Contacts of the helix formed by residues 24 - 31 (chain A) in PDB entry 3SRF
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.1 4.7 - - - +
23A ASP* 1.3 89.1 + - - +
25A PHE* 1.3 61.6 + - - +
26A LEU* 3.3 20.2 - - + +
27A GLU* 3.3 19.7 - - + +
28A HIS* 2.8 28.1 + - - +
389A PHE* 3.9 3.4 - - - -
392A LYS* 6.0 0.2 - - - -
396B GLU* 3.5 33.6 - - + +
399B ARG* 4.6 17.3 + - + +
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Residues in contact with PHE 25 (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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24A THR* 1.3 69.1 - - - +
26A LEU* 1.3 65.1 + - - +
28A HIS* 3.3 23.2 - + - +
29A MET* 3.2 40.8 + - + +
352A LEU* 6.3 3.1 - - + -
389A PHE* 3.8 23.0 - + + -
392A LYS* 3.2 31.9 - - - +
25B PHE* 4.9 25.4 - + - -
353B ASP* 6.0 1.3 - - - -
392B LYS* 4.0 9.0 - - - -
396B GLU* 3.1 21.2 + - - +
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Residues in contact with LEU 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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24A THR* 3.2 10.3 - - + -
25A PHE* 1.3 77.9 - - - +
27A GLU* 1.3 60.4 + - - +
29A MET* 3.3 12.0 + - - +
30A CYS* 3.1 32.7 + - - -
314B GLY* 4.0 25.8 - - - +
317B ASN* 4.4 8.1 - - + +
318B ARG* 4.4 10.5 - - + -
353B ASP 6.1 0.4 - - - +
393B LEU* 4.8 11.0 - - + -
396B GLU* 3.3 36.2 + - + +
397B LEU* 3.7 28.9 - - + -
400B ALA* 4.0 14.8 - - + -
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Residues in contact with GLU 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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22A ALA* 3.9 13.2 - - + +
24A THR* 3.2 24.3 + - + +
26A LEU* 1.3 77.7 - - - +
28A HIS* 1.3 66.3 + - - +
30A CYS* 3.5 3.6 + - - +
31A ARG* 3.3 59.4 + - - +
318B ARG* 2.8 36.6 + - - -
400B ALA* 5.9 1.0 - - - +
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Residues in contact with HIS 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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16A GLN 5.5 0.7 - - - -
19A ALA* 2.7 61.7 + - + +
20A ALA* 4.6 1.6 - - - -
22A ALA* 3.5 10.7 - - + +
24A THR 2.8 13.6 + - - +
25A PHE* 3.3 28.9 - + - +
27A GLU* 1.3 79.3 - - - +
29A MET* 1.3 66.4 + - + +
31A ARG 3.4 3.5 + - - -
32A LEU* 3.6 8.5 + - + +
386A ALA 5.3 0.9 - - - -
387A ALA* 2.6 31.1 + - - -
388A MET 3.6 15.5 - - - -
389A PHE* 3.5 30.9 + + + -
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Residues in contact with MET 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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25A PHE* 3.2 34.0 + - + +
26A LEU* 3.6 13.2 - - - +
28A HIS* 1.3 84.0 - - + +
30A CYS* 1.3 62.5 - - - +
32A LEU* 3.1 31.6 + - + +
310B LYS* 3.3 48.9 - - + +
311B MET* 3.4 12.2 - - - -
313B ILE* 4.4 1.1 - - + -
314B GLY* 4.2 14.6 - - - +
353B ASP* 3.9 43.3 - - + +
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Residues in contact with CYS 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 LEU* 3.1 28.1 + - - +
27A GLU* 3.9 8.7 - - - +
28A HIS 3.4 0.2 - - - -
29A MET* 1.3 79.1 - - - +
31A ARG* 1.3 58.8 + - - +
32A LEU 3.4 0.2 - - - -
311B MET* 3.6 8.0 - - - +
314B GLY* 3.6 31.4 - - - -
315B ARG* 2.8 44.9 + - + -
318B ARG* 3.6 38.8 - - - +
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Residues in contact with ARG 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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13A GLN* 5.6 0.2 + - - -
16A GLN* 4.3 1.6 - - - +
18A HIS* 3.2 70.8 + - + +
19A ALA* 3.7 18.8 + - - +
21A MET* 3.0 34.2 + - - +
22A ALA* 3.7 3.7 + - - +
27A GLU* 3.3 46.5 + - - +
28A HIS 3.9 0.4 - - - +
29A MET 3.1 1.0 - - - -
30A CYS* 1.3 77.1 - - - +
32A LEU* 1.3 63.9 + - - +
33A ASP* 3.1 11.3 + - - +
315B ARG* 4.7 4.0 - - - +
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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