Contacts of the helix formed by residues 28 - 37 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23M GLU 3.5 5.3 + - - -
24M VAL 3.6 7.9 - - - -
25M PHE* 2.7 20.7 + - - +
27M LEU* 1.3 85.5 - - - +
29M ASP* 1.3 59.8 + - - -
31M PHE* 3.5 1.0 - - - +
32M LYS* 3.0 34.0 - - - +
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Residues in contact with ASP 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M VAL 4.5 1.5 + - - -
25M PHE* 3.1 11.9 + - + +
28M GLY* 1.3 69.0 - - - -
30M ARG* 1.3 56.6 + - - +
31M PHE 2.5 17.4 + - - -
32M LYS* 2.9 7.5 + - - +
33M ASN* 2.9 28.0 + - + +
34M PHE 3.5 1.6 + - - -
271M TYR* 4.6 5.4 - - - -
272M THR* 5.4 2.8 - - - +
275M GLU* 3.6 25.8 - - - +
449M LYS* 5.7 1.1 - - + +
452M ILE* 4.1 25.3 - - + +
453M TYR* 3.6 30.8 + - - +
456M LYS* 4.1 19.3 + - - +
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Residues in contact with ARG 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M PHE 3.3 4.3 + - - +
26M ALA 3.1 18.6 - - - +
27M LEU* 3.2 19.8 - - - +
29M ASP* 1.3 73.4 - - - +
31M PHE* 1.3 68.6 + - - +
33M ASN* 5.3 0.4 - - - -
34M PHE* 2.9 62.4 - - + +
250M ARG* 4.5 1.2 - - - +
251M ASP* 2.7 45.1 + - - +
259M VAL* 4.1 9.6 - - + -
449M LYS* 3.0 39.4 - - + +
452M ILE* 5.8 3.3 - - + +
167P ASP 5.9 0.8 + - - -
168P ASN* 5.8 2.4 + - - +
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Residues in contact with PHE 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M LEU* 3.0 21.5 - - + +
28M GLY 3.5 1.3 - - - +
29M ASP 2.5 4.9 + - - -
30M ARG* 1.3 80.1 - - - +
32M LYS* 1.3 75.3 + - + +
34M PHE* 3.0 18.9 - + - +
35M ILE* 2.8 43.2 + - + +
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Residues in contact with LYS 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M GLY* 3.0 31.0 + - - +
29M ASP* 2.9 10.6 + - - +
31M PHE* 1.3 97.4 - - + +
33M ASN* 1.3 51.9 + - - +
35M ILE* 3.0 8.9 - - - +
36M SER* 2.8 33.4 + - - -
271M TYR* 2.8 24.5 + - + +
275M GLU* 3.1 35.9 + - - +
456M LYS* 4.8 2.8 - - - +
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Residues in contact with ASN 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M ASP* 2.9 16.0 + - + +
30M ARG* 5.3 0.2 - - - -
32M LYS* 1.3 70.8 - - - +
34M PHE* 1.3 59.1 + - - +
35M ILE 2.5 17.7 + - - -
36M SER* 2.6 19.0 + - - -
37M ASN* 2.7 28.0 + - - +
259M VAL* 5.2 6.6 - - - +
264M GLN* 5.1 3.6 + - - -
267M ARG* 4.9 2.0 + - - +
268M ILE* 4.0 23.5 - - - +
271M TYR* 3.5 33.7 - - + +
447M SER* 5.1 0.7 + - - -
452M ILE* 3.9 29.6 - - + +
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Residues in contact with PHE 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M ASP 3.5 1.2 + - - -
30M ARG* 2.9 62.0 - - + +
31M PHE* 3.0 31.6 - + - +
33M ASN* 1.3 82.5 + - - +
35M ILE* 1.3 54.3 + - + +
37M ASN* 3.6 6.6 - - - +
38M CYS* 2.7 29.9 - - - -
248M LYS* 5.7 5.4 - - + -
249M ALA* 2.8 30.0 - - + +
250M ARG* 3.3 17.7 - - - -
259M VAL* 4.0 21.3 - - + -
167P ASP 5.9 1.6 - - - -
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Residues in contact with ILE 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M PHE* 2.8 28.5 + - + +
32M LYS* 3.0 19.5 - - - +
33M ASN 2.5 8.2 + - - -
34M PHE* 1.3 78.1 - - + +
36M SER* 1.3 67.0 + - - +
37M ASN 3.4 0.9 - - - -
38M CYS* 3.1 23.2 + - + +
39M LYS* 3.3 49.8 + - + +
248M LYS* 5.7 6.5 - - - +
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Residues in contact with SER 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M LYS 2.8 13.0 + - - -
33M ASN* 2.6 18.6 + - - -
35M ILE* 1.3 75.9 - - - +
37M ASN* 1.3 53.0 + - - -
38M CYS 2.7 12.1 + - - -
39M LYS* 5.6 0.4 - - - -
40M THR* 2.6 32.9 + - - -
45M VAL* 5.0 10.7 - - - +
48M LEU* 5.7 8.0 - - - +
49M ILE* 5.8 1.7 - - - +
267M ARG* 5.7 5.1 - - - +
271M TYR* 3.7 31.2 - - - +
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Residues in contact with ASN 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ASN* 2.7 42.8 + - - +
34M PHE* 3.6 6.9 - - - +
36M SER* 1.3 71.4 - - - +
38M CYS* 1.3 58.0 + - - -
40M THR 3.7 13.9 - - - -
41M GLU* 3.9 13.5 - - - +
249M ALA* 3.4 23.7 + - - +
259M VAL* 5.4 2.3 - - - +
261M GLY* 4.0 9.5 - - - -
262M TYR 3.6 27.4 + - - +
263M GLY 5.4 0.2 - - - -
264M GLN* 4.9 13.3 + - - +
267M 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