Contacts of the helix formed by residues 281 - 293 (chain B) in PDB entry 1II7
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 SER 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B GLY* 1.3 76.4 - - - -
282B GLU* 1.3 66.0 + - - +
283B GLU* 3.7 10.2 + - - +
284B GLU* 3.2 23.3 + - - +
285B ILE* 2.9 23.0 + - - +
309B ARG* 5.9 4.7 - - - +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B SER* 1.3 73.6 - - - +
283B GLU* 1.3 59.5 + - - +
285B ILE* 3.3 3.1 + - - +
286B ARG* 2.8 30.5 + - + +
308B TRP* 6.1 1.0 - - - +
310B LYS 5.9 0.2 - - - +
312B PHE* 3.3 65.2 - - + +
316B GLU* 4.8 7.9 - - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B SER* 3.2 9.4 + - - +
282B GLU* 1.3 79.5 - - - +
284B GLU* 1.3 62.8 + - - +
286B ARG* 3.2 14.2 + - - +
287B LYS* 3.2 18.0 + - - +
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B TRP* 3.1 35.1 + - + +
242B GLY* 3.3 21.4 - - - +
279B LYS 4.2 4.7 - - - +
280B GLY* 4.0 15.3 - - - -
281B SER* 3.2 17.7 + - - +
283B GLU* 1.3 75.6 - - - +
285B ILE* 1.3 55.8 + - - +
286B ARG 3.0 1.8 - - - -
287B LYS* 2.7 16.9 + - + +
288B ALA* 2.7 33.4 + - - +
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 3.6 28.0 - - + -
279B LYS 4.2 4.5 - - - +
280B GLY 3.6 20.9 - - - +
281B SER 2.9 17.6 + - - +
282B GLU 3.5 4.0 - - - +
284B GLU* 1.3 76.8 - - - +
286B ARG* 1.3 63.5 + - - +
288B ALA* 3.4 1.0 + - - +
289B ILE* 3.1 27.4 + - + +
306B ILE* 3.2 34.3 - - + -
307B GLY 4.0 6.5 - - - +
308B TRP* 4.6 2.9 - - + -
312B PHE* 4.1 17.3 - - + -
317B ILE* 3.9 26.9 - - + -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU* 2.8 15.7 + - + +
283B GLU* 3.2 15.7 - - - +
285B ILE* 1.3 79.8 - - - +
287B LYS* 1.3 64.0 + - - +
289B ILE* 3.5 7.3 + - - +
290B LYS* 3.2 18.9 + - - +
316B GLU* 3.3 31.6 + - - +
317B ILE* 5.8 3.8 - - - -
320B LEU* 5.2 6.6 - - + +
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B TRP* 4.7 15.7 - - + -
242B GLY 5.3 5.6 + - - +
243B ILE* 5.4 9.1 - - - +
283B GLU 3.2 8.1 + - - +
284B GLU* 2.7 17.1 + - + +
286B ARG* 1.3 77.0 - - - +
288B ALA* 1.3 59.0 + - - +
290B LYS* 2.7 36.0 + - + +
291B ARG* 3.1 42.0 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B TRP* 3.6 42.1 - - + +
245B PHE* 3.2 17.0 - - + -
278B ILE* 3.9 22.9 - - + -
284B GLU 2.7 17.7 + - - +
285B ILE 3.7 5.2 - - - +
287B LYS* 1.3 72.4 - - - +
289B ILE* 1.3 56.9 + - - +
291B ARG* 3.0 16.5 + - - -
292B LEU 3.0 9.9 + - - -
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 3.4 27.8 - - + -
285B ILE* 3.1 19.1 + - + +
286B ARG* 3.7 6.5 - - - +
288B ALA* 1.3 72.3 - - - +
290B LYS* 1.3 64.4 + - - +
291B ARG 3.2 0.2 - - - -
292B LEU* 3.7 18.1 - - + +
293B ILE* 3.1 23.7 + - - +
304B LEU* 4.4 8.3 - - + -
306B ILE* 5.3 0.4 - - + -
317B ILE* 4.0 42.2 - - + -
320B LEU* 3.9 23.3 - - + -
321B LEU* 4.2 17.5 - - + -
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ARG 3.2 11.8 + - - +
287B LYS* 2.7 18.4 + - + +
289B ILE* 1.3 78.5 - - - +
291B ARG* 1.3 74.3 + - + +
293B ILE* 4.1 13.3 - - + +
294B PRO* 3.9 11.6 - - - +
320B LEU* 5.2 4.9 - - + -
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B TRP* 3.9 31.6 - - + -
243B ILE 4.2 8.1 + - - -
244B LYS* 5.7 0.4 - - - +
245B PHE* 4.2 5.4 - - + -
287B LYS* 3.1 41.6 + - - +
288B ALA 3.0 9.2 + - - +
290B LYS* 1.3 94.8 - - - +
292B LEU* 1.3 62.2 + - - +
294B PRO* 3.3 18.1 - - - +
295B LEU* 3.7 10.2 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B TYR* 4.1 15.3 - - + -
245B PHE* 3.7 21.1 - - + -
276B VAL* 3.8 28.3 - - + -
288B ALA 3.0 8.4 + - - +
289B ILE* 3.4 20.6 + - + +
291B ARG* 1.3 76.4 - - - +
293B ILE* 1.3 55.7 + - - +
295B LEU* 2.7 37.7 + - + +
296B ILE* 3.4 30.0 + - + +
302B VAL* 5.3 0.7 - - + -
304B LEU* 3.8 28.7 - - + -
321B LEU* 4.3 13.7 - - + -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE 3.1 16.6 - - - +
290B LYS* 4.1 10.3 - - + +
292B LEU* 1.3 76.7 - - - +
294B PRO* 1.3 71.5 - - + +
296B ILE* 3.1 26.8 + - - +
320B LEU* 3.6 50.0 - - + +
321B LEU* 4.4 13.0 - - + +
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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