Contacts of the helix formed by residues 308 - 312 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C TYR* 4.0 10.7 - - - -
307C PHE* 1.3 73.8 + - - +
309C THR* 1.3 66.4 + - - +
310C ASP 3.3 2.0 - - - -
311C LEU* 3.0 30.7 + - - +
312C HIS* 3.3 12.1 - - - -
363C ASN* 5.0 2.6 + - - -
366C ALA* 4.9 3.6 - - - -
82D ILE* 4.5 0.4 - - - +
120D ASN* 4.3 6.9 - - - +
121D ILE* 3.5 19.3 - - - +
151D GLU* 2.9 35.6 + - - +
425D TYR* 5.6 1.1 - - - -
429D MSE 6.4 0.4 - - - -
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Residues in contact with THR 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C PRO* 6.2 0.2 - - - +
306C ASN* 3.3 16.1 + - + +
307C PHE 3.1 2.7 + - - -
308C SER* 1.3 80.6 + - - +
310C ASP* 1.3 65.5 + - - +
312C HIS* 3.3 24.1 + - - +
313C SER* 4.3 1.6 + - - -
82D ILE* 4.3 5.5 - - + +
83D GLY* 5.0 1.4 + - - -
86D TYR* 4.2 17.0 - - + +
87D LEU* 6.0 2.0 - - + -
119D GLN* 2.5 45.0 + - + +
120D ASN* 3.6 11.6 + - - +
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Residues in contact with ASP 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C SER 4.8 0.2 - - - +
305C ALA* 3.5 13.0 - - + +
306C ASN* 2.7 49.7 + - - +
307C PHE* 3.9 16.7 - - + -
308C SER 3.3 0.2 - - - -
309C THR* 1.3 80.4 - - - +
311C LEU* 1.3 55.7 + - - +
312C HIS 3.0 6.1 - - - -
313C SER* 3.5 18.1 + - - +
314C LEU* 2.8 36.6 + - + +
315C GLY 3.1 3.5 + - - -
87D LEU* 6.0 2.1 - - - +
283D GLU* 4.3 15.1 - - - +
286D LYS* 5.7 1.9 + - - -
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR* 4.5 3.1 - - + +
307C PHE* 3.6 33.8 - - + -
308C SER* 3.0 31.2 + - - +
310C ASP* 1.3 78.0 - - - +
312C HIS* 1.3 59.5 + - - +
313C SER 3.3 1.3 - - - -
315C GLY* 3.3 26.4 + - - -
316C GLN 4.4 0.2 + - - -
366C ALA* 5.8 1.3 - - + -
370C THR* 3.6 38.8 - - + +
374C HIS* 3.8 11.2 - - + +
291D GLU* 4.9 0.2 - - - +
422D VAL* 3.9 15.4 - - - +
425D TYR* 3.7 38.5 - - + +
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C SER 3.3 14.6 - - - -
309C THR 3.6 7.4 - - - +
310C ASP 3.0 0.8 - - - -
311C LEU* 1.3 81.8 + - - +
313C SER* 1.3 56.5 + - - +
82D ILE* 3.1 37.1 - - + +
83D GLY* 3.7 19.3 - - - +
149D THR* 3.8 12.2 - - + +
151D GLU* 2.7 34.1 + - - -
287D GLN* 3.0 27.4 + - - +
291D GLU* 3.6 10.6 - - - +
422D VAL* 5.6 1.1 - - - -
425D TYR* 3.3 19.5 + - - -
426D LYS* 4.9 8.7 + - - -
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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