Contacts of the helix formed by residues 25 - 32 (chain C) in PDB entry 4QGC
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B GLU* 3.6 39.7 - - + +
400B ARG* 4.7 16.6 - - - +
401B LEU* 3.5 15.6 - - + +
24C ASP* 1.3 86.8 + - + +
26C PHE* 1.3 64.8 + - - +
27C LEU 4.0 0.9 - - - -
28C GLU* 2.9 35.9 + - - +
29C HIS* 3.1 20.6 + - - +
390C TYR* 3.8 7.4 - - - -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LYS* 6.0 0.4 - - - -
393B GLN* 3.7 17.0 - - - +
397B GLU* 2.9 20.3 + - - +
25C THR* 1.3 72.5 - - - +
27C LEU* 1.3 64.7 + - - +
29C HIS* 3.2 6.3 + + + +
30C MET* 3.1 59.9 + - + +
388C ALA 4.0 18.2 - - - -
390C TYR* 3.8 32.6 - - + -
393C GLN* 5.3 4.9 - - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLY* 3.5 31.9 - - - +
318B ASN* 4.4 11.0 - - + +
319B ARG* 4.1 12.6 - - + +
397B GLU* 3.0 17.5 + - + +
398B LEU* 3.6 37.9 - - + +
401B LEU* 3.9 23.1 - - + -
25C THR* 3.1 0.6 - - - +
26C PHE* 1.3 76.7 - - - +
28C GLU* 1.3 65.5 + - - +
30C MET* 3.1 9.4 + - + +
31C CYS* 3.0 29.8 + - - -
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ARG* 4.8 7.6 - - - +
401B LEU* 3.4 32.9 - - + +
24C ASP* 3.5 27.9 - - - +
25C THR* 2.9 26.7 + - - +
27C LEU* 1.3 78.0 - - - +
29C HIS* 1.3 62.7 + - - +
31C CYS* 3.2 8.7 + - - +
32C ARG* 3.0 58.8 + - - +
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Residues in contact with HIS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C THR 3.1 13.8 + - - +
26C PHE* 3.2 17.5 - + - +
27C LEU 3.1 0.2 - - - -
28C GLU* 1.3 79.5 - - - +
30C MET* 1.3 60.6 + - - +
32C ARG* 3.7 12.3 + - - +
33C LEU* 3.6 17.0 + - - +
387C ALA 3.0 27.1 + - - +
388C ALA* 3.7 19.5 - - - -
389C ILE 3.0 25.2 + - - -
390C TYR* 4.0 18.3 - + + -
447C ARG* 4.4 15.0 - - - -
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Residues in contact with MET 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LYS* 3.6 54.3 - - + +
312B MET* 3.3 15.8 - - - -
315B GLY* 4.6 7.9 - - - -
354B ASP* 4.7 12.6 - - - +
26C PHE* 3.1 53.7 + - + +
27C LEU* 3.1 10.3 + - + +
29C HIS* 1.3 76.7 - - - +
31C CYS* 1.3 64.8 + - - +
32C ARG 3.1 1.8 - - - -
33C LEU* 3.2 31.8 + - + +
388C ALA* 4.6 10.5 - - - +
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Residues in contact with CYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B MET* 3.7 3.6 - - - +
315B GLY 3.5 31.9 - - - -
316B ARG* 2.8 49.1 + - + +
319B ARG* 3.3 43.7 - - - +
27C LEU* 3.0 24.7 + - - +
28C GLU* 3.2 3.8 + - - +
30C MET* 1.3 75.7 - - - +
32C ARG* 1.3 59.6 + - + +
33C LEU 3.3 0.4 + - - -
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ARG* 4.8 2.2 - - - +
319B ARG* 4.4 13.3 - - - +
28C GLU* 3.0 49.1 + - - +
29C HIS* 4.0 10.3 - - - +
30C MET 3.1 0.6 - - - -
31C CYS* 1.3 77.3 - - - +
33C LEU* 1.3 65.4 + - - +
34C ASP* 3.4 8.7 + - - +
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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