Contacts of the helix formed by residues 313 - 328 (chain A) in PDB entry 1BK6
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 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU 3.8 4.6 + - - +
312A SER* 1.3 71.6 + - - +
314A LEU* 1.3 64.6 + - - +
315A VAL 3.1 0.4 - - - -
316A GLN* 3.4 28.9 - - - +
317A THR* 3.0 32.8 + - - -
352A SER* 5.4 1.3 - - - +
353A PRO* 5.6 7.4 - - + -
354A LYS* 4.9 12.0 - - + +
357A ILE* 4.1 16.2 - - + -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 5.3 6.3 - - + -
275A VAL* 3.8 32.0 - - + +
279A TRP* 4.6 1.2 + - - -
312A SER* 2.9 17.1 - - - +
313A THR* 1.3 87.3 - - - +
315A VAL* 1.3 58.1 + - - +
317A THR* 5.1 1.1 - - - -
318A PRO* 3.0 22.5 - - - +
491B GLN* 6.0 4.0 - - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 4.9 2.7 - - + -
274A LEU* 3.8 23.3 - - + -
275A VAL* 4.0 16.6 - - + +
278A CYS* 4.7 3.0 - - - -
307A LEU* 3.9 24.7 - - + +
310A HIS* 3.5 51.1 - - + +
312A SER* 3.0 10.8 + - - +
314A LEU* 1.3 79.2 - - - +
316A GLN* 1.3 64.3 + - - +
317A THR 3.4 0.4 - - - -
318A PRO* 3.4 5.7 - - - +
319A ALA* 3.1 22.3 + - - +
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Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 4.4 4.7 - - - +
308A LEU* 3.4 28.8 - - - +
309A SER* 4.5 0.9 - - - -
310A HIS* 2.6 26.6 - - + +
311A GLU* 4.6 2.0 - - - -
312A SER 3.2 13.0 + - - +
313A THR* 3.4 29.5 - - - +
315A VAL* 1.3 79.5 - - - +
317A THR* 1.3 57.0 + - - +
319A ALA* 4.0 3.3 - - - +
320A LEU* 3.0 33.4 + - - +
349A LEU* 4.5 14.8 - - + +
352A SER* 5.2 3.4 + - - -
357A ILE* 3.9 15.6 - - + +
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TRP* 3.7 25.8 - - + -
313A THR* 3.0 18.7 + - - -
314A LEU* 4.7 1.1 - - - -
316A GLN* 1.3 76.9 - - - +
318A PRO* 1.4 68.8 - - - +
320A LEU* 3.8 4.0 - - - +
321A ARG* 3.2 32.7 + - - +
354A LYS* 5.6 2.1 - - - +
357A ILE* 4.2 19.9 - - - +
360A GLU* 4.3 2.7 - - - +
491B GLN* 4.3 11.3 + - + +
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Residues in contact with PRO 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL 4.3 1.8 - - - +
278A CYS* 3.6 16.2 - - + +
279A TRP* 3.5 55.2 - - + +
282A SER* 3.7 8.1 - - - -
314A LEU 3.0 29.2 - - - +
315A VAL* 3.4 8.5 - - - +
317A THR* 1.4 91.5 - - + +
319A ALA* 1.3 64.8 + - - +
321A ARG* 3.4 7.9 + - + +
322A ALA* 3.2 19.6 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A CYS* 4.6 10.5 - - - -
304A LEU* 4.2 21.1 - - + +
307A LEU* 4.4 14.1 - - + +
308A LEU* 4.0 13.9 - - + -
315A VAL 3.1 18.3 + - - +
316A GLN* 4.0 3.8 - - - +
318A PRO* 1.3 81.4 - - - +
320A LEU* 1.3 63.1 + - - +
322A ALA* 3.4 3.2 + - - +
323A VAL* 3.1 27.7 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.8 13.6 - - + +
316A GLN 3.0 19.7 + - - +
317A THR* 3.8 4.5 - - - +
319A ALA* 1.3 78.1 - - - +
321A ARG* 1.3 56.8 + - - +
323A VAL* 3.7 6.7 - - + +
324A GLY* 2.9 27.4 + - - -
346A LEU* 4.1 11.4 - - + -
349A LEU* 4.1 28.0 - - + -
357A ILE* 3.8 28.3 - - + +
360A GLU* 3.7 31.4 - - + +
361A ALA 3.9 3.8 - - - +
363A TRP* 4.8 1.2 - - - -
364A THR* 3.8 17.4 + - - +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TRP* 4.3 13.8 - - + -
282A SER* 4.1 12.6 - - - +
317A THR* 3.2 29.7 + - - +
318A PRO* 3.7 9.0 - - + +
