Contacts of the helix formed by residues 270 - 280 (chain B) in PDB entry 4OIV
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 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ARG 3.4 9.6 - - - +
269B MET* 1.3 89.5 - - - +
271B GLN* 1.3 64.0 + - - +
272B GLU* 2.9 26.9 - - - +
273B ILE* 3.0 29.9 + - + +
274B THR* 3.3 9.0 + - - +
297B ASN* 3.6 19.7 - - - +
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Residues in contact with GLN 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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269B MET 3.3 4.4 + - - -
270B PRO* 1.3 70.3 - - - +
272B GLU* 1.3 71.6 + - + +
274B THR* 3.6 9.6 - - - +
275B ASN* 2.7 55.4 + - - +
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Residues in contact with GLU 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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270B PRO* 2.9 26.5 - - - +
271B GLN* 1.3 99.4 + - + +
273B ILE* 1.3 65.0 + - + +
275B ASN* 3.2 8.8 + - - +
276B LYS* 3.2 34.0 + - - +
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Residues in contact with ILE 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 MET* 3.9 19.1 - - + -
270B PRO* 3.0 32.1 + - + +
272B GLU* 1.3 80.5 - - + +
274B THR* 1.3 62.8 + - - +
276B LYS* 3.3 22.3 + - + +
277B ILE* 3.6 7.7 + - + +
290B ILE* 4.9 4.2 - - + +
293B GLU* 3.7 44.9 - - + +
294B MET* 3.3 38.1 - - + +
297B ASN* 4.3 6.3 - - + -
461B ASN* 6.0 0.9 - - - +
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Residues in contact with THR 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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269B MET* 3.6 27.8 - - + +
270B PRO 3.5 14.1 - - - +
271B GLN* 3.3 11.0 + - - +
273B ILE* 1.3 74.1 - - - +
275B ASN* 1.3 70.3 + - - +
277B ILE* 3.5 29.5 + - + +
278B LEU* 4.2 3.1 + - - +
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Residues in contact with ASN 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 GLN* 2.7 43.8 + - - +
272B GLU* 3.6 7.6 + - - +
273B ILE 3.2 0.2 - - - -
274B THR* 1.3 79.8 + - - +
276B LYS* 1.3 64.8 + - - +
278B LEU* 3.3 10.2 + - - +
279B LYS* 3.1 28.9 + - + +
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Residues in contact with LYS 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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458A TRP* 3.6 5.8 - - + -
272B GLU* 3.2 23.4 + - - +
273B ILE* 3.4 16.8 - - + +
275B ASN* 1.3 73.5 - - - +
277B ILE* 1.3 67.2 + - - +
279B LYS* 3.7 1.6 - - - -
280B GLU* 2.9 41.2 + - + +
286B GLU* 4.3 3.8 - - - +
290B ILE* 3.8 29.2 - - + -
293B GLU* 2.7 33.4 + - - +
355B ARG* 3.1 7.3 + - - -
462B ASP* 2.5 41.8 + - - +
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Residues in contact with ILE 277 (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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273B ILE* 3.6 6.0 + - + +
274B THR* 3.5 28.8 + - - +
275B ASN 3.2 1.2 - - - -
276B LYS* 1.3 78.1 - - - +
278B LEU* 1.3 57.0 + - - +
282B PHE* 3.5 8.1 - - - -
290B ILE* 4.1 18.2 - - + -
294B MET* 3.7 27.4 - - + -
349B SER 5.3 5.8 - - - +
351B LEU* 3.8 9.3 - - + +
352B LEU* 3.8 42.2 - - + +
355B ARG* 2.9 32.4 + - - +
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Residues in contact with LEU 278 (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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274B THR 4.2 2.8 + - - +
275B ASN* 3.3 9.0 + - - +
276B LYS 3.2 0.4 - - - -
277B ILE* 1.3 79.7 - - - +
279B LYS* 1.3 92.8 + - + +
280B GLU 3.7 0.7 - - - -
282B PHE* 3.9 14.6 - - - -
351B LEU* 4.8 16.5 - - + +
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Residues in contact with LYS 279 (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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275B ASN* 3.1 22.3 + - + +
276B LYS* 3.2 1.5 + - - -
278B LEU* 1.3 104.8 - - + +
280B GLU* 1.3 68.8 + - + +
281B GLU 3.8 0.5 + - - -
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Residues in contact with GLU 280 (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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454A MET* 5.7 1.7 - - - +
276B LYS* 2.9 38.4 + - + +
279B LYS* 1.3 83.0 - - + +
281B GLU* 1.3 73.0 + - - +
282B PHE* 3.3 11.3 - - - -
286B GLU* 3.2 30.7 - - - +
290B ILE* 3.9 5.2 - - + -
355B ARG* 2.8 19.3 + - - +
462B ASP* 4.9 2.1 - - - +
464B LYS* 3.7 34.2 + - - +
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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