Contacts of the helix formed by residues 313 - 330 (chain A) in PDB entry 4AY6
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 CYS 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A SER* 1.3 75.9 - - - +
314A PRO* 1.4 64.7 - - - +
315A THR* 3.4 14.8 - - - -
316A HIS* 2.8 46.2 - - + -
317A ALA* 3.1 18.7 + - - +
346A VAL* 3.2 14.1 - - + +
347A PHE* 4.5 2.0 - - - -
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Residues in contact with PRO 314 (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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312A SER 3.1 12.6 - - - +
313A CYS* 1.4 83.8 - - - +
315A THR* 1.3 54.0 + - - +
317A ALA* 3.4 2.8 + - + +
318A ASP* 2.7 39.2 + - - +
347A PHE* 3.9 38.5 - - + -
350A PHE* 5.1 0.3 - - - -
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A CYS* 3.3 11.4 - - - -
314A PRO* 1.3 75.7 - - - +
316A HIS* 1.3 70.0 + - - +
318A ASP* 3.0 9.0 + - + +
319A SER* 3.0 21.7 + - - -
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Residues in contact with HIS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A CYS* 2.8 35.1 - - + +
315A THR* 1.3 74.2 - - - +
317A ALA* 1.3 66.2 + - - +
319A SER* 3.0 16.0 + - - -
320A LEU* 3.1 28.3 + - + +
342A LYS* 5.7 5.1 - - + +
346A VAL* 3.6 30.3 - - + +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A CYS 3.1 10.7 + - - +
314A PRO* 3.6 7.4 - - + +
316A HIS* 1.3 78.4 - - - +
318A ASP* 1.3 63.6 + - - +
320A LEU* 3.1 17.2 + - - +
321A ASN* 2.9 20.4 + - - +
343A ALA* 3.5 24.1 - - - +
346A VAL* 4.0 3.1 - - + +
347A PHE* 3.7 15.9 - - + -
350A PHE* 3.8 17.2 - - + -
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PRO* 2.7 22.4 + - - +
315A THR* 3.0 12.1 + - + +
317A ALA* 1.3 74.4 - - - +
319A SER* 1.3 60.3 + - - +
321A ASN* 3.4 5.0 + - - +
322A ASN* 3.1 32.3 + - - +
350A PHE* 3.4 26.5 - - - -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A THR* 3.0 11.3 + - - -
316A HIS* 3.0 12.2 + - - -
318A ASP* 1.3 73.6 - - - +
320A LEU* 1.3 68.4 + - - +
322A ASN* 3.0 16.4 + - - +
323A LEU* 2.9 30.2 + - - +
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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
----------------------------------------------------------
316A HIS* 3.1 25.5 + - + +
317A ALA* 3.1 17.0 + - - +
319A SER* 1.3 80.9 + - - +
321A ASN* 1.3 57.6 + - - +
323A LEU* 3.0 15.4 + - + +
324A ALA* 2.8 29.9 + - - +
339A LEU* 4.4 22.1 - - + +
342A LYS* 4.0 29.4 - - + +
343A ALA* 3.6 35.9 - - + +
346A VAL* 4.2 12.6 - - + -
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA 2.9 11.5 + - - +
318A ASP 3.4 9.9 - - - +
320A LEU* 1.3 73.9 - - - +
322A ASN* 1.3 62.5 + - - +
324A ALA* 3.0 6.0 + - - +
325A ASN* 2.9 40.1 + - - +
340A TYR* 3.4 29.0 - - - -
343A ALA* 4.3 4.5 - - + +
350A PHE* 3.9 22.4 - - + -
352A ALA* 4.5 5.4 - - - +
353A ALA* 3.6 17.3 - - - +
356A ASN* 3.5 21.4 + - - +
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Residues in contact with ASN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASP* 3.1 28.2 + - - -
319A SER* 3.0 13.6 + - - +
321A ASN* 1.3 77.3 + - - +
323A LEU* 1.3 64.2 + - + +
325A ASN* 3.9 12.5 + - - +
326A ILE* 3.4 26.9 + - + +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 2.9 19.6 + - - +
320A LEU* 3.3 19.3 - - + +
322A ASN* 1.3 78.9 - - + +
324A ALA* 1.3 67.3 + - - +
326A ILE* 2.9 31.7 + - + +
327A LYS* 3.0 19.6 + - + +
339A LEU* 3.9 18.6 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU 2.8 15.0 + - - +
321A ASN 3.5 3.8 - - - +
323A LEU* 1.3 72.0 - - - +
325A ASN* 1.3 58.2 + - - +
327A LYS* 2.8 21.3 + - - +
328A ARG* 2.9 13.9 + - - +
336A ALA* 3.7 8.8 - - - +
339A LEU* 3.6 27.0 - - + +
340A TYR* 3.4 38.1 - - + +
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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
----------------------------------------------------------
321A ASN* 2.9 32.1 + - - +
322A ASN* 4.0 13.0 + - - +
324A ALA* 1.3 74.4 - - - +
326A ILE* 1.3 61.5 + - + +
328A ARG* 3.7 5.1 + - - +
329A GLU* 3.3 30.3 + - - +
340A TYR* 2.9 28.9 + - - -
356A ASN* 3.8 10.7 + - - +
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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
----------------------------------------------------------
322A ASN* 3.4 17.0 + - + +
323A LEU* 2.9 27.3 + - + +
325A ASN* 1.3 81.0 - - + +
327A LYS* 1.3 64.4 + - + +
329A GLU* 2.9 25.3 + - - +
330A GLN* 3.2 34.8 + - + +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.0 16.8 + - - +
324A ALA 2.8 7.7 + - - +
326A ILE* 1.3 81.2 - - - +
328A ARG* 1.3 60.7 + - - +
330A GLN* 3.6 28.0 + - - +
332A ASN* 3.1 39.4 + - + +
335A GLU* 4.3 18.8 - - + -
336A ALA* 4.0 18.4 - - - +
339A LEU* 3.7 20.2 - - + -
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Residues in contact with ARG 328 (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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324A ALA 2.9 14.2 + - - +
325A ASN* 3.7 8.1 - - - +
327A LYS* 1.3 75.2 - - - +
329A GLU* 1.3 67.0 + - - +
331A GLY* 2.7 28.3 + - - -
332A ASN 4.6 4.3 - - - +
333A ILE* 4.5 15.1 - - + +
336A ALA* 4.1 11.8 - - + +
340A TYR* 4.1 15.4 + - - +
356A ASN* 4.0 15.0 + - - +
359A SER* 3.1 34.9 + - - -
360A VAL* 3.5 25.6 - - + +
363A GLN* 3.5 22.6 + - - -
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASN* 3.3 15.7 + - - +
326A ILE* 2.9 12.7 + - - +
328A ARG* 1.3 86.6 - - - +
330A GLN* 1.3 55.1 + - + +
331A GLY* 2.8 15.7 + - - -
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Residues in contact with GLN 330 (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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326A ILE* 3.2 30.5 + - + +
327A LYS* 3.6 34.0 + - - +
329A GLU* 1.3 73.8 - - + +
331A GLY* 1.3 50.2 + - - +
332A ASN* 2.5 27.6 + - + +
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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
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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