Contacts of the helix formed by residues 270 - 280 (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 GLU 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A HIS* 3.4 52.9 + - + +
268A THR* 3.0 39.3 - - + +
269A ASP* 1.3 72.9 - - - +
271A PHE* 1.3 59.2 + - + +
273A LEU* 4.2 2.7 - - - -
274A ASN* 2.9 38.9 + - - +
308A THR* 6.1 0.2 - - - +
312A TYR* 3.4 31.6 - - + +
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Residues in contact with PHE 271 (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* 4.2 18.4 - + - -
83A HIS* 4.3 37.9 - + + -
99A GLN* 4.2 4.7 - - - +
102A LYS* 3.5 39.3 - - + +
110A ASN* 6.4 0.2 - - - +
269A ASP* 3.3 9.5 + - - +
270A GLU* 1.3 79.0 - - + +
272A THR* 1.3 57.5 + - - +
274A ASN* 3.9 7.2 - - + +
275A ARG* 3.0 34.0 + - - +
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Residues in contact with THR 272 (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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110A ASN* 5.6 3.5 + - - -
116A GLU* 4.2 3.1 - - - +
258A ARG* 4.1 19.6 + - - +
262A ALA* 3.8 16.6 - - + -
269A ASP* 2.5 32.2 + - - +
270A GLU 3.3 0.2 - - - -
271A PHE* 1.3 75.2 - - - +
273A LEU* 1.3 67.3 + - - +
275A ARG* 3.3 24.8 + - - +
276A ILE* 2.9 45.3 + - + +
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Residues in contact with LEU 273 (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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259A LEU* 3.7 26.9 - - + +
262A ALA* 4.5 4.2 - - + +
263A LEU* 3.8 39.3 - - + -
268A THR* 4.2 12.1 - - + -
269A ASP 3.2 12.8 + - - +
270A GLU 3.7 3.6 - - - +
272A THR* 1.3 79.0 - - - +
274A ASN* 1.3 58.8 + - - +
276A ILE* 4.1 0.5 - - - +
277A MET* 2.9 48.3 + - + +
300A LEU* 5.6 0.4 - - + -
304A ILE* 4.7 7.6 - - + -
308A THR* 4.2 8.1 - - + -
312A TYR* 3.7 17.5 - - - +
316A LEU* 4.0 20.9 - - + -
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Residues in contact with ASN 274 (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* 4.1 5.4 + - - +
83A HIS* 3.9 23.6 - - - +
84A LEU* 3.9 25.4 + - + +
87A ALA* 5.5 2.2 - - + -
95A PHE* 4.8 5.8 - - + -
270A GLU* 2.9 20.0 + - - +
271A PHE* 3.9 8.7 - - + +
273A LEU* 1.3 74.4 - - - +
275A ARG* 1.3 65.3 + - - +
277A MET* 4.8 1.6 - - - -
278A VAL* 3.0 31.4 + - + +
312A TYR* 2.7 40.5 + - - -
316A LEU* 4.2 3.6 - - - +
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Residues in contact with ARG 275 (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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95A PHE* 4.0 12.3 - - + -
96A ASP* 5.4 0.4 - - - +
99A GLN* 3.4 37.3 + - + +
102A LYS* 3.6 15.2 - - - +
110A ASN* 6.0 0.6 - - - +
113A ALA* 3.8 19.4 - - - +
116A GLU* 2.6 40.3 + - - +
117A ILE* 3.6 27.1 - - - +
121A ARG* 4.6 4.5 - - - +
258A ARG* 3.5 9.5 - - - +
271A PHE* 3.0 19.6 + - - +
272A THR* 3.3 26.3 + - - +
274A ASN* 1.3 77.8 - - - +
276A ILE* 1.3 52.2 + - - +
279A SER* 2.5 45.9 + - - +
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Residues in contact with ILE 276 (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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116A GLU* 3.7 28.0 - - - +
255A LEU* 4.0 17.9 - - + +
258A ARG* 3.6 31.0 - - + -
259A LEU* 3.7 33.4 - - + -
272A THR* 2.9 23.0 + - + +
275A ARG* 1.3 72.6 - - - +
277A MET* 1.3 68.7 + - - +
279A SER* 3.8 4.9 - - - -
280A ARG* 3.0 37.9 + - + +
285A LEU* 4.9 1.0 - - + +
288A ILE* 4.3 10.5 - - + -
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Residues in contact with MET 277 (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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259A LEU* 4.3 11.2 - - + -
273A LEU* 2.9 30.2 + - + +
274A ASN 4.2 1.8 - - - +
276A ILE* 1.3 75.9 - - - +
278A VAL* 1.3 61.9 + - + +
281A SER* 3.2 26.3 + - - -
285A LEU* 3.9 19.0 - - + +
300A LEU* 4.0 21.3 - - + -
304A ILE* 3.5 28.3 - - + -
316A LEU* 3.6 39.3 - - + +
319A ILE* 3.5 14.9 - - + +
320A CYS* 3.8 20.0 - - + +
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Residues in contact with VAL 278 (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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51A ASN* 5.9 3.1 - - - +
54A ARG* 5.6 1.3 - - - +
84A LEU* 3.4 30.3 - - + -
87A ALA* 3.8 34.1 - - + +
88A LEU* 4.1 20.6 - - + +
95A PHE* 4.1 17.7 - - + -
274A ASN 3.0 19.8 + - - +
277A MET* 1.3 74.6 - - - +
279A SER* 1.3 64.9 + - - +
281A SER* 2.7 25.3 + - - +
282A GLU 4.7 0.2 + - - -
319A ILE* 4.6 2.7 - - + -
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Residues in contact with SER 279 (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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6A TRP* 5.8 2.1 - - - -
95A PHE* 4.3 10.3 - - - -
96A ASP* 4.1 7.6 - - - -
116A GLU* 5.3 0.5 + - - -
121A ARG* 3.1 32.4 + - - -
275A ARG* 2.5 31.8 + - - +
276A ILE* 3.8 4.5 + - - +
278A VAL* 1.3 75.6 - - - +
280A ARG* 1.3 65.2 + - - +
281A SER 3.9 0.2 + - - -
282A GLU 4.9 0.9 + - - -
283A ILE* 3.6 20.6 - - - +
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Residues in contact with ARG 280 (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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120A THR* 3.8 20.2 + - - -
121A ARG* 3.8 25.7 - - - +
125A GLN* 5.0 3.4 + - - +
251A THR* 3.9 15.0 - - - +
255A LEU* 3.5 18.1 - - + +
276A ILE* 3.0 23.2 + - + +
277A MET 4.2 0.2 - - - -
279A SER* 1.3 88.7 - - - +
281A SER* 1.3 65.4 + - - +
282A GLU 3.2 3.1 - - - -
283A ILE* 3.0 37.9 + - - +
284A ASP* 2.8 44.5 + - - +
285A LEU* 3.1 19.5 + - + +
288A ILE* 3.8 20.6 - - + -
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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