4 1.7 - - - +
261W GLY* 4.1 9.3 - - - -
262W TYR 3.6 27.8 + - - +
264W GLN* 4.8 12.7 + - - +
267W ARG* 4.6 17.0 - - + +
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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