Contacts of the helix formed by residues 278 - 291 (chain A) in PDB entry 1I4A
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LYS* 4.9 0.9 - - - +
246A SER* 2.8 34.9 + - - +
249A PHE* 4.5 1.0 - - - -
274A ARG* 2.9 45.8 + - - +
277A ILE* 1.3 78.2 - - + +
279A MET* 1.3 59.9 + - - +
280A LEU* 3.2 3.4 - - - -
281A ASP* 3.1 9.4 + - + +
282A ILE* 2.9 34.3 + - - +
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Residues in contact with MET 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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253A LEU* 5.4 0.7 - - + -
270A VAL 4.5 0.4 - - - +
271A MET* 3.7 40.2 - - + +
274A ARG* 3.6 14.9 + - + +
275A ALA* 3.7 42.7 + - - +
277A ILE 3.9 0.6 - - - -
278A ASP* 1.3 77.1 - - - +
280A LEU* 1.3 70.3 + - + +
282A ILE* 3.2 14.1 + - + +
283A ARG* 2.9 29.8 + - - +
294A LEU* 3.9 18.2 - - - -
313A LEU 3.5 8.5 - - - +
314A CYS 3.2 25.6 - - - +
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Residues in contact with LEU 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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275A ALA 5.8 1.6 - - - +
278A ASP* 3.2 1.5 - - - -
279A MET* 1.3 84.4 - - + +
281A ASP* 1.3 59.2 + - - +
283A ARG* 3.3 36.2 + - - +
284A ALA* 3.1 25.5 + - - +
314A CYS 5.9 0.2 - - - +
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 4.1 4.9 - - - +
246A SER* 2.9 29.2 + - - +
278A ASP* 3.1 10.9 + - + +
280A LEU* 1.3 76.7 - - - +
282A ILE* 1.3 62.8 + - - +
284A ALA* 4.3 9.6 - - - +
285A ASN* 2.7 43.4 + - - -
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Residues in contact with ILE 282 (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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246A SER* 3.8 20.0 - - - +
249A PHE* 3.7 15.5 - - + -
250A ALA* 3.7 16.5 - - - +
253A LEU* 3.6 25.8 - - + -
270A VAL* 5.0 2.9 - - + -
274A ARG* 3.6 21.5 - - + -
278A ASP* 2.9 41.1 + - - +
279A MET* 3.5 24.0 - - + +
281A ASP* 1.3 76.4 - - - +
283A ARG* 1.3 58.5 + - - +
286A PHE* 2.8 28.0 + - + +
294A LEU* 4.5 4.0 - - + -
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Residues in contact with ARG 283 (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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279A MET* 2.9 21.4 + - + +
280A LEU* 3.4 33.4 - - - +
282A ILE* 1.3 75.4 - - - +
284A ALA* 1.3 65.8 + - - +
286A PHE* 3.2 6.6 + - - +
287A LYS* 3.1 24.3 + - - +
294A LEU* 4.1 24.4 + - + -
314A CYS* 3.2 33.7 + - - -
315A GLY* 3.5 14.8 + - - -
316A GLY* 3.1 29.5 + - - -
317A ASP 3.9 4.0 + - - -
318A ASP* 2.9 46.4 + - - +
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Residues in contact with ALA 284 (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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280A LEU 3.1 14.2 + - - +
281A ASP* 3.3 18.1 + - - +
283A ARG* 1.3 76.5 - - - +
285A ASN* 1.3 63.5 + - - +
287A LYS* 3.4 4.7 + - - +
288A ARG* 3.1 23.1 + - - +
318A ASP* 5.4 2.2 - - - -
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Residues in contact with ASN 285 (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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244A ASN* 2.9 29.2 + - - +
246A SER* 3.5 7.9 - - - +
247A ALA* 3.6 22.2 - - + +
250A ALA* 4.1 2.9 - - + -
281A ASP* 2.7 51.6 + - - +
282A ILE 3.8 3.6 - - - +
284A ALA* 1.3 75.8 - - - +
286A PHE* 1.3 60.6 + - - +
288A ARG* 3.0 25.6 + - - +
289A LEU* 2.9 37.0 + - + +
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Residues in contact with PHE 286 (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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250A ALA* 3.6 33.4 - - + +
253A LEU* 4.5 2.2 - - + -
254A TYR* 3.9 20.6 - + + -
257A MET* 4.6 0.4 - - + -
282A ILE* 2.8 19.6 + - + +
283A ARG* 3.5 7.9 - - - +
285A ASN* 1.3 78.8 - - - +
287A LYS* 1.3 57.8 + - - +
290A TYR* 2.8 51.8 + + + +
292A LYS 3.2 18.2 - - - -
294A LEU* 3.6 38.8 - - + -
297A PHE* 3.5 48.0 - + + -
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Residues in contact with LYS 287 (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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283A ARG 3.1 15.5 + - - +
284A ALA* 3.9 5.2 - - - +
286A PHE* 1.3 76.7 - - - +
288A ARG* 1.3 59.6 + - - +
291A GLY* 2.7 45.6 + - - +
292A LYS* 3.1 26.8 + - - +
293A SER* 4.7 4.2 - - - +
318A ASP* 4.2 36.8 - - + -
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Residues in contact with ARG 288 (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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244A ASN* 3.9 10.5 - - - +
247A ALA* 4.1 6.1 - - - +
284A ALA 3.1 18.1 + - - +
285A ASN* 3.0 30.5 + - - +
286A PHE 3.2 0.2 - - - -
287A LYS* 1.3 78.2 - - - +
289A LEU* 1.3 93.0 + - - +
291A GLY* 4.4 1.6 + - - -
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Residues in contact with LEU 289 (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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247A ALA* 4.2 14.6 - - + +
250A ALA* 4.2 15.3 - - + -
251A GLU* 4.7 2.2 - - + +
285A ASN 2.9 21.9 + - - +
288A ARG* 1.3 113.0 - - - +
290A TYR* 1.3 98.3 + - + +
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Residues in contact with TYR 290 (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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250A ALA 4.0 9.2 - - - -
251A GLU* 3.3 33.1 + - - +
254A TYR* 3.4 64.3 - + + +
255A LYS* 4.9 0.9 - - - +
286A PHE* 2.8 50.5 + + + +
289A LEU* 1.3 104.4 - - + +
291A GLY* 1.3 56.4 + - - +
292A LYS* 3.0 15.4 + - - +
297A PHE* 4.8 4.2 - - + -
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Residues in contact with GLY 291 (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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287A LYS* 2.7 41.8 + - - -
288A ARG 4.4 1.8 + - - -
289A LEU 3.8 1.0 - - - -
290A TYR* 1.3 70.9 - - - +
292A LYS* 1.3 67.7 + - - +
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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