Contacts of the helix formed by residues 315 - 330 (chain A) in PDB entry 2AA0
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 GLY 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A THR 3.4 0.6 + - - -
314A ASN* 1.3 72.0 - - - +
316A ALA* 1.3 64.3 + - - +
317A GLY 3.3 3.0 - - - +
318A ASP* 3.4 10.8 + - - +
319A ALA* 3.1 24.3 + - - +
348A VAL* 4.2 7.6 - - - +
354A PHE* 3.9 19.5 - - - +
1001A MTP 3.7 22.1 + - - -
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR* 3.2 17.9 + - - +
314A ASN 3.2 3.8 + - - -
315A GLY* 1.3 77.8 - - - +
317A GLY* 1.3 58.1 + - - +
319A ALA* 3.3 3.2 + - - +
320A PHE* 2.9 26.3 + - - +
345A ALA* 3.6 9.7 - - + +
348A VAL* 5.0 0.9 - - - -
349A ILE* 3.5 27.5 - - + +
1002A MTP 2.9 30.8 + - + +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN* 5.3 0.7 - - - -
313A THR 4.7 0.8 + - - -
315A GLY* 3.3 1.2 - - - +
316A ALA* 1.3 78.6 - - - +
318A ASP* 1.3 62.7 + - - +
320A PHE* 3.2 4.3 + - - +
321A VAL* 3.1 27.6 + - - +
1002A MTP 2.9 13.3 + - - -
3001A ACT 3.4 30.4 - - - +
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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
----------------------------------------------------------
70A SER* 2.5 40.5 + - - +
73A ASN* 3.4 27.2 + - + +
74A SER* 2.7 32.8 + - - +
196A ASN* 4.8 5.6 + - - +
315A GLY* 3.4 8.9 + - - +
316A ALA 3.3 0.6 - - - -
317A GLY* 1.3 75.7 - - - +
319A ALA* 1.3 57.5 + - - +
321A VAL* 3.4 2.9 + - - -
322A GLY 3.0 16.5 + - - -
354A PHE 6.0 0.4 - - - +
1001A MTP 2.9 26.5 + - - -
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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
----------------------------------------------------------
77A VAL* 4.2 17.1 - - + +
315A GLY 3.1 17.9 + - - +
316A ALA 3.7 4.0 - - - +
318A ASP* 1.3 72.9 - - - +
320A PHE* 1.3 67.4 + - - +
322A GLY* 3.2 1.4 + - - -
323A GLY 2.9 19.6 + - - -
344A CYS* 3.5 24.0 - - + +
345A ALA* 4.0 3.1 - - - -
348A VAL* 3.7 28.3 - - + -
354A PHE 5.3 2.4 + - - +
356A LEU* 5.2 0.2 - - + -
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Residues in contact with PHE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 4.2 15.3 - + - -
276A VAL* 4.1 21.3 - - + -
278A THR* 3.8 27.6 - - + -
284A VAL* 4.3 2.5 - - + -
316A ALA 2.9 14.9 + - - +
317A GLY* 3.4 9.2 - - - +
319A ALA* 1.3 76.9 - - - +
321A VAL* 1.3 72.7 + - + +
323A GLY 3.2 0.5 + - - -
324A PHE* 3.0 25.0 + + - +
338A ILE* 3.6 34.5 - - + -
341A GLY* 3.2 35.5 + - - +
342A ASN* 3.4 25.6 - - - -
345A ALA* 4.2 2.0 - - + +
1002A MTP 4.0 14.8 - - - +
3001A ACT 4.9 1.8 - - + -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.9 6.5 - - - +
165A TYR* 3.6 32.1 - - + +
196A ASN* 3.7 22.4 - - - +
221A PHE* 3.9 31.2 - - + -
317A GLY 3.1 12.8 + - - +
318A ASP* 3.7 7.0 - - - +
320A PHE* 1.3 79.0 - - + +
322A GLY* 1.3 63.5 + - - +
324A PHE* 3.2 5.2 + - - +
325A LEU* 2.9 37.1 + - + +
3001A ACT 4.1 5.2 - - + -
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Residues in contact with GLY 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.5 27.8 - - - -
77A VAL* 3.8 11.8 - - - +
78A VAL* 3.5 9.8 - - - +
318A ASP 3.0 13.1 + - - -
319A ALA 3.2 4.0 + - - -
321A VAL* 1.3 78.1 - - - +
323A GLY* 1.3 55.4 + - - +
325A LEU* 4.8 0.7 - - - -
326A TYR* 3.0 29.1 + - - +
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Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.8 2.7 - - - +
319A ALA 2.9 11.5 + - - -
320A PHE 3.7 2.2 - - - -
322A GLY* 1.3 76.4 - - - +
324A PHE* 1.3 61.9 + - - +
326A TYR* 3.2 4.5 + - - +
327A ALA* 3.0 19.4 + - - +
340A CYS* 3.3 20.8 - - - -
341A GLY* 4.0 5.4 - - - -
