Contacts of the helix formed by residues 310 - 320 (chain A) in PDB entry 1AII
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 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A SER* 1.3 75.2 + - - +
311A ASP* 1.3 67.4 + - - -
313A GLU* 3.3 7.9 + - - +
314A ILE* 3.2 27.7 + - - +
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Residues in contact with ASP 311 (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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39A GLU* 3.5 36.4 - - - +
40A LYS* 3.6 22.7 + - - -
43A ILE* 4.0 8.6 - - + +
81A PHE* 3.8 28.4 - - + -
310A GLY* 1.3 70.6 - - - -
312A TYR* 1.3 65.7 + - - +
314A ILE* 3.2 6.9 + - - +
315A THR* 3.0 27.7 + - - -
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Residues in contact with TYR 312 (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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80A HIS* 3.7 36.8 - + + -
81A PHE* 3.9 16.7 - - + +
84A LEU* 4.0 13.2 - - + -
270A GLU* 3.4 38.8 + - + +
273A LEU* 3.7 8.9 - - + +
274A ASN* 2.7 34.3 + - - -
308A THR* 3.8 23.1 - - + -
309A SER 3.7 8.7 - - - +
310A GLY 3.2 0.2 - - - -
311A ASP* 1.3 79.6 - - - +
313A GLU* 1.3 60.8 + - - +
315A THR* 3.4 2.8 + - - -
316A LEU* 3.1 43.4 + - + +
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Residues in contact with GLU 313 (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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304A ILE* 4.3 2.4 - - - +
305A LYS* 3.4 41.0 + - - +
308A THR* 3.3 34.8 - - - +
309A SER* 3.3 33.3 + - - -
310A GLY 3.6 4.6 + - - +
311A ASP 3.3 0.2 - - - -
312A TYR* 1.3 80.3 - - - +
314A ILE* 1.3 65.9 + - - +
316A LEU* 3.4 4.4 + - - +
317A LEU* 3.0 36.6 + - + +
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Residues in contact with ILE 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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40A LYS* 4.1 32.3 - - + +
43A ILE* 4.0 24.2 - - + -
310A GLY 3.2 19.9 + - - +
311A ASP* 3.2 8.3 + - - +
313A GLU* 1.3 79.0 - - + +
315A THR* 1.3 61.2 + - - +
317A LEU* 3.2 8.8 + - + +
318A LYS* 2.8 38.0 + - + +
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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
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43A ILE* 3.3 25.2 - - - +
47A THR* 3.5 23.3 - - + -
81A PHE* 3.4 8.7 - - - -
84A LEU* 3.6 29.6 - - + -
85A MET* 4.1 9.2 - - - -
88A LEU* 4.1 10.1 - - + -
311A ASP 3.0 17.7 + - - -
312A TYR 3.8 0.7 - - - -
314A ILE* 1.3 75.9 - - - +
316A LEU* 1.3 56.8 + - - +
318A LYS* 3.2 2.9 + - - +
319A ILE* 3.0 33.7 + - + +
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Residues in contact with LEU 316 (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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84A LEU* 3.7 21.1 - - + -
273A LEU* 4.0 17.3 - - + -
274A ASN* 4.2 12.3 - - - +
277A MET* 3.6 35.6 - - + +
304A ILE* 3.8 23.1 - - + -
308A THR* 4.1 10.5 - - + +
312A TYR* 3.1 50.0 + - + +
313A GLU 3.9 0.4 - - - +
315A THR* 1.3 74.9 - - - +
317A LEU* 1.3 57.4 + - - +
319A ILE* 3.3 5.2 + - + +
320A CYS* 2.8 29.6 + - - +
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Residues in contact with LEU 317 (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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301A TYR* 3.4 68.6 - - + +
304A ILE* 3.6 19.3 - - + -
305A LYS* 3.9 16.2 - - + +
313A GLU* 3.0 46.5 + - + +
314A ILE* 3.2 9.8 + - + +
316A LEU* 1.3 74.9 - - - +
318A LYS* 1.3 61.7 + - + +
320A CYS* 3.4 5.4 - - - +
321A GLY* 3.2 17.8 + - - -
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Residues in contact with LYS 318 (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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12A THR 5.6 0.7 - - - +
13A VAL* 5.3 1.9 - - - +
43A ILE* 3.6 24.7 - - + -
44A SER* 4.4 9.2 - - - +
47A THR* 3.4 33.2 + - + +
48A GLU* 3.2 35.1 + - - +
314A ILE* 2.8 25.0 + - + +
315A THR 3.2 4.7 + - - +
317A LEU* 1.3 76.2 - - + +
319A ILE* 1.3 63.3 + - - +
321A GLY* 3.2 13.8 + - - -
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Residues in contact with ILE 319 (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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12A THR* 2.7 29.6 + - - -
13A VAL* 4.3 13.6 - - + +
47A THR* 4.3 15.3 - - + -
84A LEU* 3.9 27.1 - - + -
88A LEU* 4.0 20.2 - - + -
277A MET* 3.5 33.9 - - + +
278A VAL* 4.6 3.8 - - + -
281A SER* 3.9 14.8 - - - +
285A LEU* 3.8 5.5 - - + +
315A THR* 3.0 25.3 + - + +
316A LEU* 3.3 7.4 + - - +
318A LYS* 1.3 73.9 - - - +
320A CYS* 1.3 62.6 + - - +
321A GLY* 3.0 0.9 + - - -
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Residues in contact with CYS 320 (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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12A THR* 3.3 9.9 - - - +
277A MET* 3.8 12.3 - - + +
285A LEU* 4.3 4.3 - - - -
289A ARG* 2.8 39.8 + - - -
300A LEU* 4.2 16.6 - - - -
301A TYR* 3.9 27.6 - - + -
304A ILE* 4.3 3.1 - - + -
316A LEU 2.8 17.9 + - - +
317A LEU* 3.4 11.9 - - - +
318A LYS 3.3 0.2 - - - -
319A ILE* 1.3 75.7 - - - +
321A GLY* 1.3 55.6 + - - +
322A GLY 3.4 17.7 - - - -
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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
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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