Contacts of the helix formed by residues 264 - 269 (chain B) in PDB entry 5AM8
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 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 3.9 22.7 - - - +
229B VAL* 3.6 32.5 - - + -
233B LEU* 4.6 7.4 - - + -
252B LEU 3.7 20.4 - - - +
253B LEU* 3.8 30.1 - - + +
254B GLY 3.9 2.5 - - - +
261B TRP* 3.1 20.0 + - + +
263B ASN* 1.3 76.6 - - - +
265B TYR* 1.3 66.2 + - - +
266B ASP* 3.1 3.8 - - - -
267B MET* 3.0 25.5 + - + +
268B VAL* 3.4 18.3 + - + +
430B LEU* 5.0 2.5 - - + -
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TRP 3.9 0.8 + - - -
262B GLU 3.1 20.3 + - - +
263B ASN 3.4 0.4 - - - -
264B ILE* 1.3 76.2 - - - +
266B ASP* 1.3 61.2 + - - +
268B VAL* 3.1 1.0 + - - -
269B VAL* 2.9 67.0 + - + +
275B PRO 5.3 1.0 + - - -
276B ASN* 4.4 15.0 - - - -
277B LEU* 3.8 17.2 + - + +
278B ASP* 4.6 14.4 - - + +
423B ASN* 3.5 28.7 + - - +
426B LEU* 4.3 6.3 - - + -
427B LYS* 3.5 53.2 - - + -
430B LEU* 3.7 17.0 - - + -
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Residues in contact with ASP 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 2.8 35.0 + - - -
263B ASN 4.7 2.0 + - - -
264B ILE* 3.8 2.6 - - - +
265B TYR* 1.3 85.3 - - + +
267B MET* 1.3 77.3 + - - +
269B VAL* 3.9 15.1 - - - +
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Residues in contact with MET 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 3.8 32.1 - - - +
232B ALA* 4.0 10.1 - - + +
233B LEU* 3.4 40.2 - - + +
235B ARG* 3.9 16.8 + - - -
236B ARG* 3.8 45.5 - - + +
237B TYR* 4.8 2.0 - - - -
264B ILE* 3.0 16.7 + - + +
266B ASP* 1.3 92.4 + - - +
268B VAL* 1.3 62.7 + - + +
269B VAL* 5.4 0.2 - - - -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 3.5 24.9 - - + -
229B VAL* 4.4 12.6 - - + -
232B ALA* 3.4 28.9 - - + -
233B LEU* 6.0 0.2 - - + -
235B ARG* 5.3 2.0 - - - +
264B ILE* 3.7 26.9 - - + +
265B TYR 3.1 6.7 + - - +
267B MET* 1.3 83.9 - - + +
269B VAL* 1.3 69.9 + - - +
270B PRO* 3.0 8.1 - - - +
426B LEU* 3.7 20.9 - - + -
430B LEU* 3.9 20.0 - - + -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 2.9 52.8 + - + +
266B ASP* 3.9 16.8 - - - +
267B MET 3.7 0.4 - - - -
268B VAL* 1.3 75.2 - - - +
270B PRO* 1.3 74.5 - - - +
271B PHE 4.1 4.7 - - - +
272B PRO* 3.6 31.4 - - + +
423B ASN* 3.7 19.3 - - - +
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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
------------------------------------------------------------
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