319A ALA 3.3 0.4 - - - -
320A LEU* 1.3 77.8 - - - +
322A ALA* 1.3 57.2 + - - +
324A GLY* 4.0 0.7 - - - -
325A ASN* 2.9 45.6 + - - +
360A GLU* 3.0 40.6 + - - -
363A TRP* 4.5 12.0 - - - -
491B GLN 3.0 27.3 + - - -
492B ASN* 4.6 0.2 - - - +
493B GLU* 3.4 38.7 + - - +
131D ALA 5.3 3.8 - - - -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A CYS 5.0 0.9 - - - +
281A ILE* 4.4 3.6 - - + -
282A SER* 3.7 28.6 - - - +
285A SER* 4.3 8.5 - - - +
304A LEU* 3.7 22.9 - - + -
318A PRO 3.2 12.9 + - - +
319A ALA 3.9 1.6 - - - +
320A LEU 3.2 0.2 - - - -
321A ARG* 1.3 76.2 - - - +
323A VAL* 1.3 66.7 + - - +
324A GLY 3.2 0.2 - - - -
325A ASN* 3.0 17.0 + - - +
326A ILE* 3.0 19.1 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 5.4 0.9 - - + +
304A LEU* 4.3 25.4 - - + +
305A VAL* 4.8 6.5 - - + -
308A LEU* 4.3 17.0 - - + -
319A ALA 3.1 18.7 + - - +
320A LEU* 3.7 12.1 - - + +
322A ALA* 1.3 73.8 - - - +
324A GLY* 1.3 64.9 + - - +
326A ILE* 3.1 22.3 + - + +
327A VAL* 3.3 12.8 + - - +
337A VAL* 4.1 11.2 - - + -
342A VAL* 3.6 27.6 - - + -
346A LEU* 5.8 0.2 - - + -
364A THR* 4.3 11.9 - - + -
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Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A LEU 2.9 11.4 + - - -
323A VAL* 1.3 79.4 - - - +
325A ASN* 1.3 61.3 + - - +
327A VAL* 3.2 22.8 + - - +
328A THR* 3.7 8.3 + - - -
363A TRP* 3.6 22.9 - - - -
364A THR* 3.5 23.1 - - - -
367A ASN* 4.7 1.4 + - - -
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Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A SER 3.5 22.8 + - - -
285A SER* 3.6 23.1 - - - +
286A ASP* 4.0 15.1 - - - +
292A ILE* 3.7 9.1 - - - +
321A ARG* 2.9 33.6 + - - +
322A ALA* 3.0 9.4 + - - +
324A GLY* 1.3 76.5 - - - +
326A ILE* 1.3 59.0 + - - +
328A THR* 2.9 28.8 + - - +
363A TRP* 3.6 15.8 - - - -
131D ALA 4.2 12.0 + - - +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A SER* 4.8 10.1 - - - +
292A ILE* 4.0 27.8 - - + +
295A VAL* 4.2 24.7 - - + -
296A ILE* 4.3 8.3 - - + -
301A PRO* 4.3 22.2 - - + -
304A LEU* 4.5 11.9 - - + -
322A ALA 3.0 14.3 + - - +
323A VAL* 3.1 10.9 + - + +
325A ASN* 1.3 73.1 - - - +
327A VAL* 1.3 52.8 + - - +
328A THR 2.6 15.4 + - - -
329A GLY* 2.8 16.5 + - - -
333A GLN* 4.0 12.6 - - - +
334A THR* 4.5 1.4 + - - -
337A VAL* 3.3 26.5 - - + -
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL 3.3 8.2 + - - +
324A GLY* 3.2 16.6 - - - +
326A ILE* 1.3 72.9 - - - +
328A THR* 1.3 56.6 + - - +
329A GLY 3.3 0.9 - - - -
334A THR* 3.5 22.0 - - + +
337A VAL* 4.1 23.3 - - + -
364A THR* 3.7 27.6 - - + +
367A ASN* 3.5 21.2 - - + +
368A ILE* 3.8 29.4 - - + -
128D LYS* 2.9 27.2 + - - -
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY 5.5 3.8 - - - +
292A ILE* 4.4 8.1 - - + -
324A GLY 3.7 9.0 + - - -
325A ASN* 2.9 22.7 + - - +
326A ILE 2.6 5.5 + - - -
327A VAL* 1.3 73.0 - - - +
329A GLY* 1.3 66.1 + - - +
363A TRP* 4.7 2.6 - - - -
367A ASN* 4.3 6.0 + - - -
128D LYS* 3.7 23.6 - - + +
129D LYS 3.8 18.6 + - - -
130D ALA* 4.3 22.7 - - + +
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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
------------------------------------------------------------
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