344A CYS* 3.7 25.4 - - - -
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Residues in contact with PHE 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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219A ILE* 3.9 22.2 - - + -
221A PHE* 3.6 33.2 - + + -
274A LEU* 3.9 24.2 - - + -
276A VAL* 4.2 12.6 - - + -
320A PHE* 3.0 22.1 + + + +
321A VAL 3.5 7.9 - - - +
323A GLY* 1.3 74.9 - - - +
325A LEU* 1.3 62.3 - - + +
327A ALA* 3.3 2.6 + - - +
328A LEU* 2.9 31.9 + - + +
334A VAL* 4.3 4.7 - - + -
337A CYS* 3.5 47.6 - - + +
338A ILE* 3.8 24.2 - - + -
341A GLY* 3.8 1.8 - - - -
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Residues in contact with LEU 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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15A VAL* 4.4 20.3 - - + +
74A SER* 5.6 2.0 - - - -
75A VAL* 6.2 1.1 - - + -
78A VAL* 4.3 12.1 - - + -
163A ILE* 3.8 23.8 - - + +
165A TYR* 4.0 28.9 - - + -
194A THR* 4.0 19.7 - - + +
221A PHE* 4.3 11.9 - - + -
321A VAL* 2.9 36.6 + - + +
322A GLY* 3.9 3.8 - - - +
324A PHE* 1.3 74.5 - - + +
326A TYR* 1.3 66.7 + - - +
328A LEU* 3.3 11.8 + - + +
329A SER* 3.0 23.2 + - - -
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Residues in contact with TYR 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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78A VAL* 4.5 14.1 - - - +
81A LEU* 3.5 57.0 + - + -
82A LEU* 3.7 34.1 - - + -
322A GLY 3.0 14.4 + - - +
323A GLY 3.2 6.0 + - - +
325A LEU* 1.3 75.4 - - - +
327A ALA* 1.3 66.7 + - - +
329A SER* 2.6 24.9 + - - -
330A GLN* 3.3 33.9 + - + +
332A LYS* 5.8 3.8 - - + -
340A CYS* 3.9 13.7 - - - -
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Residues in contact with ALA 327 (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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323A GLY 3.0 16.8 + - - +
324A PHE 3.6 4.5 - - - +
326A TYR* 1.3 82.5 - - - +
328A LEU* 1.3 57.6 + - - +
330A GLN* 2.9 16.8 + - - -
331A GLY 3.3 0.2 + - - -
332A LYS* 3.2 45.1 + - + +
337A CYS* 3.6 24.7 - - - -
340A CYS* 3.9 11.2 - - + -
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Residues in contact with LEU 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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163A ILE* 4.0 21.9 - - + +
192A ILE* 4.0 25.8 - - + -
219A ILE* 3.8 29.8 - - + -
272A THR* 6.2 1.1 - - + -
324A PHE* 2.9 21.7 + - + +
325A LEU* 3.5 19.1 - - + +
327A ALA* 1.3 77.9 - - - +
329A SER* 1.3 57.3 + - - +
331A GLY* 2.9 20.8 + - - +
332A LYS 4.7 5.6 - - - +
337A CYS* 3.5 16.3 - - - -
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Residues in contact with SER 329 (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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14A ARG* 4.1 27.5 + - - -
15A VAL* 4.8 3.1 - - - -
82A LEU* 4.4 7.7 - - - +
163A ILE* 3.5 18.5 - - - +
325A LEU 3.0 12.7 + - - -
326A TYR* 2.6 25.8 + - - -
328A LEU* 1.3 77.5 - - - +
330A GLN* 1.3 72.3 + - - +
331A GLY 3.2 1.4 + - - -
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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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14A ARG* 5.8 2.6 + - - +
82A LEU* 4.0 11.6 - - - +
326A TYR* 3.3 50.7 + - + +
327A ALA* 2.9 9.8 + - - +
329A SER* 1.3 90.9 + - - +
331A GLY* 1.3 62.4 + - - +
332A LYS* 3.3 15.9 + - + +
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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
------------------------------------------------------------
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