Contacts of the helix formed by residues 280 - 290 (chain B) in PDB entry 5IYB
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 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B VAL* 1.3 90.4 + - - +
281B ASP* 1.3 65.6 + - - +
283B ASP* 3.1 30.1 + - - +
284B ILE* 3.1 21.8 + - - +
20I CYS 3.4 15.6 + - - -
21I ASN* 3.7 23.4 - - - +
22I ASN* 3.3 5.4 - - - +
148S PRO* 5.6 6.1 - - - +
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG* 3.0 27.2 + - - -
280B SER* 1.3 70.3 - - - +
282B ARG* 1.3 56.8 + - - +
284B ILE* 3.1 9.8 + - - +
285B LEU* 2.7 39.0 + - - +
305B LEU* 3.9 35.1 - - + +
309B PHE* 4.3 10.5 - - - -
16I PHE* 4.4 6.5 - - + -
21I ASN 3.8 0.8 + - - -
22I ASN* 3.4 13.1 + - - +
23I MET* 3.1 33.8 + - + +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B SER 3.3 0.4 - - - -
281B ASP* 1.3 77.7 - - - +
283B ASP* 1.3 63.7 + - - +
285B LEU* 3.3 3.3 + - + +
286B GLU* 2.6 51.5 + - + +
292B PHE* 4.2 22.9 - - + -
559B ALA* 5.3 6.3 - - - +
14I ILE* 3.6 24.9 - - + -
16I PHE* 3.6 20.2 - - + -
21I ASN* 3.3 48.0 + - - +
34S ALA* 3.3 37.2 + - - +
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 5.0 16.6 - - + -
279B VAL* 5.5 0.5 + - - +
280B SER* 3.1 33.1 + - - +
281B ASP 3.1 0.6 - - - -
282B ARG* 1.3 91.5 + - - +
284B ILE* 1.3 59.5 + - - +
286B GLU* 3.5 16.9 - - - +
287B HIS* 3.0 33.8 + - + +
21I ASN* 4.1 5.8 + - - -
32S ASN* 4.9 6.2 + - - -
34S ALA* 5.5 0.7 - - - +
148S PRO* 5.9 2.9 - - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ILE* 3.9 35.0 - - + -
273B PHE* 4.0 34.8 - - + -
274B ARG* 4.3 17.7 - - + +
278B PHE* 4.3 16.8 - - + +
280B SER 3.1 14.9 + - - +
281B ASP* 3.1 16.9 + - - +
283B ASP* 1.3 74.9 - - - +
285B LEU* 1.3 63.4 + - + +
287B HIS* 3.1 8.9 + - - +
288B ILE* 2.9 46.5 + - + +
305B LEU* 4.8 0.9 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ASP 2.7 21.3 + - - +
282B ARG* 3.7 5.4 - - + +
284B ILE* 1.3 76.1 - - + +
286B GLU* 1.3 58.5 + - - +
288B ILE* 3.9 7.2 - - + -
289B ILE* 2.4 49.0 + - + +
292B PHE* 6.3 2.0 - - + -
298B MET* 3.9 20.2 - - + +
301B VAL* 3.8 37.7 - - + -
305B LEU* 3.8 28.7 - - + -
16I PHE* 3.5 34.5 - - + -
23I MET* 5.4 0.2 - - - -
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ARG* 2.6 35.5 + - + +
283B ASP* 3.5 19.3 - - - +
285B LEU* 1.3 74.8 - - - +
287B HIS* 1.3 63.1 + - + +
289B ILE* 4.5 5.4 - - - -
290B TYR* 3.8 13.0 + - - +
292B PHE* 5.9 4.2 - - + -
557B SER* 4.2 7.6 - - - -
558B PRO* 3.8 41.9 - - + +
559B ALA* 3.3 34.0 + - + +
32S ASN* 4.0 19.0 + - - +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B PHE* 4.2 12.0 - + + -
278B PHE* 3.4 24.9 - + - -
283B ASP* 3.0 16.1 + - + +
284B ILE* 3.3 10.8 - - - +
286B GLU* 1.3 79.9 - - + +
288B ILE* 1.3 57.9 + - - +
290B TYR* 3.4 24.8 + - - -
359B THR* 4.1 1.9 + - - +
362B ALA* 3.0 33.8 + - + +
363B TYR* 3.0 71.5 + + - +
366B GLY* 3.8 10.2 - - - -
558B PRO* 5.2 2.0 - - + -
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ILE* 4.5 7.4 - - + -
273B PHE* 4.6 8.1 - - + -
284B ILE* 2.9 37.9 + - + +
285B LEU* 3.5 8.5 - - + +
287B HIS* 1.3 78.0 - - - +
289B ILE* 1.3 61.0 + - + +
290B TYR* 3.8 6.1 - - - -
297B MET* 3.4 22.7 - - + -
301B VAL* 4.3 26.2 - - + -
366B GLY* 4.4 16.4 - - - +
369B VAL* 4.3 27.4 - - + -
370B HIS* 3.0 27.9 + - - +
373B LEU* 5.7 0.4 - - + -
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 2.4 41.6 + - + +
286B GLU* 4.5 3.6 - - - +
288B ILE* 1.3 69.6 - - + +
290B TYR* 1.3 60.5 + - - +
291B ASP* 2.3 24.4 + - + +
292B PHE* 3.7 21.8 - - + +
294B ASP* 4.1 14.6 - - + +
297B MET* 3.2 46.4 - - + -
298B MET* 3.7 37.2 - - + -
370B HIS* 4.2 7.1 - - + -
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Residues in contact with TYR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B GLU* 3.8 15.1 + - - +
287B HIS* 3.4 24.2 + - - -
288B ILE 3.8 1.8 - - - -
289B ILE* 1.3 73.7 - - - +
291B ASP* 1.3 64.7 + - + +
292B PHE* 3.2 4.7 + - - +
363B TYR* 4.3 2.9 + + - -
367B TYR* 3.7 19.4 + + - +
370B HIS* 3.4 47.8 - + + -
558B PRO* 4.5 13.0 - - + -
559B ALA* 3.8 18.3 - - - +
562B ALA* 3.3 35.9 - - + +
566B LYS* 4.1 21.3 - - - -
573B TRP* 3.3 39.6 - + - -
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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