Contacts of the helix formed by residues 27 - 46 (chain 7) in PDB entry 6AH0
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 27 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257 ASP 3.2 5.5 + - - -
267 THR* 1.3 75.6 - - - +
287 LYS* 1.3 70.4 + - - +
297 TRP 3.2 2.9 - - - +
307 GLU* 3.3 6.3 + - - +
317 TRP* 3.2 17.3 + - - -
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Residues in contact with LYS 28 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267 THR 3.7 2.0 + - - -
277 THR* 1.3 71.5 - - - +
297 TRP* 1.3 68.3 + - - +
317 TRP* 3.1 1.2 + - - -
327 LEU* 3.1 15.6 + - - -
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Residues in contact with TRP 29 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277 THR* 3.2 1.4 - - - +
287 LYS* 1.3 76.3 - - - +
307 GLU* 1.3 64.2 + - - +
327 LEU* 2.9 1.7 + - - -
337 VAL* 2.9 19.4 + - - -
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Residues in contact with GLU 30 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277 THR* 3.3 9.0 + - - +
287 LYS 3.3 0.6 - - - -
297 TRP* 1.3 73.5 - - - +
317 TRP* 1.3 64.0 + - - +
337 VAL* 3.0 3.6 + - - +
347 ASN* 2.9 21.5 + - - -
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Residues in contact with TRP 31 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277 THR 3.2 9.8 + - - -
287 LYS 3.1 6.7 + - - -
307 GLU* 1.3 74.8 - - - +
327 LEU* 1.3 63.9 + - - +
347 ASN* 3.2 2.8 + - - +
357 GLN* 3.1 17.3 + - - -
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Residues in contact with LEU 32 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12951 TYR* 6.5 0.9 - - - +
287 LYS 3.1 8.1 + - - -
297 TRP 2.9 7.2 + - - -
317 TRP* 1.3 73.0 - - - +
337 VAL* 1.3 68.7 + - - +
357 GLN* 3.1 2.6 + - - +
367 HIS* 2.9 19.4 + - - -
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Residues in contact with VAL 33 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297 TRP 2.9 13.5 + - - -
307 GLU* 3.0 3.1 + - - +
327 LEU* 1.3 76.0 - - - +
347 ASN* 1.3 66.9 + - - +
367 HIS* 3.1 3.7 + - - +
377 ARG* 3.0 16.3 + - - -
757 PRO 5.0 12.6 - - - -
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Residues in contact with ASN 34 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207 GLY* 6.4 2.9 - - - -
307 GLU 2.9 13.6 + - - -
317 TRP 3.2 4.7 + - - -
337 VAL* 1.3 75.4 - - - +
357 GLN* 1.3 65.4 + - - +
377 ARG* 2.9 14.2 + - - -
387 ASP* 3.0 10.7 + - - -
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Residues in contact with GLN 35 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317 TRP 3.1 13.4 + - - -
327 LEU* 3.1 2.8 + - - +
347 ASN* 1.3 75.4 - - - +
367 HIS* 1.3 63.0 + - - +
387 ASP* 3.8 2.4 - - - +
397 SER* 2.9 20.8 + - - -
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Residues in contact with HIS 36 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327 LEU 2.9 13.9 + - - -
337 VAL* 3.5 4.5 - - - +
347 ASN 3.1 0.2 - - - -
357 GLN* 1.3 73.5 - - - +
377 ARG* 1.3 67.5 + - - +
397 SER* 2.8 14.2 + - - -
407 TYR* 3.0 7.6 + - - -
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Residues in contact with ARG 37 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337 VAL 3.0 8.7 + - - -
347 ASN 2.9 10.2 + - - -
367 HIS* 1.3 68.7 - - - +
387 ASP* 1.3 54.0 + - - +
407 TYR* 2.4 27.6 + - - +
417 CYS 3.0 10.4 + - - -
727 MET* 5.2 13.6 + - - +
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Residues in contact with ASP 38 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12811 ILE* 6.4 0.2 - - - -
1143 ARG* 5.9 7.6 - - - +
347 ASN 3.0 12.7 + - - -
357 GLN* 3.9 2.9 - - - +
377 ARG* 1.3 73.9 - - - +
397 SER* 1.3 64.5 + - - +
417 CYS* 3.9 2.2 - - - +
427 SER* 3.0 20.4 + - - -
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Residues in contact with SER 39 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12811 ILE* 5.8 8.2 - - - +
357 GLN 2.9 11.8 + - - -
367 HIS* 2.8 10.2 + - - +
387 ASP* 1.3 78.1 - - - +
407 TYR* 1.3 61.6 + - - +
427 SER* 3.3 2.6 + - - +
437 TYR* 2.9 17.3 + - - -
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Residues in contact with TYR 40 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367 HIS 3.0 6.2 + - - -
377 ARG* 2.4 18.4 + - - +
397 SER* 1.3 71.4 - - - +
417 CYS* 1.3 53.6 + - - +
437 TYR* 2.3 31.0 + - - +
447 MET 2.9 10.6 + - - -
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Residues in contact with CYS 41 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 CYS* 5.0 5.5 - - - -
1133 ARG 4.3 20.7 - - - +
1143 ARG* 5.5 3.8 - - - +
377 ARG 3.0 9.7 + - - -
387 ASP* 3.4 3.2 + - - +
407 TYR* 1.3 73.0 - - - +
427 SER* 1.3 57.1 + - - +
447 MET* 4.0 3.3 - - - +
457 GLY* 3.0 21.3 + - - -
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Residues in contact with SER 42 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 CYS* 5.6 8.0 + - - +
387 ASP 3.0 12.8 + - - -
397 SER* 3.6 4.5 - - - +
407 TYR 2.7 4.6 + - - -
417 CYS* 1.3 75.5 - - - +
437 TYR* 1.3 53.3 + - - +
457 GLY* 2.5 23.2 + - - -
467 HIS* 2.7 15.4 + - - -
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Residues in contact with TYR 43 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397 SER 2.9 10.2 + - - -
407 TYR* 2.3 17.4 + - - +
427 SER* 1.3 69.8 - - - +
447 MET* 1.3 61.0 + - - +
467 HIS* 3.8 13.8 + - - +
477 PHE* 5.5 0.3 - - - -
497 LEU* 5.8 2.0 - - - +
507 LEU* 4.1 17.4 - - - +
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Residues in contact with MET 44 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407 TYR 2.9 10.6 + - - -
417 CYS* 4.3 3.6 - - - +
437 TYR* 1.3 75.8 - - - +
457 GLY* 1.3 63.1 + - - +
467 HIS 5.0 0.2 - - - -
477 PHE* 5.1 2.3 + - - -
657 ARG* 6.5 1.6 - - - +
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Residues in contact with GLY 45 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623 ILE 5.2 5.7 - - - +
633 ARG* 5.4 5.3 - - - -
1123 CYS* 5.8 6.3 - - - -
417 CYS 3.0 14.8 + - - -
427 SER* 2.5 15.8 + - - -
447 MET* 1.3 75.1 - - - +
467 HIS* 1.3 57.5 + - - -
477 PHE* 3.0 9.5 + - - -
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Residues in contact with HIS 46 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427 SER 2.7 15.2 + - - -
437 TYR* 3.8 3.9 + - - +
447 MET 3.6 0.6 - - - -
457 GLY* 1.3 67.7 - - - +
477 PHE* 1.3 69.5 + - - +
487 ASP 2.9 4.1 + - - -
497 LEU* 2.9 15.2 + - - -
507 LEU 3.1 7.8 + - - -
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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