Contacts of the helix formed by residues 287 - 295 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286E GLY* 1.3 75.7 - - - -
288E LEU* 1.3 68.0 + - - +
289E PHE* 3.7 6.8 - - - +
290E ASP* 2.7 38.6 + - - +
291E TYR* 2.9 20.3 + - - +
336E SER 3.6 9.6 - - - -
337E LYS* 3.7 19.0 - - - +
339E ILE 3.0 12.8 - - - -
340E LEU* 3.8 7.7 - - - +
341E VAL* 4.3 1.3 - - - -
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Residues in contact with LEU 288 (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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286E GLY 3.9 0.6 + - - -
287E SER* 1.3 71.1 - - - +
289E PHE* 1.3 57.4 + - - +
291E TYR* 3.4 10.7 - - + +
292E LEU* 2.8 64.0 + - + +
305E LEU* 3.9 20.2 - - + -
309E THR* 4.9 1.6 - - - +
336E SER* 3.3 14.1 - - - +
339E ILE* 2.7 36.3 + - + +
341E VAL* 4.3 5.8 - - + +
347E CYS* 4.6 11.9 - - - -
407E VAL* 3.7 30.3 - - + -
411E ILE* 4.1 12.6 - - + -
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Residues in contact with PHE 289 (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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287E SER* 3.7 3.8 - - - +
288E LEU* 1.3 77.1 - - - +
290E ASP* 1.3 75.5 + - - +
292E LEU* 3.5 4.2 + - - +
293E ASN* 2.7 46.9 + - - -
336E SER* 2.9 24.5 + - - +
337E LYS* 3.5 50.3 - - + -
424E TYR* 3.1 44.1 - + - -
426E LEU* 3.8 11.7 - - + -
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Residues in contact with ASP 290 (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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211E ILE 5.6 1.9 - - - +
285E HIS 4.6 7.4 - - - +
286E GLY* 4.5 2.6 - - - -
287E SER* 2.7 32.4 + - - +
289E PHE* 1.3 91.4 - - - +
291E TYR* 1.3 58.0 + - - +
293E ASN* 3.2 6.8 + - - +
294E ARG* 2.9 31.5 + - - +
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Residues in contact with TYR 291 (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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285E HIS* 4.0 31.7 + + + +
287E SER 2.9 12.6 + - - +
288E LEU* 3.1 9.4 + - + +
290E ASP* 1.3 78.6 - - - +
292E LEU* 1.3 70.4 + - + +
294E ARG* 3.3 1.2 + - - -
295E TYR* 2.8 74.9 + + + +
297E VAL* 5.4 12.2 - - + +
305E LEU* 4.1 22.6 - - + +
341E VAL* 3.5 38.6 - - + +
345E GLY* 4.9 8.5 - - - -
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Residues in contact with LEU 292 (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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288E LEU* 2.8 44.7 + - + +
289E PHE 4.0 1.3 - - - +
291E TYR* 1.3 91.3 - - + +
293E ASN* 1.3 60.8 + - - +
295E TYR* 2.8 9.5 - - + +
296E THR 6.5 0.4 - - - -
297E VAL* 5.6 5.4 - - + -
305E LEU* 4.4 8.7 - - + -
336E SER* 5.2 2.2 - - - -
410E GLU* 3.7 38.1 - - + +
411E ILE* 4.0 12.6 - - + +
414E ARG* 2.7 44.7 + - + -
424E TYR* 3.7 18.6 - - + -
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Residues in contact with ASN 293 (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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289E PHE* 2.7 53.5 + - - +
290E ASP* 3.2 7.3 + - - +
292E LEU* 1.3 78.2 - - - +
294E ARG* 1.3 59.6 + - - +
414E ARG* 3.8 7.8 + - - -
424E TYR* 2.9 40.4 - - - +
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Residues in contact with ARG 294 (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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290E ASP 2.9 16.5 + - - +
291E TYR* 3.8 3.6 - - - +
293E ASN* 1.3 78.7 - - - +
295E TYR* 1.3 103.6 + - + +
414E ARG* 4.9 1.1 - - - -
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Residues in contact with TYR 295 (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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285E HIS* 4.5 15.6 + + - -
291E TYR* 2.8 66.3 + + + +
292E LEU* 2.8 26.4 - - + +
294E ARG* 1.3 133.1 + - + +
296E THR* 1.3 74.9 + - - +
414E ARG* 2.8 13.4 + - - +
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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