Contacts of the helix formed by residues 311 - 321 (chain B) in PDB entry 1OX4
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 PRO 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LEU* 3.8 26.7 - - + -
276B LEU* 4.1 4.0 - - + +
300B THR* 5.5 4.3 - - - +
302B PHE* 3.5 41.5 - - + -
305B CYS* 3.8 11.0 - - - -
309B ASP 3.4 8.1 - - - +
310B THR* 1.3 88.2 - - + +
312B MET* 1.3 64.5 + - - +
314B GLU* 2.9 21.3 + - + +
315B VAL* 3.3 12.1 + - - +
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 3.9 29.2 - - + -
254B LEU* 4.4 2.6 - - - +
296B PHE* 3.8 29.2 - - + -
298B ASN* 3.5 39.7 - - + +
300B THR* 5.0 3.2 + - + +
310B THR* 3.2 12.5 - - + +
311B PRO* 1.3 78.8 - - - +
313B LEU* 1.3 63.2 + - - +
315B VAL* 3.0 28.3 + - + -
316B LEU* 3.2 31.7 + - + +
329B VAL* 4.1 4.5 - - + -
353B TYR* 3.8 17.5 - - + -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 3.7 16.2 - - + +
308B LYS 4.2 9.9 - - - +
310B THR* 3.4 18.6 - - - +
311B PRO 3.2 0.4 - - - -
312B MET* 1.3 77.2 - - - +
314B GLU* 1.3 56.6 - - - +
316B LEU* 3.5 5.9 + - + +
317B LYS* 3.0 28.3 + - - +
352B LEU* 3.6 32.1 - - + -
353B TYR* 3.5 48.5 - - + +
356B SER* 3.4 27.9 - - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.4 23.6 - - + -
310B THR 3.9 1.9 + - - +
311B PRO* 2.9 16.3 + - + +
313B LEU* 1.3 76.3 - - - +
315B VAL* 1.3 61.1 + - - +
317B LYS* 3.7 17.9 + - - +
318B GLN* 2.8 67.8 + - + +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.8 0.7 - - + -
254B LEU* 3.6 24.7 - - + -
276B LEU* 4.2 11.0 - - + -
279B PRO* 3.8 27.8 - - + -
280B VAL* 3.8 18.5 - - + +
296B PHE* 3.9 21.3 - - + -
311B PRO 3.5 14.1 - - - +
312B MET* 3.3 22.0 - - + +
314B GLU* 1.3 77.9 - - - +
316B LEU* 1.3 52.5 + - - +
318B GLN* 3.7 0.5 - - - -
319B ALA* 2.8 37.1 + - - +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 3.7 34.1 - - + -
312B MET* 3.2 18.3 + - + +
313B LEU* 3.7 7.0 - - - +
315B VAL* 1.3 77.6 - - - +
317B LYS* 1.3 59.3 + - - +
319B ALA* 3.2 3.9 + - - +
320B ALA* 2.8 33.3 + - - +
327B LEU* 4.1 16.4 - - + +
328B THR 5.3 0.2 - - - +
329B VAL* 4.3 8.1 - - + -
353B TYR* 3.7 35.9 - - + +
356B SER* 3.6 14.4 - - - +
357B GLY* 4.5 1.8 - - - -
358B ALA* 3.8 25.1 - - + +
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Residues in contact with LYS 317 (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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15B GLN* 3.8 28.9 + - - +
313B LEU 3.0 16.0 + - - +
314B GLU* 3.7 21.0 + - - +
316B LEU* 1.3 80.7 - - - +
318B GLN* 1.3 78.3 + - - +
320B ALA* 3.5 12.2 + - - +
321B LYS* 3.7 24.5 + - - +
356B SER* 3.1 19.4 + - - +
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 5.2 7.0 - - + -
280B VAL* 3.7 27.5 - - + +
284B GLN* 5.1 2.8 + - - -
314B GLU* 2.8 48.4 + - + +
317B LYS* 1.3 82.1 - - - +
319B ALA* 1.3 64.2 + - - +
321B LYS* 3.3 53.7 + - - +
322B THR* 4.5 2.3 + - - -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 4.4 13.8 - - + +
283B ALA* 4.5 11.4 - - + -
284B GLN* 5.2 2.5 - - - -
296B PHE* 4.2 23.3 - - + -
315B VAL 2.8 22.5 + - - +
316B LEU 3.7 3.1 - - - +
318B GLN* 1.3 73.1 - - - +
320B ALA* 1.3 57.8 + - - +
321B LYS 3.0 3.1 + - - -
322B THR* 3.3 3.6 + - - -
323B VAL* 3.0 36.8 + - + +
327B LEU* 4.3 7.4 - - + -
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Residues in contact with ALA 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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15B GLN* 4.0 24.2 - - + -
16B SER* 4.5 12.5 + - - +
19B ASN* 3.0 16.2 + - - +
316B LEU 2.8 17.1 + - - +
317B LYS 3.7 6.7 - - - +
318B GLN 3.2 0.6 - - - -
319B ALA* 1.3 76.7 - - - +
321B LYS* 1.3 60.2 + - - +
322B THR 3.3 0.6 + - - -
323B VAL 4.3 11.7 + - - +
324B PHE* 4.3 8.5 - - - -
327B LEU* 4.4 8.0 - - + +
357B GLY* 4.3 12.3 - - - -
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 5.7 1.8 - - - +
19B ASN* 3.4 25.7 - - - +
23B HIS* 5.6 2.4 - - - +
317B LYS* 3.7 25.9 - - - +
318B GLN* 3.3 48.7 + - - +
319B ALA 3.0 1.2 + - - -
320B ALA* 1.3 79.4 - - - +
322B THR* 1.3 68.9 + - + +
324B PHE* 3.5 15.2 - - - -
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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
------------------------------------------------------------
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