Contacts of the helix formed by residues 273 - 281 (chain B) in PDB entry 2IPG
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 LYS 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B NAP 2.9 24.3 + - - +
37B LEU* 5.5 0.2 - - - -
271B SER* 3.2 7.9 + - - +
272B LEU* 1.3 86.6 - - + +
274B GLU* 1.3 65.4 + - - +
275B GLU* 4.5 4.0 - - + +
276B ARG* 3.1 51.2 + - + +
277B ILE* 3.2 18.1 + - - +
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Residues in contact with GLU 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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37B LEU* 5.6 0.6 - - - +
40B ILE* 3.6 42.4 - - + +
272B LEU 4.0 2.4 + - - -
273B LYS* 1.3 72.5 - - - +
275B GLU* 1.3 63.9 + - - +
277B ILE* 3.2 18.7 + - - +
278B LYS* 3.2 43.7 + - - +
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Residues in contact with GLU 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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273B LYS* 3.2 4.1 - - + +
274B GLU* 1.3 80.6 - - - +
276B ARG* 1.3 60.9 + - + +
278B LYS* 3.7 20.3 + - - +
279B GLU* 3.1 26.8 + - + +
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Residues in contact with ARG 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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2B NAP 2.9 89.3 + - + +
271B SER* 3.2 16.8 - - - +
273B LYS* 3.1 31.8 + - + +
275B GLU* 1.3 79.0 - - + +
277B ILE* 1.3 65.5 + - - +
278B LYS 3.2 0.2 - - - -
279B GLU* 4.0 7.9 - - - +
280B ASN* 3.0 33.1 + - - -
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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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21B PHE* 3.2 31.4 - - + -
37B LEU* 5.2 4.9 - - + +
40B ILE* 4.4 9.9 - - + -
41B ALA* 3.8 32.8 - - + +
44B ALA* 4.1 6.7 - - + -
46B PHE* 3.5 30.0 - - + -
269B ASN* 4.9 2.5 - - - +
271B SER* 3.2 33.0 - - - +
273B LYS 3.2 15.8 + - - +
274B GLU* 3.2 10.1 + - - +
276B ARG* 1.3 77.3 - - - +
278B LYS* 1.3 64.4 + - - +
280B ASN* 3.5 9.5 + - - +
281B MET* 3.8 1.7 + - - +
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Residues in contact with LYS 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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40B ILE* 5.4 2.7 - - + -
44B ALA* 4.3 22.2 - - + +
274B GLU* 3.2 44.8 + - + +
275B GLU* 3.8 22.4 + - - +
277B ILE* 1.3 78.5 - - + +
279B GLU* 1.3 62.3 + - - +
281B MET* 3.2 19.9 + - - +
282B GLN* 4.0 6.5 + - - +
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Residues in contact with GLU 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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2B NAP 2.7 29.6 + - - -
251B THR* 3.1 39.2 + - - +
253B ALA* 4.4 0.2 - - - +
254B LEU* 3.5 11.7 - - + +
275B GLU* 3.1 17.7 + - + +
276B ARG* 3.6 9.2 - - - +
278B LYS* 1.3 80.3 - - - +
280B ASN* 1.3 53.9 + - - +
282B GLN* 2.8 56.1 + - - +
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Residues in contact with ASN 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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2B NAP 2.8 48.5 + - - -
19B LEU* 4.0 5.4 - - + +
46B PHE* 4.5 4.0 - - + -
219B LEU* 4.5 0.4 - - - +
253B ALA* 4.5 2.8 - - - +
254B LEU* 4.1 3.6 - - - +
257B LEU* 3.8 28.3 - - + +
269B ASN* 3.0 31.8 - - - +
271B SER* 4.8 0.9 - - - -
276B ARG 3.0 14.1 + - - +
277B ILE* 3.8 6.9 - - - +
278B LYS 3.4 0.6 - - - -
279B GLU* 1.3 76.7 + - - +
281B MET* 1.3 60.5 + - - +
282B GLN 3.0 1.1 + - - -
283B VAL* 3.2 25.1 + - - +
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Residues in contact with MET 281 (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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6B HIS* 6.2 0.2 - - - -
19B LEU* 3.3 32.5 - - + +
44B ALA* 3.4 24.2 - - + +
45B GLY* 3.6 19.7 - - - +
46B PHE* 3.6 36.3 - - + -
277B ILE 3.8 1.9 + - - +
278B LYS* 3.2 14.4 + - - +
279B GLU 3.0 1.2 + - - -
280B ASN* 1.3 73.1 - - - +
282B GLN* 1.3 57.9 + - + +
283B VAL* 3.0 10.4 + - - -
284B PHE* 3.5 34.8 + - + +
285B GLU* 5.1 1.0 - - - +
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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