Contacts of the helix formed by residues 50 - 55 (chain E) in PDB entry 3IFS
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 ASP 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E HIS* 5.5 3.9 + - - -
38E LYS* 4.9 10.6 + - - +
46E LEU 4.6 0.2 + - - -
47E GLY 3.9 3.9 + - - +
49E VAL* 1.3 89.0 - - - +
51E LEU* 1.3 60.3 + - - +
52E PRO* 3.2 3.8 - - - -
53E LEU* 3.0 7.5 + - + +
54E GLN* 2.9 56.3 + - + +
238E ARG* 2.7 39.4 + - - +
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Residues in contact with LEU 51 (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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47E GLY 3.4 18.6 + - - +
48E TRP* 3.7 18.4 - - + +
49E VAL 3.5 0.2 - - - -
50E ASP* 1.3 76.4 - - - +
52E PRO* 1.4 70.1 - - + +
54E GLN* 4.4 3.4 - - - +
55E TYR* 3.0 48.0 + - + +
202E PRO* 5.4 7.9 - - + -
205E VAL* 4.9 3.6 - - + -
209E PHE 4.9 2.9 - - - +
212E LEU* 3.9 32.8 - - + +
213E THR* 3.7 31.9 - - + -
231E MSE 5.1 1.1 - - + -
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Residues in contact with PRO 52 (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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48E TRP 3.6 9.0 - - - +
49E VAL 3.8 5.2 - - - +
50E ASP 3.3 5.6 - - - -
51E LEU* 1.4 93.4 - - + +
53E LEU* 1.3 61.8 + - - +
55E TYR* 3.4 9.5 - - - -
212E LEU* 4.8 5.8 - - + -
231E MSE 3.0 29.3 - - + +
234E ALA* 3.7 21.3 - - + +
235E ALA* 3.5 34.2 - - - +
238E ARG* 4.4 5.4 - - + -
399E TYR* 3.9 17.0 - - + -
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Residues in contact with LEU 53 (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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50E ASP* 3.0 6.5 + - + +
52E PRO* 1.3 78.8 - - - +
54E GLN* 1.3 60.8 + - + +
55E TYR* 3.5 1.3 - - - -
57E LYS* 2.5 29.8 + - - -
235E ALA* 3.8 24.7 - - + +
238E ARG* 3.1 47.1 - - - +
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Residues in contact with GLN 54 (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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47E GLY 5.8 0.3 - - - +
50E ASP* 2.9 41.5 + - + +
51E LEU* 4.8 2.0 - - - -
53E LEU* 1.3 80.3 - - + +
55E TYR* 1.3 68.1 + - - +
56E ASP* 3.5 1.4 + - - -
57E LYS* 3.4 3.3 + - - +
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Residues in contact with TYR 55 (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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51E LEU* 3.0 34.9 + - + +
52E PRO 3.4 17.0 - - - -
53E LEU* 4.5 1.1 - - - -
54E GLN* 1.3 76.9 - - - +
56E ASP* 1.3 62.3 + - - +
57E LYS* 2.7 68.7 + - + +
60E PHE* 3.7 45.1 - + + -
212E LEU 5.6 2.0 - - - +
231E MSE 3.2 36.9 - - + +
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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