Contacts of the helix formed by residues 279 - 286 (chain A) in PDB entry 2IHU
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 PRO 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ASP* 4.4 7.0 - - - +
278A PHE* 1.4 99.9 - - + +
280A ALA* 1.3 57.9 + - - +
281A LEU 3.5 2.7 - - - -
282A GLN* 4.0 18.6 - - + -
283A THR* 2.8 34.6 + - - +
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Residues in contact with ALA 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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272A MET* 3.8 22.2 - - + -
273A ASP* 3.1 11.6 + - - +
276A LEU* 4.0 11.9 - - + -
278A PHE* 2.8 19.0 + - + +
279A PRO* 1.3 70.2 - - - +
281A LEU* 1.3 60.0 + - - +
283A THR* 3.4 1.8 + - - -
284A MET* 3.0 29.9 + - - +
364A LEU* 3.5 31.3 - - + +
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Residues in contact with LEU 281 (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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268A VAL* 3.8 20.0 - - + -
269A THR 4.5 2.0 - - - +
270A GLY* 4.6 7.9 - - - +
272A MET* 3.6 29.2 - - + -
273A ASP* 2.9 23.2 + - - +
279A PRO 3.5 0.2 - - - -
280A ALA* 1.3 72.1 - - - +
282A GLN* 1.3 60.4 + - - +
284A MET* 4.4 2.9 - - + -
285A PHE* 2.9 42.6 + - + +
306A MET* 3.8 21.1 - - + +
309A LYS* 3.7 27.7 - - + +
570A ALA* 3.8 29.4 - - + -
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Residues in contact with GLN 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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273A ASP* 5.0 1.4 + - - +
279A PRO* 3.6 22.1 + - + +
280A ALA 3.4 0.2 - - - -
281A LEU* 1.3 78.1 - - - +
283A THR* 1.3 57.6 + - - +
286A ALA* 2.8 50.8 + - + +
309A LYS* 3.8 20.7 - - - +
310A GLY* 3.4 27.9 + - - +
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Residues in contact with THR 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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278A PHE* 3.5 13.7 - - - -
279A PRO* 2.8 26.5 + - - +
280A ALA 3.7 4.5 - - - -
281A LEU 3.4 0.2 - - - -
282A GLN* 1.3 76.8 - - - +
284A MET* 1.3 63.0 + - - +
287A PRO* 4.2 5.1 - - - +
359A HIS* 4.1 4.7 - - - -
360A ASP 3.9 8.4 - - - +
361A ILE* 3.8 25.1 - - - +
363A PRO* 4.3 11.4 - - + +
364A LEU* 3.7 32.8 - - + +
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Residues in contact with MET 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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248A ILE* 3.8 33.0 - - + +
265A TYR* 3.1 34.8 - - - +
266A GLY* 4.7 0.9 - - - +
267A ALA 4.4 10.1 - - - +
268A VAL* 4.7 2.5 - - + -
272A MET* 4.4 14.4 - - + -
280A ALA 3.0 18.1 + - - +
281A LEU* 3.7 6.5 - - + +
283A THR* 1.3 78.3 - - - +
285A PHE* 1.3 80.7 + - + +
288A VAL* 3.7 2.4 - - - +
359A HIS* 2.8 27.5 + - - -
361A ILE* 4.0 13.2 - - - -
364A LEU* 3.9 19.7 - - + +
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Residues in contact with PHE 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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220A VAL* 4.4 11.2 - - + -
222A VAL* 4.4 10.1 - - + -
248A ILE* 3.8 23.3 - - + -
268A VAL* 3.9 27.8 - - + -
281A LEU* 2.9 26.2 + - + +
284A MET* 1.3 96.9 - - + +
286A ALA* 1.3 61.0 + - - +
287A PRO* 3.4 4.5 - - - -
288A VAL* 3.1 21.9 + - + +
291A VAL* 5.1 2.0 - - + -
302A LEU* 5.2 3.4 - - + -
306A MET* 3.4 24.9 - - + -
307A TRP* 3.6 38.1 - - + +
309A LYS* 4.0 6.5 - - + -
313A LYS* 2.8 24.2 + - - -
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Residues in contact with ALA 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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281A LEU 4.3 0.2 + - - -
282A GLN* 2.8 51.2 + - + +
285A PHE* 1.3 73.6 - - - +
287A PRO* 1.4 61.5 - - + +
309A LYS* 3.5 11.8 + - - +
310A GLY* 3.8 3.3 - - - -
311A ILE* 3.2 28.6 + - - +
313A LYS* 3.3 4.5 + - - -
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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