Contacts of the helix formed by residues 312 - 322 (chain B) in PDB entry 1ADI
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 THR 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B LEU* 3.6 21.5 - - + +
311B ASP* 1.3 69.4 - - - +
313B VAL* 1.3 60.8 + - - +
315B VAL* 4.0 7.1 - - + +
316B ARG* 3.1 38.6 + - - +
343B LEU* 4.3 13.2 - - + -
344B CYS 2.4 33.2 + - - +
345B VAL* 3.7 9.2 - - - -
402B ILE* 4.9 7.2 - - + -
405B LEU* 3.7 31.3 - - + +
406B THR* 4.8 10.4 - - + +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ASP* 3.3 12.9 + - - +
312B THR* 1.3 74.7 - - - +
314B ALA* 1.3 67.0 + - - +
316B ARG* 3.1 12.3 + - - +
317B ARG* 3.0 17.0 + - - +
344B CYS* 4.5 0.4 - - - -
345B VAL 4.3 4.7 - - - +
346B ALA* 3.7 31.0 - - - +
347B TYR* 3.7 23.3 - - + -
355B VAL 4.9 0.2 - - - +
356B THR* 3.6 6.8 - - - +
357B THR* 3.6 41.7 - - - +
358B THR* 3.6 11.9 + - + +
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Residues in contact with ALA 314 (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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9B THR 5.4 0.9 - - - -
11B TRP* 4.5 10.8 - - + -
227B LEU* 3.9 28.8 - - + +
311B ASP* 3.2 27.4 + - + +
313B VAL* 1.3 79.9 - - - +
315B VAL* 1.3 58.7 - - + +
317B ARG* 2.9 20.8 + - - +
318B ALA* 3.1 11.1 + - - +
347B TYR* 4.3 2.7 - - - +
358B THR* 3.7 13.9 - - + +
365B TRP* 5.6 1.3 - - + -
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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
----------------------------------------------------------
9B THR* 4.7 6.7 - - - +
10B GLN* 4.7 11.7 - - + +
266B LEU* 4.1 23.1 - - + -
310B LEU* 3.9 16.8 - - + -
311B ASP 3.0 22.6 + - - +
312B THR* 4.0 7.4 - - + -
314B ALA* 1.3 78.1 - - + +
316B ARG* 1.3 61.6 + - - +
318B ALA* 3.0 18.8 + - - +
319B VAL* 3.0 12.0 + - + +
327B PHE* 3.7 29.2 - - + -
402B ILE* 5.7 0.7 - - + -
406B THR* 4.4 12.3 - - + -
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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
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312B THR* 3.1 35.3 + - - +
313B VAL* 3.1 8.5 + - - +
315B VAL* 1.3 76.5 - - - +
317B ARG* 1.3 62.4 + - - +
319B VAL* 3.2 10.2 + - + +
320B GLN* 3.2 23.5 + - - +
345B VAL 3.5 24.4 + - - -
356B THR* 3.7 38.9 + - - +
405B LEU* 2.3 60.9 + - - +
406B THR* 4.1 17.0 - - + +
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Residues in contact with ARG 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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203A ASP* 2.6 38.2 + - - -
205A SER* 3.0 18.2 + - - -
206A ASP* 3.7 4.8 - - - +
227B LEU* 4.9 10.8 - - + -
232B HIS 5.3 4.7 - - - +
313B VAL 3.0 10.6 + - - +
314B ALA* 2.9 12.4 + - - +
316B ARG* 1.3 76.2 - - - +
318B ALA* 1.3 63.1 + - - +
320B GLN* 2.9 46.2 + - - +
321B LEU* 3.2 29.1 + - + +
357B THR* 3.6 8.1 - - - +
358B THR* 2.8 46.3 + - + +
359B PRO 5.2 2.6 + - - -
360B LEU* 6.0 1.6 - - - +
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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
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9B THR* 3.4 38.8 - - + +
226B THR* 3.7 26.0 - - + +
227B LEU* 5.1 1.9 - - + +
314B ALA 3.1 7.5 + - - +
315B VAL 3.0 9.7 + - - +
317B ARG* 1.3 74.2 - - - +
319B VAL* 1.3 65.5 + - + +
321B LEU 4.8 0.4 - - - +
322B ASN* 3.1 29.5 + - - +
324B LEU* 4.4 2.0 - - - +
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Residues in contact with VAL 319 (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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258A TYR* 4.9 4.4 + - - +
315B VAL 3.0 13.4 + - - +
316B ARG* 3.5 13.0 - - + +
317B ARG 3.2 0.4 - - - -
318B ALA* 1.3 74.3 - - + +
320B GLN* 1.3 67.5 + - - +
322B ASN 3.3 0.7 + - - -
323B SER* 2.8 23.3 + - - -
324B LEU* 3.3 22.0 + - + +
327B PHE* 4.0 20.0 - - + -
406B THR* 4.3 14.4 - - - +
408B VAL* 3.4 35.0 - - + -
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Residues in contact with GLN 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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205A SER* 3.3 13.9 + - - +
206A ASP* 2.8 34.1 + - - +
209A ASP* 3.8 37.3 + - + +
253A GLY 4.6 4.0 - - - +
255A GLY* 3.6 12.6 + - - -
258A TYR* 4.2 7.7 - - - -
316B ARG 3.2 10.8 + - - +
317B ARG* 2.9 41.4 + - - +
319B VAL* 1.3 82.4 - - - +
321B LEU* 1.3 65.7 + - + +
323B SER* 3.2 8.8 + - - -
357B THR* 5.3 1.2 + - - +
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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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205A SER* 3.4 27.4 - - - +
249A ALA* 5.6 0.7 - - - +
253A GLY* 3.5 18.5 - - - +
254A LEU 4.6 1.6 - - - +
255A GLY* 3.6 14.3 + - - +
256A PRO* 3.8 6.2 - - - +
226B THR* 4.3 11.4 - - + +
227B LEU* 5.4 2.0 - - + -
232B HIS* 3.4 46.0 - - + +
244B THR* 4.2 27.5 + - + -
246B GLY* 4.9 0.3 + - - -
317B ARG* 3.2 28.4 + - + +
318B ALA* 4.5 2.9 - - - +
320B GLN* 1.3 79.3 - - + +
322B ASN* 1.3 61.5 + - - +
323B SER 3.5 0.2 - - - -
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Residues in contact with ASN 322 (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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256A PRO* 4.4 1.1 - - - -
7B LEU* 3.8 17.8 - - - +
9B THR* 4.6 4.4 - - - +
226B THR* 2.9 29.4 + - - +
244B THR* 3.0 31.2 - - - -
245B ALA* 3.1 16.0 + - + +
262B VAL* 3.6 20.6 - - + +
318B ALA* 3.1 24.0 + - - +
321B LEU* 1.3 75.6 - - - +
323B SER* 1.3 79.1 + - - +
324B LEU* 2.9 12.7 + - + +
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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