Contacts of the helix formed by residues 308 - 313 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C ILE* 4.4 0.2 - - - +
120C ASN* 4.2 5.9 - - - +
121C ILE* 3.7 18.8 - - - +
151C GLU* 2.7 37.0 + - - +
425C TYR* 5.6 1.3 - - - -
429C MSE 6.4 0.2 - - - -
274D TYR* 4.2 8.7 - - - -
307D PHE* 1.3 74.4 + - - +
309D THR* 1.3 68.1 + - - +
310D ASP 3.2 2.9 - - - -
311D LEU* 2.9 30.6 + - - +
312D HIS* 3.3 11.4 - - - -
363D ASN* 5.0 2.6 + - - -
366D ALA* 5.1 3.4 - - - -
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Residues in contact with THR 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ILE* 4.3 6.0 - - + +
83C GLY* 5.0 2.3 + - - +
86C TYR* 4.0 28.7 - - + +
87C LEU* 5.7 2.2 - - + -
119C GLN* 2.6 35.2 + - + +
120C ASN* 3.8 10.2 + - - +
306D ASN* 3.3 14.8 + - + +
307D PHE 3.2 3.9 + - - -
308D SER* 1.3 77.8 + - - +
310D ASP* 1.3 68.1 + - - +
312D HIS* 3.1 26.3 + - - +
313D SER* 4.1 2.4 + - - -
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Residues in contact with ASP 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 6.1 0.9 - - - +
283C GLU* 4.4 14.5 - - - +
286C LYS* 5.8 1.2 + - - -
304D SER 4.8 0.3 - - - +
305D ALA* 3.4 12.7 - - + +
306D ASN* 2.8 48.7 + - - +
307D PHE* 3.8 17.4 - - + -
309D THR* 1.3 81.4 - - - +
311D LEU* 1.3 55.6 + - - +
312D HIS 2.9 5.8 - - - -
313D SER* 3.3 16.6 + - - +
314D LEU* 2.7 38.0 + - + +
315D GLY 3.1 3.5 + - - -
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C GLU* 4.9 0.2 - - - +
422C VAL* 3.9 15.2 - - - +
425C TYR* 3.8 37.5 + - + +
274D TYR* 4.4 3.4 - - + +
307D PHE* 3.6 39.6 - - + -
308D SER* 2.9 31.8 + - - +
310D ASP* 1.3 77.3 - - - +
312D HIS* 1.3 58.6 + - - +
313D SER 3.3 1.3 - - - -
315D GLY* 3.4 24.3 + - - -
366D ALA* 5.8 1.6 - - + -
370D THR* 3.6 24.7 - - + +
374D HIS* 3.8 21.8 - - + +
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Residues in contact with HIS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ILE* 3.3 31.6 - - + +
83C GLY* 3.7 20.0 - - - +
149C THR* 3.7 28.9 - - + +
151C GLU* 2.9 21.1 + - - -
287C GLN* 3.0 27.4 + - - +
291C GLU* 3.4 11.7 - - - +
422C VAL* 5.6 1.3 - - - -
425C TYR* 3.2 18.7 + - - -
426C LYS* 4.7 10.3 + - - -
308D SER 3.3 13.9 - - - -
309D THR 3.1 8.4 + - - +
310D ASP 2.9 1.2 - - - -
311D LEU* 1.3 82.4 - - - +
313D SER* 1.3 56.2 + - - +
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 4.1 15.4 - - - +
283C GLU* 4.9 4.5 + - - -
286C LYS 4.2 0.7 - - - +
287C GLN* 3.6 32.2 - - - -
290C GLY 4.4 0.7 - - - -
291C GLU* 3.4 27.4 + - - +
309D THR 4.4 1.3 + - - -
310D ASP* 3.2 26.2 + - - +
311D LEU 3.3 0.8 - - - -
312D HIS* 1.3 80.1 - - - +
314D LEU* 1.3 82.4 + - - +
315D GLY 3.6 0.9 - - - -
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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