Contacts of the helix formed by residues 311 - 324 (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 HIS 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ILE* 4.0 9.3 - - + +
288B ASN* 3.2 37.0 + - + -
309B THR 3.6 2.2 + - - -
310B LEU* 1.3 73.0 - - - +
312B PRO* 1.3 77.7 - - + +
313B LYS* 3.0 43.7 - - + +
314B ILE* 2.9 25.8 + - + +
315B SER 3.1 8.8 + - - -
357B GLN* 2.8 27.6 + - + +
358B LYS* 4.2 20.0 - - + -
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Residues in contact with PRO 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU 3.2 5.3 - - - +
311B HIS* 1.3 99.5 - - + +
313B LYS* 1.3 62.0 + - + +
315B SER* 3.3 10.5 + - - +
316B LYS* 3.2 24.9 + - - +
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Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR* 6.2 1.6 - - - -
287B ILE* 3.8 22.9 - - + +
288B ASN* 2.9 36.3 + - - +
311B HIS* 3.0 20.7 - - + +
312B PRO* 1.3 79.4 - - + +
314B ILE* 1.3 59.1 + - - +
316B LYS* 4.0 7.0 - - + +
317B LEU* 3.0 28.4 + - - +
383B SER* 5.1 0.2 + - - -
384B ILE* 3.8 42.1 - - + +
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 4.4 8.3 - - + -
287B ILE* 3.6 36.8 - - + -
310B LEU* 4.2 15.3 - - + -
311B HIS* 2.9 10.0 + - + +
313B LYS* 1.3 76.9 - - - +
315B SER* 1.3 66.1 + - - +
316B LYS 3.1 1.1 - - - -
317B LEU* 3.2 8.0 + - + +
318B ILE* 3.0 39.9 + - + +
330B PRO* 5.6 0.4 - - + -
357B GLN 3.7 14.4 - - - +
358B LYS 3.6 15.0 - - - +
359B GLY 3.4 23.8 - - - +
360B ILE* 4.2 15.0 - - + -
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 6.4 0.2 - - - -
310B LEU* 4.2 26.0 + - - +
311B HIS 3.1 7.8 + - - -
312B PRO* 3.3 18.0 + - - +
314B ILE* 1.3 76.0 - - - +
316B LYS* 1.3 63.8 + - - +
318B ILE* 3.4 5.6 + - - +
319B GLU* 3.3 21.7 + - - +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO 3.2 15.8 + - - +
313B LYS* 4.0 5.8 - - - +
314B ILE 3.1 0.4 - - - -
315B SER* 1.3 78.8 + - - +
317B LEU* 1.3 65.2 + - - +
318B ILE 3.4 0.2 + - - -
319B GLU* 3.4 7.0 + - - +
320B ASP* 2.9 57.0 + - - +
382B LYS 5.3 0.4 + - - -
383B SER* 3.2 25.5 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 3.8 32.1 - - + -
313B LYS 3.0 19.3 + - - +
314B ILE* 3.5 10.1 - - + +
316B LYS* 1.3 75.9 - - - +
318B ILE* 1.3 65.1 + - - +
320B ASP* 3.4 1.0 + - - +
321B LEU* 3.0 52.1 + - + +
328B THR* 3.9 3.8 - - + +
360B ILE* 3.7 31.4 - - + -
362B LEU* 5.5 0.7 - - + -
380B ILE* 4.0 18.6 - - + -
383B SER* 3.6 17.2 + - - +
384B ILE* 4.3 7.9 - - + -
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Residues in contact with ILE 318 (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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217A LEU* 4.2 13.7 - - + -
310B LEU* 4.2 13.2 - - + -
314B ILE* 3.0 31.0 + - + +
315B SER* 3.7 5.8 - - - +
317B LEU* 1.3 75.6 - - - +
319B GLU* 1.3 58.6 + - - +
321B LEU* 3.4 1.4 + - - +
322B LYS* 2.9 54.4 + - - +
326B ILE 4.9 0.3 - - - +
328B THR* 3.7 23.4 + - - +
329B ARG 4.2 0.4 - - - -
330B PRO* 3.9 29.6 - - + -
360B ILE* 3.5 23.3 - - + -
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B SER 3.3 12.8 + - - +
316B LYS* 3.4 7.3 + - - +
318B ILE* 1.3 76.4 - - - +
320B ASP* 1.3 70.2 + - - +
322B LYS* 3.2 9.4 + - + +
323B ASN* 3.0 44.8 + - - +
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Residues in contact with ASP 320 (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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316B LYS* 2.9 48.9 + - - +
317B LEU 3.7 2.5 - - - +
319B GLU* 1.3 76.0 - - - +
321B LEU* 1.3 62.9 + - + +
323B ASN* 3.2 19.2 + - - +
324B LYS* 3.2 37.5 + - - +
383B SER* 2.6 31.6 + - - +
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Residues in contact with LEU 321 (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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317B LEU* 3.0 44.4 + - + +
318B ILE 4.0 2.2 - - - +
320B ASP* 1.3 76.2 - - + +
322B LYS* 1.3 60.4 + - - +
324B LYS* 3.1 16.8 + - + +
325B GLN 3.3 0.2 + - - -
326B ILE* 2.7 59.9 + - + +
328B THR* 3.6 20.6 - - + -
376B ILE* 4.7 1.8 - - + +
379B LEU* 3.8 39.3 - - + +
380B ILE* 3.7 19.5 - - + +
383B SER* 5.5 0.9 - - - -
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.6 29.3 - - - +
318B ILE* 2.9 33.7 + - - +
319B GLU* 3.2 10.5 + - + +
321B LEU* 1.3 78.5 - - - +
323B ASN* 1.3 59.7 + - - +
325B GLN* 3.0 25.0 + - - +
326B ILE 3.4 11.4 + - - +
327B GLU* 5.8 6.1 - - - +
328B THR 4.9 5.6 + - - +
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU* 3.0 37.9 + - - +
320B ASP* 3.5 12.6 + - - +
321B LEU 3.1 0.2 - - - -
322B LYS* 1.3 78.5 - - - +
324B LYS* 1.3 60.1 + - + +
325B GLN* 3.1 17.3 + - - +
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ASP* 3.2 36.8 + - - +
321B LEU* 3.1 12.5 + - + +
323B ASN* 1.3 78.1 - - - +
325B GLN* 1.3 61.9 - - - +
326B ILE* 3.0 19.7 + - + +
379B LEU* 3.5 63.6 + - + +
382B LYS* 5.4 3.0 - - - +
383B SER* 4.8 3.4 - - - +
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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