Contacts of the helix formed by residues 50 - 54 (chain F) in PDB entry 1F1H
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179E TYR* 3.6 16.8 + - - -
210E HIS* 5.5 0.2 - - - -
212E GLU* 5.1 0.3 - - - +
269E HIS* 5.8 4.9 - - - -
339E ARG* 4.7 8.8 + - - +
344E ARG* 4.2 15.7 - - - +
359E ARG* 5.4 10.0 + - - +
473E TL 3.3 12.8 - - - -
1475E ADP 3.1 30.5 + - - +
49F PHE* 1.4 72.2 - - - +
51F GLY* 1.3 56.9 + - - +
52F SER* 3.1 9.2 + - - -
53F SER* 2.9 28.8 + - - -
63F SER 4.6 0.2 - - - -
64F ASP* 4.3 7.4 - - - -
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Residues in contact with GLY 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E TYR* 6.1 0.4 - - - -
49F PHE* 3.3 29.8 - - - +
50F ASP* 1.3 72.2 - - - +
52F SER* 1.3 50.1 + - - +
53F SER* 1.8 29.5 + - - -
54F ILE* 2.5 22.6 + - - +
57F TRP* 5.8 2.5 - - - +
58F LYS* 5.9 0.2 - - - -
63F SER 3.8 10.8 + - - -
65F MET* 5.8 2.5 - - - -
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Residues in contact with SER 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E GLU* 4.3 24.6 + - - +
339E ARG* 3.5 19.2 + - - +
50F ASP* 3.1 3.7 + - - -
51F GLY* 1.3 71.9 - - - +
53F SER* 1.3 59.3 + - - -
54F ILE 3.4 6.5 + - - +
57F TRP 5.7 1.6 - - - -
58F LYS* 4.3 22.6 - - - +
59F GLY 4.7 5.6 - - - +
60F ILE* 5.6 2.7 - - - -
63F SER* 3.0 40.3 + - - +
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E TYR* 3.2 41.2 - - - +
213E VAL* 4.7 8.0 - - - +
473E TL 3.3 9.2 - - - -
50F ASP* 2.9 26.1 + - - -
51F GLY* 1.8 22.6 + - - -
52F SER* 1.3 72.4 + - - +
54F ILE* 1.4 59.8 + - - +
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Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E TYR* 4.4 19.7 - - + +
180E PHE* 4.5 10.1 - - + -
21F PHE* 4.5 18.2 - - + -
23F ASP* 4.5 18.2 - - + +
29F GLN* 4.6 12.6 - - - +
49F PHE* 4.9 7.6 - - + -
51F GLY* 2.5 32.5 + - - +
52F SER 4.2 0.3 - - - +
53F SER* 1.4 76.3 - - - +
55F GLY* 1.4 71.5 + - - +
57F TRP* 4.0 40.7 - - + -
58F LYS* 3.6 28.4 + - - +
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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