Contacts of the helix formed by residues 256 - 268 (chain B) in PDB entry 3PEJ
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 ASN 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B LYS* 3.4 19.4 + - - +
252B THR 4.8 2.3 - - - +
253B ASN* 3.4 37.0 + - - +
254B LEU 3.2 2.2 - - - -
255B LEU* 1.3 79.6 - - - +
257B ASP* 1.3 59.3 + - - +
258B LYS* 3.4 3.1 - - + +
259B LYS* 3.3 9.2 + - + +
260B LEU* 2.9 32.4 + - - +
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Residues in contact with ASP 257 (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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139B LYS* 4.7 7.0 - - - +
255B LEU 3.7 2.6 + - - -
256B ASN* 1.3 71.5 - - - +
258B LYS* 1.3 66.1 + - + +
260B LEU* 3.6 5.0 + - - +
261B MET* 3.1 55.8 + - - +
277B LEU* 4.5 1.8 - - - +
279B HIS* 3.3 30.7 + - - +
280B GLU* 4.2 14.1 + - - +
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Residues in contact with LYS 258 (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 ASN* 3.4 2.7 - - + +
257B ASP* 1.3 82.9 - - + +
259B LYS* 1.4 61.4 + - - +
261B MET* 3.6 8.0 + - - +
262B ASP* 3.1 24.1 + - - +
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Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLU* 2.8 34.5 + - - +
253B ASN* 3.4 37.7 - - + +
254B LEU* 4.2 9.6 - - + +
256B ASN* 3.3 12.8 + - + +
258B LYS* 1.4 74.9 - - - +
260B LEU* 1.4 60.6 + - - +
262B ASP* 3.2 12.2 + - + +
263B LEU* 2.9 45.3 + - + +
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Residues in contact with LEU 260 (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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99B PHE* 6.3 0.2 - - + -
100B LEU* 4.5 15.3 - - + -
135B ILE* 4.1 12.8 - - + -
137B ALA* 4.2 17.3 - - + +
144B LEU* 3.8 32.5 - - + -
254B LEU* 3.3 24.9 - - + +
255B LEU 4.4 5.6 - - - +
256B ASN 2.9 18.8 + - - +
257B ASP* 4.1 3.6 - - - +
259B LYS* 1.4 72.0 - - - +
261B MET* 1.3 53.9 + - - +
263B LEU* 3.3 8.5 + - + +
264B ILE* 2.8 42.7 + - + +
277B LEU* 4.0 26.7 - - + -
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Residues in contact with MET 261 (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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257B ASP* 3.1 39.6 + - - +
258B LYS* 3.8 6.3 - - - +
259B LYS 3.3 0.2 - - - -
260B LEU* 1.3 74.8 - - - +
262B ASP* 1.3 55.7 + - - +
264B ILE 3.5 0.2 + - - -
265B SER* 3.0 32.3 + - - -
277B LEU* 3.6 15.2 - - + +
279B HIS* 3.4 35.2 - - + +
327B THR* 5.7 2.2 - - + -
329B MET* 3.6 27.3 - - + +
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Residues in contact with ASP 262 (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 LYS 3.1 12.7 + - - +
259B LYS* 3.3 14.8 + - + +
261B MET* 1.3 78.7 - - - +
263B LEU* 1.4 70.6 + - - +
265B SER* 3.4 6.0 + - - -
266B LYS* 3.1 34.8 + - - +
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Residues in contact with LEU 263 (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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97B GLU* 3.6 42.8 - - + +
100B LEU* 3.8 21.5 - - + -
254B LEU* 3.8 29.8 - - + -
259B LYS* 2.9 35.0 + - + +
260B LEU* 3.8 7.0 - - + +
262B ASP* 1.4 77.4 + - - +
264B ILE* 1.4 60.0 + - - +
266B LYS* 3.5 9.6 + - + +
267B TYR* 3.0 50.0 + - + +
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Residues in contact with ILE 264 (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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100B LEU* 3.9 13.5 - - + -
104B ILE* 4.8 5.6 - - + +
135B ILE* 3.7 30.7 - - + -
260B LEU* 2.8 29.2 + - + +
261B MET 4.1 2.9 - - - +
263B LEU* 1.4 67.9 - - - +
265B SER* 1.3 58.7 + - - +
267B TYR 3.3 1.2 + - - -
268B SER* 2.6 42.7 + - - +
275B ILE* 3.7 27.1 - - + -
277B LEU* 3.8 38.4 - - + -
329B MET* 3.7 21.8 - - + -
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Residues in contact with SER 265 (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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261B MET 3.0 19.0 + - - -
262B ASP* 3.6 6.1 - - - -
264B ILE* 1.3 76.4 - - - +
266B LYS* 1.3 61.2 + - - +
268B SER* 3.5 13.6 + - - -
269B GLN* 4.5 4.2 + - - -
329B MET* 4.8 11.1 - - - +
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Residues in contact with LYS 266 (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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262B ASP* 3.1 29.1 + - - +
263B LEU* 3.5 11.2 - - + +
264B ILE 3.3 0.2 - - - -
265B SER* 1.3 77.8 - - - +
267B TYR* 1.4 89.2 + - + +
268B SER 3.7 0.5 + - - -
269B GLN* 4.2 13.0 + - - +
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Residues in contact with TYR 267 (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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97B GLU* 3.1 39.8 + - - +
98B VAL* 3.7 13.4 - - - +
100B LEU* 3.9 11.7 - - + -
101B ARG* 3.5 69.1 - - + +
104B ILE* 4.1 18.4 - - + +
263B LEU* 3.0 32.6 + - + +
264B ILE 3.3 0.9 + - - -
266B LYS* 1.4 101.6 - - + +
268B SER* 1.3 56.7 + - - +
269B GLN* 3.4 5.5 + - - -
271B ILE* 4.1 10.2 - - - +
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Residues in contact with SER 268 (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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104B ILE* 5.1 0.9 - - - -
264B ILE* 2.6 26.7 + - - +
265B SER* 3.5 11.4 + - - -
266B LYS 3.5 1.0 - - - -
267B TYR* 1.3 78.3 - - - +
269B GLN* 1.3 64.7 + - - +
270B PHE 3.7 1.6 - - - -
271B ILE* 3.6 22.1 + - - +
275B ILE* 3.5 29.8 - - - -
329B MET 4.8 2.4 + - - -
330B ASN* 4.5 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
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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