Contacts of the helix formed by residues 25 - 32 (chain X) in PDB entry 3GX4
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 TYR 25 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24X THR* 1.3 73.1 + - - +
26X GLY* 1.3 63.1 - - - +
28X ILE* 3.2 5.2 + - - +
29X ALA 3.2 15.9 + - - -
38X ALA* 4.2 4.9 - - - +
41X VAL* 3.7 15.5 - - + +
42X GLY* 3.8 33.0 - - - -
45X MET* 4.8 2.0 - - + -
59X VAL* 3.9 21.3 + - + +
60X ILE* 2.8 47.3 + - - -
61X ASN* 3.3 14.1 - - - -
67X SER* 3.5 16.0 + - - -
69X ARG* 4.7 0.7 + - - -
78X GLN* 5.2 0.3 + - - -
207Y 6OG 2.6 52.4 + + - -
208Y C 3.6 24.7 - - - +
209Y T 2.8 8.5 - - - +
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Residues in contact with GLY 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X THR* 3.9 2.2 - - - -
25X TYR* 1.3 76.8 - - - +
27X GLU* 1.3 63.1 + - - -
29X ALA* 3.1 4.9 + - - +
30X ARG* 3.1 34.1 + - - -
35X PRO 5.2 0.2 - - - +
38X ALA* 3.9 18.3 - - - +
62X SER* 5.5 0.4 - - - -
209Y T 2.7 19.2 + - - -
210Y A 6.0 1.3 - - - -
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Residues in contact with GLU 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X SER* 3.7 12.1 - - - +
24X THR* 2.7 39.9 + - + +
26X GLY* 1.3 71.1 - - - -
28X ILE* 1.3 54.8 + - + +
30X ARG* 2.6 36.3 + - - +
31X TYR* 2.7 36.4 + - - +
105X MET* 4.8 16.4 - - + -
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Residues in contact with ILE 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL* 4.4 10.8 - - + -
13X ALA* 3.9 32.5 - - + -
14X VAL* 4.7 11.2 - - + -
17X ILE* 5.0 4.9 - - + -
23X SER* 3.7 21.1 - - - +
24X THR 3.1 16.5 + - - +
25X TYR* 3.5 7.0 - - - +
27X GLU* 1.3 76.4 - - + +
29X ALA* 1.3 73.2 + - - +
31X TYR* 3.0 9.5 + - + -
32X VAL* 2.9 26.9 + - + +
41X VAL* 4.0 19.5 - - + -
59X VAL* 5.0 7.4 - - + -
106X TRP* 5.6 7.0 - - + -
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Residues in contact with ALA 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X TYR 3.2 3.2 + - - -
26X GLY* 3.1 12.3 + - - +
28X ILE* 1.3 83.3 - - - +
30X ARG* 1.3 62.8 + - - +
32X VAL* 3.2 8.7 + - - +
34X MET* 2.9 40.4 + - - +
35X PRO 4.1 6.7 - - - +
37X TYR 3.9 0.7 - - - -
38X ALA* 3.8 18.8 - - + +
41X VAL* 3.6 24.5 - - + +
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Residues in contact with ARG 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X THR* 4.3 2.2 - - - +
26X GLY* 3.1 11.7 + - - -
27X GLU* 2.6 59.9 + - - +
29X ALA* 1.3 77.6 - - - +
31X TYR* 1.3 66.1 + - - +
33X GLY* 2.8 16.8 + - - -
35X PRO* 3.9 30.8 + - + +
210Y A 4.8 13.7 + - - -
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Residues in contact with TYR 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X ALA* 3.8 27.1 - - + -
16X GLU* 3.1 33.7 + - - -
27X GLU* 2.7 21.9 + - - +
28X ILE* 3.0 14.0 + - + +
30X ARG* 1.3 72.5 - - - +
32X VAL* 1.3 65.0 + - + +
33X GLY* 3.3 1.2 + - - -
106X TRP* 4.0 16.9 - + - -
108X PRO* 4.6 21.0 - - + +
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Residues in contact with VAL 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 4.2 4.7 - - + +
6X PHE* 4.2 8.3 - - + -
9X LYS* 3.9 57.4 - - + +
10X VAL* 4.0 20.6 - - + +
13X ALA* 4.1 16.8 - - + -
28X ILE* 2.9 17.4 + - + +
29X ALA* 3.3 14.8 - - - +
31X TYR* 1.3 79.0 - - + +
33X GLY* 1.3 58.0 + - - +
34X MET* 3.2 19.6 - - + +
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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