Contacts of the helix formed by residues 25 - 33 (chain A) in PDB entry 3G2G
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 THR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.7 1.9 - - - +
24A ASP* 1.3 90.0 - - + +
26A PHE* 1.3 59.5 + - - +
27A LEU 3.9 0.2 + - - -
28A GLU* 3.2 24.8 + - - +
29A HIS* 3.0 23.4 + - - +
390A TYR* 3.5 11.6 + - - -
397B GLU* 3.4 34.3 - - + +
400B ARG* 4.9 14.6 - - - -
401B LEU* 3.8 21.1 - - + +
24D ASP* 6.4 0.4 - - - -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 1.3 69.2 - - - +
27A LEU* 1.3 67.6 + - - +
29A HIS* 3.1 21.0 + + - +
30A MET* 2.9 52.7 + - + +
390A TYR* 3.7 32.6 - + + -
393A GLN* 4.2 2.2 - - - +
26B PHE* 6.4 3.8 - + - -
311B LYS* 6.2 2.5 - - + -
353B LEU 6.1 0.9 - - - -
354B ASP* 6.4 0.7 - - - -
393B GLN* 3.7 21.7 - - + +
397B GLU* 2.9 10.9 + - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 4.2 0.4 - - - +
26A PHE* 1.3 81.5 - - - +
28A GLU* 1.3 56.3 + - - +
30A MET* 3.2 14.2 + - - +
31A CYS* 2.9 33.3 + - - -
315B GLY* 3.7 33.9 - - - +
318B ASN* 4.5 9.9 - - + +
319B ARG* 4.9 9.6 - - + +
394B LEU* 5.0 10.8 - - + -
397B GLU* 2.9 17.9 + - + +
398B LEU* 3.5 39.5 - - + +
401B LEU* 4.0 25.6 - - + -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.7 12.3 - - + -
24A ASP* 4.9 2.5 - - + +
25A THR* 3.2 18.7 + - - +
27A LEU* 1.3 76.4 - - - +
29A HIS* 1.3 66.3 + - - +
31A CYS* 3.2 6.7 + - - +
32A ARG* 3.1 60.3 + - - +
319B ARG* 2.8 35.9 + - - -
401B LEU* 4.3 11.5 - - + +
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Residues in contact with HIS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN 5.3 0.7 - - - -
20A ALA* 2.7 48.9 + - + +
21A ALA* 4.4 2.9 - - + -
23A ALA* 3.4 8.4 - - + +
25A THR 3.0 14.9 + - - +
26A PHE* 3.1 26.9 + + - +
28A GLU* 1.3 76.5 - - - +
30A MET* 1.3 66.2 + - + +
32A ARG 3.1 8.7 + - - -
33A LEU* 3.4 19.6 + - + +
387A ALA 5.2 1.3 - - - -
388A ALA* 2.7 30.8 + - - -
389A ILE 3.6 14.6 - - - -
390A TYR* 3.5 31.7 + + + -
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Residues in contact with MET 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 2.9 52.2 + - + +
27A LEU* 3.2 18.8 + - - +
29A HIS* 1.3 77.3 - - + +
31A CYS* 1.3 64.6 + - - +
32A ARG 2.9 2.1 + - - -
33A LEU* 3.1 24.3 + - + +
311B LYS* 3.5 41.1 - - + +
312B MET* 3.2 17.5 - - - -
314B ILE* 4.7 0.4 - - + -
315B GLY* 4.2 10.3 - - - +
354B ASP* 3.4 39.7 - - + +
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 2.9 20.8 + - - +
28A GLU* 3.2 23.7 + - - +
30A MET* 1.3 76.1 - - - +
32A ARG* 1.3 58.4 + - - +
312B MET* 3.4 7.0 - - - +
315B GLY* 3.3 32.5 - - - -
316B ARG* 2.9 48.1 + - + -
319B ARG* 3.8 26.5 - - - +
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 4.2 0.9 - - - +
19A HIS* 3.0 69.7 + - + +
20A ALA* 3.6 24.4 + - + +
22A MET* 3.9 9.5 + - - +
23A ALA* 3.8 18.4 - - - +
24A ASP 5.7 0.4 - - - +
28A GLU* 3.1 51.0 + - - +
29A HIS 3.1 0.4 + - - -
30A MET 2.9 1.4 + - - -
31A CYS* 1.3 78.2 - - - +
33A LEU* 1.3 69.1 + - - +
34A ASP* 3.2 12.0 + - - +
316B ARG* 4.8 4.2 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 3.7 9.4 - - + +
20A ALA* 3.9 17.9 - - + -
29A HIS* 3.4 23.6 + - + +
30A MET* 3.1 17.6 + - + +
32A ARG* 1.3 76.2 - - - +
34A ASP* 1.3 60.1 + - - +
35A ILE 4.2 1.1 + - - -
353A LEU* 6.4 0.2 - - + -
388A ALA* 3.8 33.9 - - + +
307B PHE* 5.6 0.2 - - + -
308B LEU* 3.8 25.4 - - + +
309B ALA* 5.7 0.2 - - - -
311B LYS* 3.9 35.7 - - + -
312B MET* 3.5 22.7 - - - +
316B ARG* 5.0 1.9 + - - -
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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