Contacts of the helix formed by residues 350 - 358 (chain B) in PDB entry 1O69
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 GLY 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ASP* 3.1 6.0 + - - -
296B ALA* 5.3 2.0 - - - -
297B CYS* 3.6 18.1 + - - -
299B LYS* 6.1 0.6 - - - +
348B LEU* 4.3 3.0 - - - +
349B ASN* 1.3 77.7 - - - +
351B ASN* 1.3 63.7 + - - +
352B SER 3.5 2.0 - - - -
353B GLU* 3.5 15.1 + - - +
354B LEU* 3.1 24.1 + - - +
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Residues in contact with ASN 351 (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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100B ASP* 3.6 0.4 + - - -
101B CYS* 3.0 32.3 + - - +
102B ASP* 4.1 8.1 - - - +
293B GLU 4.6 1.2 - - - +
294B LEU* 3.4 23.3 - - - +
295B ASN* 2.8 48.1 + - - +
349B ASN* 3.0 13.8 + - - +
350B GLY* 1.3 80.1 - - - +
352B SER* 1.3 59.3 + - - +
354B LEU* 3.1 7.5 + - - +
355B PHE* 2.9 41.7 + - + -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 4.8 0.7 - - - -
80B PHE* 3.5 39.4 - - - +
100B ASP* 2.7 26.2 + - - -
101B CYS* 3.8 7.2 - - - -
332B TRP 5.1 0.3 - - - +
334B ALA* 3.6 9.6 + - - +
336B HIS* 3.3 24.3 - - - -
350B GLY 3.5 0.2 - - - -
351B ASN* 1.3 76.3 - - - +
353B GLU* 1.3 60.8 + - - +
355B PHE* 3.6 5.9 + - - +
356B PHE* 3.1 22.2 + - - +
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Residues in contact with GLU 353 (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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100B ASP* 5.6 0.6 - - - +
299B LYS* 5.4 6.2 + - - -
306B LYS* 3.5 34.5 - - - +
308B ILE* 3.9 26.6 - - + +
334B ALA* 5.5 0.4 - - + -
336B HIS* 2.7 37.0 + - + +
337B THR* 4.2 2.7 - - + -
348B LEU* 4.1 8.8 - - - +
350B GLY* 3.5 14.3 + - - +
351B ASN 3.2 0.6 - - - -
352B SER* 1.3 76.7 + - - +
354B LEU* 1.3 59.4 + - - +
356B PHE* 3.3 3.1 + - - +
357B GLN* 3.0 42.2 + - - +
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Residues in contact with LEU 354 (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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289B PHE* 4.0 20.4 - - + -
293B GLU* 3.7 54.1 - - + +
294B LEU* 4.6 7.2 - - + -
350B GLY 3.1 18.4 + - - +
351B ASN* 3.1 6.5 + - - +
353B GLU* 1.3 75.8 - - - +
355B PHE* 1.3 65.4 + - + +
357B GLN* 3.1 20.9 + - - +
358B LYS* 3.0 43.5 + - + +
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Residues in contact with PHE 355 (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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80B PHE* 3.9 15.9 - + + -
101B CYS* 3.7 20.2 - - - -
102B ASP 3.5 23.6 - - - -
103B GLU* 4.5 1.3 - - - -
105B TYR* 3.8 20.6 - + - -
270B LEU* 4.0 14.4 - - + -
286B LEU* 3.7 34.5 - - + -
289B PHE* 4.0 8.3 - + - -
294B LEU* 3.6 32.8 - - + -
331B LEU* 3.6 11.4 - - + +
351B ASN* 2.9 21.5 + - + +
352B SER 3.9 4.3 - - - +
354B LEU* 1.3 79.6 - - + +
356B PHE* 1.3 58.7 + - - +
359B GLY* 2.8 31.9 + - - -
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Residues in contact with PHE 356 (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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218A HIS* 3.9 26.2 - + + -
80B PHE* 5.0 0.6 - - - -
308B ILE* 3.5 55.4 - - + -
310B LEU* 3.2 39.1 - - + +
330B PRO* 3.8 12.3 - - + -
331B LEU* 3.2 38.2 + - - +
332B TRP 3.5 12.6 - - - +
333B LYS* 3.8 23.3 - - + -
334B ALA 5.7 0.7 - - - +
352B SER 3.1 18.3 + - - +
353B GLU 3.6 4.3 - - - +
355B PHE* 1.3 78.5 - - - +
357B GLN* 1.3 62.4 + - - +
359B GLY 3.7 6.9 + - - +
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Residues in contact with GLN 357 (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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308B ILE* 3.3 24.4 - - + +
309B THR 3.7 12.3 - - - +
310B LEU* 3.8 3.6 - - - +
311B HIS* 2.8 33.1 + - + +
314B ILE* 3.7 6.2 - - - +
353B GLU* 3.0 31.0 + - - +
354B LEU* 3.5 21.7 - - - +
356B PHE* 1.3 79.0 - - - +
358B LYS* 1.3 68.4 + - + +
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Residues in contact with LYS 358 (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 LEU* 3.3 11.3 - - + -
287B ILE* 2.8 59.8 + - - +
288B ASN* 3.0 21.3 + - - +
289B PHE* 4.6 6.5 - - + -
293B GLU* 2.6 30.1 + - - +
311B HIS* 4.2 23.1 - - - +
314B ILE* 3.6 6.4 - - - +
354B LEU* 3.0 32.3 + - + +
355B PHE* 3.8 0.7 - - + -
357B GLN* 1.3 85.2 - - + +
359B GLY* 1.3 59.8 + - - +
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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