Contacts of the helix formed by residues 281 - 290 (chain B) in PDB entry 4O9U
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 ASP 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 5.7 0.2 + - - -
280B ILE* 1.3 83.3 - - - +
282B VAL* 1.3 73.1 + - - +
283B GLU* 2.8 31.9 + - + +
284B ASP* 3.4 23.9 + - - +
285B ALA* 3.6 8.5 + - - +
432B LEU* 4.6 0.8 - - - +
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Residues in contact with VAL 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 ILE 4.0 0.2 + - - -
281B ASP* 1.3 77.2 + - - +
283B GLU* 1.3 83.9 + - - +
285B ALA 3.9 0.6 + - - -
286B ALA* 3.7 4.2 + - - +
432B LEU* 3.6 26.9 - - + +
433B TYR 5.5 1.1 - - - +
439B VAL* 4.2 14.6 - - + +
442B GLU* 2.9 47.6 - - + +
443B LEU* 3.4 26.7 - - + +
446B ALA* 4.6 1.9 - - - +
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Residues in contact with GLU 283 (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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25A ARG* 3.4 45.3 + - - +
281B ASP* 2.8 29.9 - - + +
282B VAL* 1.3 90.2 - - - +
284B ASP* 1.3 61.9 + - - +
285B ALA 3.1 2.2 - - - -
286B ALA* 3.0 20.4 + - - +
287B VAL* 3.0 17.3 + - + +
442B GLU* 4.9 0.7 - - - +
446B ALA* 4.1 17.2 - - + +
449B ARG* 3.4 27.9 + - - +
450B LEU* 5.4 1.0 - - - +
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 5.4 1.8 + - - -
26A VAL 5.0 0.7 - - - +
27A PRO* 4.0 6.2 - - - +
28A VAL* 3.2 53.6 + - + +
280B ILE* 3.6 27.5 - - + +
281B ASP* 3.4 19.9 + - - +
283B GLU* 1.3 77.7 - - - +
285B ALA* 1.3 58.8 + - - +
287B VAL* 3.1 23.1 - - + +
288B MET* 3.4 14.9 + - - +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 4.4 7.5 - - + +
281B ASP 3.6 6.4 + - - +
282B VAL 4.0 2.7 - - - +
283B GLU 3.1 0.8 - - - -
284B ASP* 1.3 74.8 - - - +
286B ALA* 1.3 56.7 + - - +
287B VAL 3.0 5.1 + - - -
288B MET* 3.3 4.5 + - - +
289B LEU* 3.0 34.9 + - + +
406B ILE* 4.1 24.9 - - + +
432B LEU* 3.8 20.2 - - + -
443B LEU* 3.6 20.2 - - + -
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL 3.7 5.0 + - - +
283B GLU 3.0 11.2 + - - +
285B ALA* 1.3 78.0 - - - +
287B VAL* 1.3 57.4 + - - +
289B LEU* 3.7 9.3 - - - +
290B ALA* 2.9 31.7 + - - +
443B LEU* 3.7 18.7 - - + +
446B ALA* 3.8 28.5 - - + +
447B LEU* 4.1 13.3 - - + +
450B LEU* 4.8 5.0 - - + +
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Residues in contact with VAL 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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27A PRO* 3.8 27.6 - - + -
28A VAL 5.2 0.4 - - - +
29A ILE* 3.8 36.1 - - + +
283B GLU* 3.0 19.4 + - + +
284B ASP* 3.1 21.5 - - + +
286B ALA* 1.3 75.3 - - - +
288B MET* 1.3 69.7 - - + +
289B LEU 3.2 0.5 + - - -
290B ALA* 3.3 2.9 + - - -
291B TYR* 3.2 35.0 - - + +
450B LEU* 4.5 16.6 - - + -
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Residues in contact with MET 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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29A ILE* 5.6 13.7 - - + -
280B ILE* 5.1 4.7 - - + -
284B ASP 3.4 12.3 + - - +
285B ALA 3.3 7.0 + - - +
287B VAL* 1.3 79.5 - - + +
289B LEU* 1.3 59.9 + - - +
290B ALA 3.5 0.2 - - - -
291B TYR* 3.9 3.4 + - - +
292B ALA* 3.5 24.6 + - - +
370B VAL* 3.9 15.3 - - + +
404B ASN* 3.4 41.3 - - + +
406B ILE* 4.5 16.8 - - + -
430B ARG* 4.2 28.5 - - - +
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Residues in contact with LEU 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 ALA* 3.0 31.0 + - + +
286B ALA* 3.7 7.2 - - - +
287B VAL 3.1 0.2 - - - -
288B MET* 1.3 76.9 - - - +
290B ALA* 1.3 59.5 + - - +
291B TYR 3.2 6.0 + - - -
292B ALA* 4.1 8.2 + - - +
295B VAL* 4.2 18.2 - - + -
297B PHE* 5.6 2.5 - - + -
315B LEU* 5.2 9.2 - - + -
319B LEU* 3.5 29.7 - - + +
322B ARG* 5.6 0.2 - - - -
324B VAL* 4.8 5.2 - - - +
370B VAL* 3.9 17.5 - - + -
372B VAL* 3.8 31.2 - - + -
406B ILE* 4.8 2.0 - - + -
443B LEU* 4.2 21.3 - - + -
447B LEU* 4.3 13.0 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.0 + - - +
287B VAL* 3.3 1.2 + - - -
289B LEU* 1.3 75.8 - - - +
291B TYR* 1.3 86.6 + - + +
292B ALA 3.8 0.9 - - - -
322B ARG* 3.7 28.0 + - - +
324B VAL* 5.4 4.0 - - - +
447B LEU* 3.9 23.1 - - + -
450B LEU* 4.9 12.3 - - + -
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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