Contacts of the helix formed by residues 19 - 27 (chain R) 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 LYS 19 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G LYS* 3.4 26.7 - - - +
154G LYS* 3.9 35.2 - - - +
155G ASP* 4.2 15.6 - - - +
230G ASP* 2.8 38.8 - - - +
235G ASP* 5.8 3.4 - - - -
17R ASP* 2.5 34.2 + - - +
18R ASP* 1.3 79.6 - - - +
20R GLN* 1.3 59.2 + - - +
22R LYS* 4.5 7.5 - - - +
23R GLU* 3.6 19.4 + - - +
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Residues in contact with GLN 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G LYS* 4.8 4.2 - - - +
157G THR* 3.9 25.3 + - - +
230G ASP* 4.0 7.6 - - + +
18R ASP* 2.6 41.6 + - - +
19R LYS* 1.3 72.5 - - - +
21R LEU* 1.3 69.9 + - - +
22R LYS 3.1 0.9 - - - -
23R GLU* 2.8 8.4 + - - +
24R VAL* 2.6 34.0 + - + +
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Residues in contact with LEU 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R LYS* 4.0 12.6 - - + +
16R TYR* 3.3 43.1 - - + +
17R ASP 3.5 6.5 + - - +
18R ASP* 3.6 18.8 - - + +
20R GLN* 1.3 79.1 - - + +
22R LYS* 1.3 66.7 + - - +
24R VAL* 3.0 18.2 + - + +
25R PHE* 2.9 16.9 - - - -
453R TYR* 3.1 33.3 - - + +
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Residues in contact with LYS 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R TRP* 4.7 18.4 - - + -
14R ASP 5.6 3.1 - - - +
16R TYR* 4.3 5.2 - - + -
17R ASP* 3.3 54.5 + - - +
19R LYS* 4.7 8.1 - - - +
20R GLN 2.8 4.0 + - - -
21R LEU* 1.3 74.2 - - - +
23R GLU* 1.3 52.0 + - - +
25R PHE* 2.7 24.8 + - + -
26R ALA* 2.6 40.8 + - + -
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Residues in contact with GLU 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ASN* 4.7 11.9 + - - +
230G ASP* 4.3 11.0 - - - +
19R LYS 3.6 15.6 + - - +
20R GLN* 2.8 11.6 + - - +
22R LYS* 1.3 76.1 - - - +
24R VAL* 1.3 55.0 + - + +
25R PHE 2.7 11.4 + - - -
26R ALA* 4.6 5.6 - - - +
27R LEU* 3.5 32.7 + - + +
28R GLY* 3.4 13.9 + - - -
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Residues in contact with VAL 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R GLN* 2.6 43.7 + - + +
21R LEU* 3.2 13.7 - - + +
22R LYS 3.0 0.8 + - - -
23R GLU* 1.3 71.0 - - + +
25R PHE* 1.3 61.5 + - - +
28R GLY* 3.6 10.5 - - - -
29R ASP* 4.5 1.2 + - - +
453R TYR* 3.9 20.7 - - + +
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Residues in contact with PHE 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R TRP* 3.4 40.6 - + - -
16R TYR* 3.4 35.9 - + + -
21R LEU 2.9 24.2 - - - -
22R LYS* 2.7 19.1 + - + -
23R GLU 2.7 3.4 + - - -
24R VAL* 1.3 82.3 - - - +
26R ALA* 1.3 85.4 + - - +
27R LEU 2.8 2.0 - - - -
28R GLY* 2.7 14.7 + - - +
29R ASP* 3.1 17.1 + - + +
30R ARG* 3.3 8.8 + - - +
449R LYS* 3.9 18.1 - - + +
450R ALA 3.9 10.8 - - - -
453R TYR* 3.3 34.1 - + + -
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Residues in contact with ALA 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R TRP* 5.7 3.6 - - + -
22R LYS* 2.6 29.1 + - + +
23R GLU* 4.5 3.4 - - - +
25R PHE* 1.3 87.1 - - + +
27R LEU* 1.3 65.3 + - + +
30R ARG* 3.1 21.1 - - - +
449R LYS* 3.5 18.7 + - + +
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Residues in contact with LEU 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R GLU* 3.5 34.3 + - + +
25R PHE 3.3 1.3 - - - -
26R ALA* 1.3 84.1 - - + +
28R GLY* 1.3 70.3 + - - +
30R ARG* 3.6 17.7 - - - +
31R PHE* 3.0 25.9 - - + +
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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