Contacts of the helix formed by residues 269 - 276 (chain B) in PDB entry 5IYB
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 ILE 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B VAL* 5.0 7.9 - - + -
256B ILE* 3.6 43.2 + - + -
258B ALA* 3.8 24.3 - - + +
260B LEU* 5.8 1.6 - - + -
267B VAL 3.5 3.9 + - - -
268B PRO* 1.3 71.2 - - - +
270B ILE* 1.3 80.8 + - + +
272B VAL* 2.9 32.2 + - + +
273B PHE* 3.2 32.3 + - + -
288B ILE* 6.1 0.2 - - + -
365B LEU* 4.3 19.7 - - + -
369B VAL* 3.9 17.3 - - + -
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Residues in contact with ILE 270 (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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256B ILE* 5.8 0.2 - - + -
268B PRO* 3.2 4.2 + - + -
269B ILE* 1.3 89.0 - - + +
271B ILE* 1.3 61.7 + - + +
273B PHE* 3.3 7.5 + - + +
274B ARG* 3.0 25.7 + - - +
284B ILE* 3.9 37.0 - - + -
288B ILE* 4.5 11.4 - - + -
301B VAL* 4.6 5.2 - - + -
304B SER* 3.6 39.0 - - - +
305B LEU* 3.9 17.3 - - + -
308B ALA* 3.7 24.0 - - + -
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Residues in contact with ILE 271 (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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267B VAL* 4.9 2.9 - - + -
268B PRO* 2.9 45.7 + - + +
270B ILE* 1.3 78.2 - - + +
272B VAL* 1.3 58.9 + - + +
274B ARG* 3.3 3.0 + - - +
275B ALA* 2.9 27.7 + - - +
307B GLU 5.7 3.4 - - - +
308B ALA* 5.2 5.2 - - - -
310B VAL* 6.4 0.4 - - + -
311B ILE* 3.9 37.0 - - + -
317B ALA* 4.2 16.6 - - + +
320B PHE* 3.6 37.7 - - + -
321B ILE* 4.7 6.7 - - + -
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Residues in contact with VAL 272 (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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258B ALA* 4.9 0.9 - - + -
260B LEU* 4.0 22.9 - - + -
267B VAL* 4.3 10.5 - - + -
268B PRO 4.0 9.2 - - - +
269B ILE* 2.9 25.8 + - + +
271B ILE* 1.3 74.3 - - + +
273B PHE* 1.3 59.9 + - - +
275B ALA* 3.4 7.5 + - - +
276B LEU* 3.0 27.6 + - + +
321B ILE* 4.8 5.6 - - + -
343B LEU* 4.3 11.0 - - + -
347B MET* 4.0 22.9 - - + -
365B LEU* 4.0 22.4 - - + -
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Residues in contact with PHE 273 (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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269B ILE* 3.2 43.3 + - + -
270B ILE* 3.3 11.0 + - + +
272B VAL* 1.3 78.1 - - - +
274B ARG* 1.3 60.8 + - - +
276B LEU* 3.2 18.8 + - + +
277B GLY 3.3 8.1 + - - -
278B PHE* 3.4 26.1 + + + +
284B ILE* 4.0 35.2 - - + -
287B HIS* 4.2 18.6 - - + -
288B ILE* 4.6 8.7 - - + -
362B ALA* 3.7 20.9 - - + -
365B LEU* 3.6 21.3 - - + -
366B GLY* 3.5 29.2 - - - -
369B VAL* 4.5 4.0 - - + -
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Residues in contact with ARG 274 (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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270B ILE* 3.0 21.2 + - - +
271B ILE* 3.3 5.8 + - - +
273B PHE* 1.3 75.3 - - - +
275B ALA* 1.3 63.2 + - - +
277B GLY* 3.2 11.8 + - - -
278B PHE 3.2 14.8 - - - +
279B VAL* 2.9 28.7 + - - +
281B ASP* 3.0 27.7 + - - -
284B ILE* 4.3 8.3 - - + +
305B LEU 5.5 0.2 + - - -
308B ALA* 3.4 24.7 + - - +
309B PHE* 4.9 3.4 - - - -
311B ILE* 3.5 35.4 - - - +
312B GLN* 3.3 48.7 + - - +
313B GLU 4.9 0.6 - - - +
314B GLN* 3.7 16.8 - - - +
317B ALA* 4.6 4.7 - - + -
22I ASN* 4.3 2.8 - - - +
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Residues in contact with ALA 275 (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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271B ILE 2.9 18.3 + - - +
272B VAL 3.5 6.1 - - - +
274B ARG* 1.3 73.6 - - - +
276B LEU* 1.3 52.5 + - - +
277B GLY 3.1 4.9 - - - -
314B GLN* 2.4 34.7 + - - +
317B ALA* 4.2 8.2 - - + +
318B LEU* 3.7 28.6 - - + +
321B ILE* 3.8 19.3 - - + -
343B LEU* 3.8 7.0 - - + +
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Residues in contact with LEU 276 (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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272B VAL* 3.0 19.5 + - + +
273B PHE* 3.2 14.1 + - + +
275B ALA* 1.3 74.6 - - - +
277B GLY* 1.3 56.3 - - - +
278B PHE* 3.7 9.9 + - + -
314B GLN* 3.3 4.4 + - - -
343B LEU* 5.0 13.0 - - + +
347B MET* 4.6 17.3 - - + -
358B GLU* 4.1 40.5 - - + +
361B LYS* 4.9 4.7 - - + -
362B ALA* 3.8 33.2 - - + +
365B LEU* 3.8 25.4 - - + -
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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