Contacts of the helix formed by residues 255 - 263 (chain B) in PDB entry 2JDQ
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 CYS 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU* 4.3 3.1 - - + +
217B LEU* 3.8 21.2 - - + +
236B LEU* 3.7 33.9 - - + -
240B CYS* 4.4 4.5 - - - -
252B VAL 3.3 20.9 + - - +
253B SER 3.1 2.0 - - - -
254B PRO* 1.3 75.2 - - - +
256B LEU* 1.3 64.4 + - - +
257B ASN 3.2 3.1 - - - -
258B VAL* 3.1 7.4 + - - +
259B LEU* 3.0 45.5 + - - +
281B LEU* 4.0 11.2 - - - -
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PHE* 4.5 6.7 - - + -
253B SER* 3.2 31.5 + - - +
254B PRO 3.3 0.2 - - - -
255B CYS* 1.3 78.1 - - - +
257B ASN* 1.3 63.1 + - - +
259B LEU* 3.6 4.1 + - + +
260B SER* 3.1 23.7 + - - -
278B LEU* 3.9 21.5 - - + -
281B LEU* 3.9 26.0 - - + -
291B ALA* 3.7 33.7 - - + +
292B VAL* 4.1 16.6 - - + +
295B ALA* 3.7 19.3 - - + +
297B VAL* 4.9 0.2 - - - +
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Residues in contact with ASN 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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254B PRO 4.2 9.0 + - - +
255B CYS 3.2 0.2 - - - -
256B LEU* 1.3 76.1 - - - +
258B VAL* 1.3 65.2 + - + +
260B SER* 3.4 3.4 + - - -
261B TRP* 2.9 68.5 + - + +
295B ALA* 5.5 6.1 - - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 4.4 27.1 - - + +
220B PHE* 3.4 48.9 - - + -
221B SER* 5.4 3.4 - - - +
236B LEU* 4.9 3.4 - - + -
254B PRO 5.2 0.9 + - - +
255B CYS 3.1 8.1 + - - +
257B ASN* 1.3 77.0 - - + +
259B LEU* 1.3 61.9 + - - +
261B TRP* 3.0 23.1 + - + +
262B LEU* 2.8 43.0 + - + +
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Residues in contact with LEU 259 (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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233B VAL* 4.3 13.9 - - + -
236B LEU* 3.7 26.0 - - + -
255B CYS* 3.0 37.4 + - - +
256B LEU* 3.8 5.2 - - - +
258B VAL* 1.3 76.4 - - - +
260B SER* 1.3 63.0 + - - +
262B LEU* 3.4 8.2 + - + +
263B LEU* 3.4 27.1 + - - +
274B ALA* 4.1 9.8 - - - +
277B ALA* 3.9 20.4 - - + -
278B LEU* 3.9 26.7 - - + -
281B LEU* 3.6 20.6 - - + -
297B VAL* 4.6 1.3 - - - -
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Residues in contact with SER 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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256B LEU 3.1 14.3 + - - -
257B ASN* 3.4 10.8 - - - -
259B LEU* 1.3 79.7 - - - +
261B TRP* 1.3 71.8 + - - +
263B LEU* 3.5 16.5 + - - +
264B PHE* 3.9 12.9 - - - -
295B ALA* 2.7 29.7 + - - -
296B GLY* 4.2 2.8 - - - -
297B VAL* 3.5 21.1 + - - +
300B ARG* 5.5 0.3 - - - +
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Residues in contact with TRP 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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221B SER* 6.1 1.1 - - - -
257B ASN* 2.9 55.6 + - + +
258B VAL* 3.0 19.1 + - + +
260B SER* 1.3 85.0 + - - +
262B LEU* 1.3 64.0 + - - +
263B LEU 3.2 0.4 - - - -
264B PHE* 3.1 32.1 + + + +
265B VAL* 4.3 3.6 + - - +
295B ALA 5.6 0.4 + - - -
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Residues in contact with LEU 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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220B PHE* 3.8 13.9 - - + -
229B THR* 4.1 16.2 - - + -
233B VAL* 3.6 36.1 - - + -
258B VAL* 2.8 38.7 + - + +
259B LEU* 3.8 10.3 - - + +
260B SER 3.4 0.2 - - - -
261B TRP* 1.3 71.4 - - + +
263B LEU* 1.3 61.2 + - - +
264B PHE 3.1 5.6 - - - -
265B VAL* 3.2 33.0 + - + +
270B VAL* 4.1 19.4 - - + +
271B LEU* 3.8 7.3 - - - +
274B ALA* 4.4 9.5 - - + +
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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
----------------------------------------------------------
259B LEU 3.4 10.7 + - - +
260B SER 3.6 9.2 - - - +
261B TRP 3.2 1.0 - - - -
262B LEU* 1.3 75.1 - - - +
264B PHE* 1.3 52.8 + - - +
265B VAL 3.4 0.4 - - - -
271B LEU* 3.8 9.7 - - + +
274B ALA* 4.0 23.6 - - + -
275B CYS* 4.2 10.8 - - - -
278B LEU* 3.8 13.0 - - + -
297B VAL* 3.7 36.6 - - + +
300B ARG* 2.7 66.6 + - + -
301B LEU* 3.9 6.5 - - + +
304B LEU* 4.1 19.5 - - + -
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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