Contacts of the helix formed by residues 24 - 31 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ALA* 3.0 5.1 - - - +
23E ASP* 1.3 86.8 + - - +
25E PHE* 1.3 59.5 + - - +
26E LEU* 3.3 12.3 - - + +
27E GLU* 3.3 30.5 - - + +
28E HIS* 2.8 28.2 + - - +
389E PHE* 3.9 4.0 - - - -
392E LYS* 6.0 0.7 - - - -
396F GLU* 3.6 34.3 - - + +
399F ARG* 4.7 15.3 + - + +
400F ALA* 6.5 0.2 - - + -
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Residues in contact with PHE 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 1.3 71.5 - - - +
26E LEU* 1.3 64.8 + - - +
28E HIS* 3.2 21.9 + + - +
29E MET* 3.2 43.1 + - + +
389E PHE* 4.3 18.0 - + + -
392E LYS* 3.1 32.2 - - - +
25F PHE* 4.9 26.7 - + - -
310F LYS* 5.8 6.5 - - - -
353F ASP* 6.1 0.7 - - - -
392F LYS* 4.6 4.0 - - - -
396F GLU* 3.4 17.7 + - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 3.3 9.6 - - + -
25E PHE* 1.3 76.5 - - - +
27E GLU* 1.3 62.2 + - - +
29E MET* 3.3 15.2 + - - +
30E CYS* 3.2 28.7 + - - -
314F GLY* 3.8 29.8 - - - +
317F ASN* 4.3 13.7 - - + +
318F ARG* 4.4 9.6 - - + -
353F ASP 6.1 0.4 - - - +
393F LEU* 4.7 12.3 - - + -
396F GLU* 3.2 34.9 + - + +
397F LEU* 3.8 27.1 - - + +
400F ALA* 4.3 13.2 - - + -
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA* 3.9 13.0 - - + +
24E THR* 3.3 24.5 - - + +
26E LEU* 1.3 77.7 - - + +
28E HIS* 1.3 63.4 + - - +
29E MET 3.4 0.2 - - - -
30E CYS* 4.0 4.9 - - - +
31E ARG* 3.3 56.4 + - - +
318F ARG* 3.3 36.5 + - - -
400F ALA* 5.4 3.6 - - - +
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Residues in contact with HIS 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN 5.7 0.4 - - - -
19E ALA* 2.8 44.4 + - + +
20E ALA* 5.1 0.7 - - - -
22E ALA* 3.5 9.4 - - + -
24E THR 2.8 14.6 + - - +
25E PHE* 3.2 27.6 - + - +
26E LEU 3.1 0.2 - - - -
27E GLU* 1.3 75.1 - - - +
29E MET* 1.3 72.0 + - + +
31E ARG 3.6 1.7 + - - -
32E LEU* 3.6 17.6 - - + +
386E ALA 5.3 1.3 - - - -
387E ALA* 2.7 30.5 + - - -
388E MET 4.0 3.4 - - - -
389E PHE* 3.6 45.9 + + + -
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Residues in contact with MET 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE* 3.2 36.2 + - + +
26E LEU* 3.3 14.1 + - - +
28E HIS* 1.3 76.2 - - + +
30E CYS* 1.3 54.4 + - - +
31E ARG 2.8 5.1 + - - -
32E LEU* 2.8 43.6 + - + +
310F LYS* 3.3 57.7 - - + +
311F MET* 3.7 10.6 - - - -
313F ILE* 4.3 0.7 - - + -
314F GLY* 4.2 14.1 - - - +
317F ASN* 5.9 0.2 - - - +
353F ASP* 4.1 33.7 - - + +
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Residues in contact with CYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 3.2 19.7 + - - +
27E GLU* 4.0 10.3 - - - +
28E HIS 3.5 0.2 - - - -
29E MET* 1.3 77.1 - - - +
31E ARG* 1.3 58.8 + - - +
32E LEU 3.4 0.2 - - - -
311F MET* 3.6 9.8 - - - +
314F GLY* 3.4 33.9 - - - -
315F ARG* 3.0 48.2 + - + +
318F ARG* 3.7 32.1 - - - +
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Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 4.4 0.3 - - - +
18E HIS* 2.9 69.1 + - + +
19E ALA* 3.7 22.6 + - + +
21E MET* 3.9 25.7 + - - +
22E ALA* 4.7 5.3 + - - -
27E GLU* 3.3 46.2 + - - +
29E MET 2.8 1.6 + - - -
30E CYS* 1.3 78.7 - - - +
32E LEU* 1.3 64.4 + - - +
33E ASP* 3.0 11.1 + - - +
315F ARG* 4.9 3.1 - - - +
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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