Contacts of the helix formed by residues 82 - 85 (chain F) 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 ILE 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308E SER* 4.3 1.8 - - - +
309E THR* 4.3 6.1 - - + +
312E HIS* 3.2 49.6 - - + +
81F GLY* 1.3 73.7 - - - +
83F GLY* 1.3 75.4 + - - +
84F GLY 3.3 0.9 + - - -
85F SER* 3.0 17.8 + - - -
86F TYR* 3.8 6.7 - - - +
118F GLY 3.6 4.9 - - - +
119F GLN* 3.6 30.1 - - + +
143F ILE 4.9 0.2 + - - -
149F THR* 3.9 5.8 - - + -
151F GLU* 3.4 24.5 - - + +
152F PRO* 3.7 22.4 - - + +
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Residues in contact with GLY 83 (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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309E THR 5.0 1.9 + - - -
312E HIS* 3.6 30.4 - - - +
313E SER* 5.8 0.2 - - - -
82F ILE* 1.3 78.5 - - - +
84F GLY* 1.3 64.5 + - - -
86F TYR* 2.9 19.4 + - - +
87F LEU* 3.0 19.2 + - - +
287F GLN* 3.5 10.6 - - - +
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Residues in contact with GLY 84 (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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82F ILE 3.3 1.0 + - - -
83F GLY* 1.3 71.0 - - - -
85F SER* 1.3 57.5 + - - +
86F TYR 3.2 3.5 + - - -
87F LEU* 4.6 1.8 - - - -
88F GLY* 4.4 11.2 + - - -
89F ALA 5.6 0.2 + - - -
207F GLY* 3.4 34.7 - - - +
208F ARG* 4.3 1.3 - - - -
210F SER* 3.5 13.2 + - - -
211F VAL* 5.3 2.6 + - - -
215F VAL* 3.6 6.6 - - - +
284F TRP* 6.5 1.1 - - - -
287F GLN* 3.5 16.1 + - - +
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Residues in contact with SER 85 (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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79F VAL* 4.3 5.4 - - - +
81F GLY* 4.1 6.9 - - - -
82F ILE 3.0 17.9 + - - -
84F GLY* 1.3 75.9 - - - +
86F TYR* 1.3 57.6 + - - +
89F ALA* 5.6 2.9 - - - +
143F ILE* 3.3 57.7 + - - +
144F SER* 4.8 2.4 + - - -
201F ILE* 4.7 6.8 - - - +
207F GLY* 5.9 1.4 - - - -
210F SER* 5.3 0.5 + - - -
215F VAL* 3.6 14.7 - - - +
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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