Contacts of the helix formed by residues 287 - 295 (chain D) in PDB entry 1IAS
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 287 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286D GLY* 1.3 75.5 - - - -
288D LEU* 1.3 65.6 + - - +
289D PHE* 3.7 6.6 - - - +
290D ASP* 2.7 38.0 + - - +
291D TYR* 2.8 21.1 + - - +
336D SER 3.6 5.4 - - - -
337D LYS* 3.6 22.5 - - - +
339D ILE 2.9 13.7 - - - -
340D LEU* 3.7 6.8 - - - +
341D VAL* 4.3 0.9 - - - -
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Residues in contact with LEU 288 (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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286D GLY 3.9 0.6 + - - -
287D SER* 1.3 70.9 - - - +
289D PHE* 1.3 57.5 + - - +
291D TYR* 3.4 9.7 - - + +
292D LEU* 2.8 63.5 + - + +
305D LEU* 3.9 19.3 - - + -
309D THR* 4.9 1.1 - - - +
336D SER* 3.2 14.1 - - - +
339D ILE* 2.7 37.3 + - + +
341D VAL* 4.3 6.0 - - + +
347D CYS* 4.5 12.6 - - - -
407D VAL* 3.7 29.8 - - + -
411D ILE* 4.1 13.7 - - + -
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Residues in contact with PHE 289 (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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287D SER* 3.7 3.4 - - - +
288D LEU* 1.3 78.0 - - - +
290D ASP* 1.3 73.9 + - - +
292D LEU* 3.6 3.5 + - - +
293D ASN* 2.7 47.4 + - - -
336D SER* 2.8 23.9 + - - +
337D LYS* 3.4 52.7 - - + -
424D TYR* 3.1 41.9 - + - -
426D LEU* 3.7 12.8 - - + -
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Residues in contact with ASP 290 (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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211D ILE 5.7 0.7 - - - +
285D HIS 4.6 6.7 - - - +
286D GLY* 4.6 2.5 - - - -
287D SER* 2.7 32.7 + - - +
289D PHE* 1.3 91.0 - - - +
291D TYR* 1.3 58.6 + - - +
293D ASN* 3.2 7.0 + - - +
294D ARG* 2.9 31.1 + - - +
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Residues in contact with TYR 291 (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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285D HIS* 3.9 30.3 + + + +
287D SER 2.8 12.7 + - - +
288D LEU* 3.4 9.6 - - + +
290D ASP* 1.3 78.6 - - - +
292D LEU* 1.3 71.8 + - + +
294D ARG* 3.3 1.2 + - - -
295D TYR* 2.8 73.8 + + + +
296D THR 6.0 0.2 - - - -
297D VAL* 5.4 12.1 - - + +
305D LEU* 4.1 22.6 - - + +
341D VAL* 3.5 37.9 - - + +
345D GLY* 4.9 9.2 - - - -
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Residues in contact with LEU 292 (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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288D LEU* 2.8 44.2 + - + +
289D PHE 4.1 0.2 - - - +
291D TYR* 1.3 90.8 - - + +
293D ASN* 1.3 61.3 + - - +
294D ARG 3.2 0.4 - - - -
295D TYR* 2.8 9.4 - - + +
296D THR 6.4 0.4 - - - -
297D VAL* 5.6 5.2 - - + -
305D LEU* 4.4 9.2 - - + -
336D SER* 5.1 2.2 - - - -
410D GLU* 3.7 39.0 - - + +
411D ILE* 4.0 11.2 - - + +
414D ARG* 2.8 44.9 + - + -
424D TYR* 3.6 20.4 - - + -
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Residues in contact with ASN 293 (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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289D PHE* 2.7 50.5 + - - +
290D ASP* 3.2 7.1 + - - +
292D LEU* 1.3 77.3 - - - +
294D ARG* 1.3 60.9 + - - +
414D ARG* 3.9 7.3 + - - -
424D TYR* 2.8 45.3 - - - +
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Residues in contact with ARG 294 (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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290D ASP 2.9 17.0 + - - +
291D TYR* 3.8 2.9 - - - +
293D ASN* 1.3 80.2 - - - +
295D TYR* 1.3 107.5 + - + +
414D ARG* 4.8 1.1 - - - -
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Residues in contact with TYR 295 (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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285D HIS* 4.5 15.5 + + - -
291D TYR* 2.8 65.2 + + + +
292D LEU* 2.8 13.1 - - + +
294D ARG* 1.3 132.5 + - + +
296D THR* 1.3 73.3 + - - +
414D ARG* 2.7 29.0 + - - +
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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