Contacts of the helix formed by residues 318 - 334 (chain W) 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 ASP 318 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235W TYR* 5.0 6.1 - - - +
317W GLY* 1.3 79.3 - - - +
319W GLY* 1.3 66.2 + - - +
320W VAL 3.3 4.0 - - - +
321W ASP* 4.0 6.7 - - - +
322W PHE* 3.0 22.1 + - - +
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Residues in contact with GLY 319 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235W TYR* 4.5 21.7 - - - +
238W ALA* 6.4 0.2 - - - -
239W VAL* 5.6 6.8 - - - -
318W ASP* 1.3 70.7 - - - +
320W VAL* 1.3 56.3 + - - +
323W LEU* 3.0 26.4 + - - -
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Residues in contact with VAL 320 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318W ASP* 3.3 1.6 - - - +
319W GLY* 1.3 75.6 - - - +
321W ASP* 1.3 56.1 + - - +
323W LEU* 3.8 0.7 - - - +
324W SER* 3.0 25.5 + - - -
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Residues in contact with ASP 321 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317W GLY* 5.9 0.9 - - - -
318W ASP* 3.5 11.3 + - - +
320W VAL* 1.3 73.9 - - - +
322W PHE* 1.3 56.8 + - - +
324W SER* 3.2 4.0 + - - +
325W TRP* 2.9 24.8 + - - -
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Residues in contact with PHE 322 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317W GLY* 5.3 1.4 - - - -
318W ASP 3.0 16.4 + - - +
319W GLY 4.3 0.2 - - - -
321W ASP* 1.3 73.3 - - - +
323W LEU* 1.3 63.7 + - - +
325W TRP* 3.7 2.0 - - - +
326W PHE* 2.9 23.4 + - - -
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Residues in contact with LEU 323 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239W VAL* 5.6 9.5 - - - +
319W GLY 3.0 20.3 + - - -
320W VAL 3.8 0.9 - - - -
322W PHE* 1.3 74.3 - - - +
324W SER* 1.3 61.5 + - - +
326W PHE* 3.9 0.7 - - - +
327W LEU* 3.0 22.0 + - - -
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Residues in contact with SER 324 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320W VAL 3.0 14.5 + - - -
321W ASP* 3.6 4.0 - - - +
323W LEU* 1.3 76.2 - - - +
325W TRP* 1.3 55.0 + - - +
327W LEU* 3.9 1.0 - - - +
328W ASN* 3.0 26.7 + - - -
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Residues in contact with TRP 325 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321W ASP 2.9 13.3 + - - -
322W PHE* 3.2 4.4 + - - +
324W SER* 1.3 72.3 - - - +
326W PHE* 1.3 58.4 + - - +
328W ASN* 4.0 0.5 - - - -
329W ALA* 3.0 24.1 + - - -
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Residues in contact with PHE 326 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322W PHE 2.9 14.6 + - - -
323W LEU* 3.9 0.9 - - - +
325W TRP* 1.3 72.4 - - - +
327W LEU* 1.3 56.8 + - - +
329W ALA* 3.1 1.8 + - - +
330W LEU* 2.9 28.9 + - - -
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Residues in contact with LEU 327 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323W LEU 3.0 16.6 + - - -
324W SER* 3.9 1.3 - - - +
326W PHE* 1.3 72.6 - - - +
328W ASN* 1.3 62.7 + - - +
330W LEU* 3.9 1.1 - - - +
331W HIS* 3.0 19.8 + - - -
361W PRO* 5.5 11.0 - - - +
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Residues in contact with ASN 328 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324W SER 3.0 16.5 + - - -
325W TRP 4.2 0.9 - - - -
327W LEU* 1.3 73.5 - - - +
329W ALA* 1.3 62.1 + - - +
331W HIS* 3.2 3.2 + - - +
332W SER* 3.1 18.7 + - - -
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Residues in contact with ALA 329 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325W TRP 3.0 16.7 + - - -
326W PHE* 3.1 3.5 + - - +
328W ASN* 1.3 73.9 - - - +
330W LEU* 1.3 63.6 - - - +
332W SER* 3.2 3.5 + - - -
333W ALA* 3.0 21.3 + - - -
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Residues in contact with LEU 330 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326W PHE 2.9 17.0 + - - -
327W LEU* 4.0 1.3 - - - +
329W ALA* 1.3 70.1 - - - +
331W HIS* 1.3 57.1 + - - +
333W ALA* 4.5 0.9 - - - +
334W LEU* 2.9 31.4 + - - +
340W LYS* 4.5 0.5 - - - +
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Residues in contact with HIS 331 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327W LEU 3.0 15.5 + - - -
328W ASN* 3.7 3.6 - - - +
329W ALA 3.2 0.4 - - - -
330W LEU* 1.3 75.9 - - - +
332W SER* 1.3 58.8 + - - +
334W LEU 2.9 13.9 - - - +
335W GLY* 4.1 3.6 - - - -
357W THR* 4.3 1.0 - - - -
358W LYS* 3.4 28.2 + - - +
360W LEU 5.8 0.4 - - - -
361W PRO* 5.4 6.5 - - - -
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Residues in contact with SER 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328W ASN 3.1 13.0 + - - -
329W ALA 3.7 3.1 - - - -
331W HIS* 1.3 79.2 - - - +
333W ALA* 1.3 55.8 + - - +
334W LEU 3.9 4.0 - - - -
335W GLY* 4.8 2.8 + - - -
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Residues in contact with ALA 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270W MET* 4.6 15.8 - - - -
271W PHE 4.6 5.2 + - - -
274W VAL* 5.8 6.1 - - - -
329W ALA 3.0 13.1 + - - -
330W LEU* 3.2 1.1 + - - +
332W SER* 1.3 78.2 - - - +
334W LEU* 1.3 58.4 + - - +
335W GLY 4.1 0.2 - - - -
338W LYS 4.9 1.0 - - - +
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Residues in contact with LEU 334 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330W LEU* 2.9 16.6 + - - +
331W HIS 2.9 14.4 - - - +
333W ALA* 1.3 75.9 - - - +
335W GLY* 1.3 53.6 + - - +
338W LYS 3.7 1.1 - - - -
339W LYS 3.1 11.4 - - - -
340W LYS* 2.4 34.9 - - - +
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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