Contacts of the helix formed by residues 314 - 327 (chain B) in PDB entry 3IO6
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 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LEU 3.0 12.6 + - - +
312B ALA 3.2 6.3 - - - +
313B LYS* 1.3 75.6 - - - +
315B PRO* 1.4 76.8 - - - +
316B ARG* 2.9 50.5 + - - +
317B ILE* 3.5 28.3 - - + +
318B ALA 3.0 18.4 + - - -
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Residues in contact with PRO 315 (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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244B VAL 4.1 6.8 - - - +
312B ALA 4.5 1.1 - - - +
313B LYS 3.2 11.2 - - - +
314B ASP* 1.4 90.3 - - - +
316B ARG* 1.3 65.1 + - + +
318B ALA* 3.7 8.7 - - + +
319B ALA* 3.2 23.2 + - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 3.4 41.4 - - + +
236B ASP* 4.2 11.7 + - - -
242B TYR* 2.7 49.1 + - - +
243B GLY* 5.7 1.3 - - - -
244B VAL* 3.7 27.9 - - + +
314B ASP* 2.9 33.6 + - - +
315B PRO* 1.3 81.4 - - + +
317B ILE* 1.3 63.7 + - - +
319B ALA* 3.2 5.4 + - - +
320B THR* 3.1 23.6 + - - -
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 4.1 18.8 - - + -
294B ASN* 6.1 0.9 - - - +
298B PRO* 6.1 4.3 - - + -
300B GLY* 3.9 37.2 - - - +
301B ALA* 4.5 3.0 - - - +
308B GLU* 4.1 14.8 - - - +
311B LEU* 4.0 33.2 - - + +
312B ALA 4.5 0.2 - - - +
314B ASP* 3.2 34.6 + - + +
316B ARG* 1.3 75.0 - - - +
318B ALA* 1.3 65.9 + - - +
320B THR* 3.3 6.4 + - - +
321B MET* 3.1 22.3 + - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 3.5 36.3 - - + +
314B ASP 3.0 9.2 + - - +
315B PRO* 3.7 9.0 - - + +
317B ILE* 1.3 78.5 - - - +
319B ALA* 1.3 59.1 + - - +
321B MET* 3.6 7.3 + - - +
322B GLU* 3.3 22.0 + - - +
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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
----------------------------------------------------------
244B VAL* 3.8 7.9 - - + +
245B THR* 3.7 35.7 - - - +
246B VAL 4.1 2.2 - - - +
315B PRO 3.2 13.9 + - - +
316B ARG 3.2 8.5 + - - +
318B ALA* 1.3 75.0 - - - +
320B THR* 1.3 63.6 + - - +
322B GLU* 3.1 11.5 + - - +
323B ASN* 3.1 30.8 + - - -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL 4.4 5.2 - - - +
112B ALA* 3.9 20.8 - - + +
114B SER* 3.1 21.5 + - - -
229B PRO* 3.7 21.1 - - + +
232B TRP* 3.6 23.6 - - - -
300B GLY* 5.9 0.7 - - - -
301B ALA* 4.2 20.0 - - + +
316B ARG 3.1 8.3 + - - -
317B ILE* 3.6 11.4 - - - -
319B ALA* 1.3 75.8 - - - +
321B MET* 1.3 62.3 + - - +
323B ASN* 3.5 2.8 + - - +
324B ALA* 3.3 20.7 + - + +
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Residues in contact with MET 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.7 19.5 - - + +
92B PHE* 4.0 21.5 - - - -
110B VAL* 4.2 10.5 - - + -
301B ALA* 3.8 17.0 - - + +
302B VAL 3.3 26.7 - - - +
308B GLU* 3.4 39.7 - - + +
317B ILE 3.1 8.3 + - - +
318B ALA* 3.7 9.4 - - - +
320B THR* 1.3 77.8 - - - +
322B GLU* 1.3 61.8 + - - +
324B ALA* 3.2 5.6 + - - +
325B GLN* 3.1 35.9 + - - +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.2 24.3 - - + +
318B ALA 3.3 11.4 + - - +
319B ALA* 3.1 14.1 + - - +
321B MET* 1.3 77.6 - - - +
323B ASN* 1.3 57.7 + - - +
325B GLN* 3.4 16.1 + - - +
326B LYS* 3.1 58.0 + - - +
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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
----------------------------------------------------------
112B ALA* 4.4 1.3 - - + -
113B LEU 3.3 19.7 - - - +
114B SER* 3.5 17.4 - - - +
245B THR 3.5 22.4 + - - -
246B VAL* 3.4 13.7 - - - +
247B LEU* 3.0 32.5 + - - +
255B SER 5.3 1.9 - - - +
257B PRO* 3.4 20.4 - - + +
319B ALA 3.1 22.3 + - - +
320B THR 3.9 4.0 - - - +
322B GLU* 1.3 73.6 - - - +
324B ALA* 1.3 59.8 + - - +
326B LYS* 3.7 6.5 + - - +
327B GLY* 3.0 18.9 + - - -
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.2 13.9 - - + -
110B VAL* 3.7 30.1 - - + -
112B ALA* 4.0 12.1 - - + +
259B VAL* 3.4 23.0 - - + +
320B THR 3.3 12.5 + - - +
321B MET* 3.2 11.6 + - - +
323B ASN* 1.3 75.9 - - - +
325B GLN* 1.3 59.9 + - - +
326B LYS 3.1 0.2 - - - -
327B GLY 3.0 17.5 + - - +
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Residues in contact with GLN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.9 22.1 - - - -
92B PHE* 3.6 31.1 - - + +
321B MET* 3.1 32.1 + - - +
322B GLU* 3.4 19.6 + - - +
324B ALA* 1.3 75.1 - - - +
326B LYS* 1.3 61.0 + - + +
327B GLY 4.2 3.1 - - - +
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Residues in contact with LYS 326 (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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127B LYS* 6.1 2.2 - - - +
246B VAL* 3.5 29.2 - - + +
247B LEU 5.5 0.4 + - - -
249B THR* 5.5 5.9 - - - +
254B PRO* 3.8 35.9 - - + +
255B SER 4.1 11.4 - - - +
256B LYS* 2.9 31.2 + - - +
322B GLU* 3.1 37.6 + - + +
323B ASN* 3.8 7.4 - - - +
325B GLN* 1.3 77.9 - - + +
327B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 6.1 0.5 - - - -
256B LYS* 3.7 5.9 + - - -
257B PRO* 3.1 24.0 - - - -
259B VAL* 4.1 2.8 - - - +
323B ASN 3.0 11.4 + - - -
324B ALA 3.0 18.2 + - - +
325B GLN 4.2 3.6 - - - +
326B LYS* 1.3 82.8 - - - +
328B GLU* 1.3 59.3 + - - -
329B ILE* 4.3 2.6 + - - +
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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
------------------------------------------------------------
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