Contacts of the helix formed by residues 28 - 37 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23U GLU 3.4 4.9 + - - -
24U VAL 3.6 7.9 - - - -
25U PHE* 2.8 20.2 + - - +
27U LEU* 1.3 85.5 - - - +
29U ASP* 1.3 61.5 + - - -
31U PHE* 3.5 1.2 - - - +
32U LYS* 3.0 32.8 - - - +
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Residues in contact with ASP 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U VAL 4.5 1.3 + - - -
25U PHE* 3.1 12.1 + - + +
28U GLY* 1.3 67.1 - - - -
30U ARG* 1.3 56.1 + - - +
31U PHE 2.4 18.5 + - - -
32U LYS* 2.8 15.8 + - - +
33U ASN* 2.9 17.4 + - + +
34U PHE 3.5 1.4 + - - -
271U TYR* 4.6 5.6 - - - -
272U THR* 5.4 2.8 - - - +
275U GLU* 3.5 26.7 - - - +
449U LYS* 5.8 0.7 - - + +
452U ILE* 4.1 26.8 - - + +
453U TYR* 3.6 34.4 + - - +
456U LYS* 4.1 17.0 + - - +
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Residues in contact with ARG 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U PHE 3.3 4.1 + - - +
26U ALA 3.1 17.7 - - - +
27U LEU* 3.1 21.2 - - - +
29U ASP* 1.3 74.0 - - - +
31U PHE* 1.3 68.5 + - - +
33U ASN* 5.3 0.4 - - - -
34U PHE* 2.9 62.8 - - + +
250U ARG* 5.7 0.6 - - - +
251U ASP* 2.7 42.6 + - - +
259U VAL* 4.1 10.5 - - + -
449U LYS* 3.0 40.5 - - + +
452U ILE* 5.8 3.0 - - - +
167X ASP 5.7 2.4 + - - -
168X ASN* 5.7 3.8 + - - +
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Residues in contact with PHE 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LEU* 3.0 21.3 - - + +
28U GLY 3.5 1.1 - - - +
29U ASP 2.4 6.1 + - - -
30U ARG* 1.3 80.0 - - - +
32U LYS* 1.3 75.4 + - + +
34U PHE* 3.0 19.1 - + - +
35U ILE* 2.8 44.3 + - + +
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Residues in contact with LYS 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U GLY* 3.0 31.3 + - - +
29U ASP* 2.8 10.6 + - - +
31U PHE* 1.3 96.3 - - + +
33U ASN* 1.3 52.0 + - - +
35U ILE* 2.9 8.7 - - - +
36U SER* 2.8 32.6 + - - -
271U TYR* 2.9 23.8 + - + +
275U GLU* 3.0 35.4 + - - +
456U LYS* 4.7 2.6 - - - +
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Residues in contact with ASN 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ASP* 2.9 20.1 + - + +
30U ARG* 5.3 0.7 - - - -
32U LYS* 1.3 69.1 - - - +
34U PHE* 1.3 58.6 + - - +
35U ILE 2.5 17.8 + - - -
36U SER* 2.5 19.0 + - - -
37U ASN* 2.7 27.0 + - - +
259U VAL* 5.2 5.9 - - - +
264U GLN* 5.1 4.2 + - - +
267U ARG* 4.9 2.4 + - - +
268U ILE* 3.9 24.8 - - - +
271U TYR* 3.5 33.2 - - + +
447U SER* 5.2 0.3 + - - -
452U ILE* 3.8 26.3 - - + +
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Residues in contact with PHE 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ASP 3.5 1.2 + - - -
30U ARG* 2.9 61.0 - - + +
31U PHE* 3.0 31.6 - + - +
33U ASN* 1.3 81.3 - - - +
35U ILE* 1.3 54.9 + - + +
37U ASN* 3.6 5.5 - - - +
38U CYS* 2.7 28.1 - - - -
248U LYS* 5.8 6.1 - - + -
249U ALA* 2.8 31.2 - - - +
250U ARG* 3.3 17.5 - - - -
259U VAL* 4.0 22.7 - - + -
167X ASP 5.7 2.7 - - - -
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Residues in contact with ILE 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U PHE* 2.8 28.1 + - + +
32U LYS* 2.9 20.0 - - - +
33U ASN 2.5 4.0 + - - -
34U PHE* 1.3 78.4 - - + +
36U SER* 1.3 67.1 + - - +
37U ASN 3.4 1.6 - - - -
38U CYS* 3.0 22.7 + - + +
39U LYS* 3.3 49.9 + - + +
248U LYS* 5.7 6.7 - - - +
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Residues in contact with SER 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U LYS 2.8 13.1 + - - -
33U ASN* 2.5 18.6 + - - -
35U ILE* 1.3 74.2 - - - +
37U ASN* 1.3 54.0 + - - -
38U CYS 2.7 12.5 + - - -
39U LYS* 5.6 0.7 - - - -
40U THR* 2.6 32.7 + - - -
45U VAL* 5.1 10.2 - - - +
48U LEU* 5.7 7.4 - - - +
49U ILE* 5.8 1.9 - - - +
267U ARG* 5.7 4.4 - - - +
271U TYR* 3.7 30.9 - - - +
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Residues in contact with ASN 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U ASN* 2.7 42.8 + - - +
34U PHE* 3.6 6.8 - - - +
36U SER* 1.3 72.3 - - - +
38U CYS* 1.3 57.8 + - - +
40U THR 3.7 15.3 - - - +
41U GLU* 3.9 13.0 - - - +
249U ALA* 3.4 24.3 + - - +
259U VAL* 5.5 1.7 - - - +
261U GLY* 4.1 10.3 - - - -
262U TYR 3.6 27.2 + - - +
264U GLN* 4.8 13.1 + - - +
267U ARG* 4.6 17.5 - - + +
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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