Contacts of the helix formed by residues 308 - 313 (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 SER 308 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274E TYR* 4.0 9.4 - - - -
307E PHE* 1.3 74.7 + - - +
309E THR* 1.3 67.3 + - - +
310E ASP 3.3 2.0 - - - -
311E LEU* 2.9 35.5 + - - +
312E HIS* 3.4 6.9 - - - -
363E ASN* 4.9 2.6 + - - -
366E ALA* 5.0 3.6 - - - -
82F ILE* 4.3 0.3 - - - +
120F ASN* 4.3 6.9 - - - +
121F ILE* 3.6 19.3 - - - +
151F GLU* 2.7 37.4 + - - +
425F TYR* 5.7 0.9 - - - -
429F MSE 6.4 0.2 - - - -
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Residues in contact with THR 309 (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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306E ASN* 3.3 15.8 + - + +
307E PHE 3.1 2.9 + - - -
308E SER* 1.3 81.8 + - - +
310E ASP* 1.3 67.7 + - - +
312E HIS* 3.2 23.6 + - - +
313E SER* 4.2 2.3 + - - -
82F ILE* 4.3 6.0 - - + +
83F GLY* 5.0 1.6 + - - +
86F TYR* 4.0 29.6 - - + +
87F LEU* 5.8 1.6 - - + -
119F GLN* 2.6 34.3 + - + +
120F ASN* 3.7 11.6 + - - +
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Residues in contact with ASP 310 (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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304E SER 4.9 0.9 - - - +
305E ALA* 3.4 12.4 - - + +
306E ASN* 2.8 49.1 + - - +
307E PHE* 3.9 16.9 - - + -
309E THR* 1.3 82.0 - - - +
311E LEU* 1.3 55.4 + - - +
312E HIS 2.9 5.8 - - - -
313E SER* 3.4 16.3 + - - +
314E LEU* 2.7 34.8 + - + +
315E GLY 3.1 3.1 + - - -
87F LEU* 5.9 2.9 - - - +
283F GLU* 4.4 15.7 - - - +
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Residues in contact with LEU 311 (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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274E TYR* 4.5 5.6 - - + +
307E PHE* 3.6 32.7 - - + -
308E SER* 2.9 31.7 + - - +
310E ASP* 1.3 77.7 - - - +
312E HIS* 1.3 58.2 + - - +
313E SER 3.3 1.1 - - - -
315E GLY* 3.4 24.3 + - - -
316E GLN 4.4 0.2 + - - -
366E ALA* 5.8 1.3 - - + -
370E THR* 3.5 25.8 - - + +
374E HIS* 3.7 23.6 - - + +
422F VAL* 4.0 15.1 - - - +
425F TYR* 3.8 39.7 - - + +
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Residues in contact with HIS 312 (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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308E SER 3.4 13.9 - - - -
309E THR 3.2 7.2 + - - +
310E ASP 2.9 0.8 - - - -
311E LEU* 1.3 81.3 + - - +
313E SER* 1.3 57.1 + - - +
82F ILE* 3.2 31.4 - - + +
83F GLY* 3.6 20.3 - - - -
149F THR* 3.8 28.4 - - + +
151F GLU* 2.9 22.0 + - - -
287F GLN* 3.1 25.6 + - - +
291F GLU* 3.4 12.1 - - - +
422F VAL* 5.6 1.3 - - - -
425F TYR* 3.3 19.8 + - - -
426F LYS* 4.7 10.2 + - - -
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Residues in contact with SER 313 (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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309E THR 5.0 0.9 - - - -
310E ASP* 3.3 27.9 + - - +
311E LEU 3.3 0.6 - - - -
312E HIS* 1.3 81.2 - - - +
314E LEU* 1.3 76.0 + - - +
315E GLY 3.6 0.7 - - - -
83F GLY* 5.8 0.2 - - - -
87F LEU* 4.1 15.2 - - - +
283F GLU* 5.0 5.0 + - - -
286F LYS* 5.2 0.9 - - - -
287F GLN* 3.6 37.5 - - - -
291F GLU* 3.3 24.9 + - - +
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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