Contacts of the helix formed by residues 255 - 263 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 4.4 4.6 - - + +
217A LEU* 3.9 18.1 - - + +
236A LEU* 3.7 28.3 - - + -
240A CYS* 4.1 12.6 - - - -
252A VAL* 3.1 22.6 + - + +
253A SER 2.9 2.0 + - - -
254A PRO* 1.3 76.3 - - - +
256A LEU* 1.3 64.1 + - - +
257A ASN 3.3 2.0 - - - -
258A VAL* 3.1 7.7 + - - +
259A LEU* 3.1 45.1 + - - +
281A LEU* 3.9 10.8 - - - -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PHE* 4.5 3.8 - - + -
253A SER* 2.9 27.8 + - - +
255A CYS* 1.3 78.1 - - - +
257A ASN* 1.3 66.1 + - - +
259A LEU* 3.4 4.8 + - + +
260A SER* 3.1 22.2 + - - -
278A LEU* 3.5 31.2 - - + -
281A LEU* 3.9 17.9 - - + -
291A ALA* 3.7 34.8 - - + +
292A VAL* 4.1 15.5 - - + +
295A ALA* 3.9 24.3 - - + +
297A VAL* 4.9 0.2 - - - +
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Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A PRO* 4.2 13.4 + - - +
255A CYS 3.3 0.6 - - - -
256A LEU* 1.3 79.8 - - - +
258A VAL* 1.3 62.2 + - + +
260A SER* 3.4 16.7 + - - -
261A TRP* 3.1 18.3 - - + -
295A ALA* 4.9 10.5 - - - +
383B PRO 6.1 1.1 - - - +
386B ILE* 4.9 7.6 - - + +
387B SER* 5.0 10.3 + - - +
390B GLN* 2.6 43.6 + - - +
391B THR* 5.3 3.8 - - - +
422B LEU 5.0 7.2 - - - +
423B GLY* 5.7 1.2 - - - +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LEU* 3.9 29.2 - - + +
220A PHE* 3.6 34.3 - - + -
236A LEU* 4.5 5.8 - - + -
254A PRO 5.1 0.6 + - - +
255A CYS 3.1 10.1 + - - +
257A ASN* 1.3 74.9 - - + +
259A LEU* 1.3 65.8 + - - +
260A SER 3.1 0.7 + - - -
261A TRP* 3.1 25.3 + - + +
262A LEU* 2.9 43.1 + - + +
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 4.4 1.6 - - + -
236A LEU* 3.4 28.3 - - + -
255A CYS* 3.1 38.5 + - - +
256A LEU* 3.7 8.5 - - - +
258A VAL* 1.3 76.4 - - - +
260A SER* 1.3 61.7 + - - +
262A LEU* 3.4 16.0 + - + +
263A LEU* 3.4 27.8 + - - +
274A ALA* 4.1 15.5 - - - +
277A ALA* 4.1 19.3 - - + -
278A LEU* 3.9 36.3 - - + -
281A LEU* 4.0 10.5 - - + -
297A VAL* 4.7 1.1 - - - -
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU 3.1 11.8 + - - -
257A ASN* 3.5 12.1 - - - -
258A VAL 3.1 0.4 + - - -
259A LEU* 1.3 79.9 - - - +
261A TRP* 1.3 61.1 + - - +
263A LEU* 3.5 12.5 + - - +
264A PHE* 3.6 15.0 - - - -
295A ALA 3.1 19.6 + - - -
297A VAL* 3.8 17.3 - - - +
300A ARG* 5.3 0.3 - - - +
421B GLU 2.7 27.9 + - - +
422B LEU* 3.8 9.9 - - - -
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Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.6 46.0 - + + -
221A SER* 5.7 0.7 - - - -
257A ASN* 3.1 23.9 + - + -
258A VAL* 3.1 27.5 + - + +
260A SER* 1.3 77.5 - - - +
262A LEU* 1.3 80.2 + - + +
263A LEU 3.2 0.7 - - - -
264A PHE* 3.0 32.5 + - + +
265A VAL* 4.1 10.0 + - + +
383B PRO* 4.0 29.5 - - + +
422B LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 4.0 7.6 - - + -
229A THR* 4.3 13.7 - - + -
233A VAL* 3.8 33.9 - - + -
258A VAL* 2.9 39.9 + - + +
259A LEU* 3.6 12.3 - - + +
260A SER 3.3 0.2 - - - -
261A TRP* 1.3 101.8 - - + +
263A LEU* 1.3 56.6 + - - +
264A PHE 3.1 1.3 - - - -
265A VAL* 3.3 29.7 + - + +
270A VAL* 4.0 22.1 - - + +
271A LEU* 3.9 6.6 - - - +
274A ALA* 4.4 9.3 - - + +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU 3.4 9.1 + - - +
260A SER 3.7 8.5 - - - +
261A TRP 3.2 1.2 - - - -
262A LEU* 1.3 75.3 - - - +
264A PHE* 1.3 57.0 + - - +
265A VAL 3.5 0.7 - - - -
271A LEU* 3.6 12.8 - - + +
274A ALA* 4.0 18.4 - - + -
275A CYS* 3.9 16.4 - - - -
278A LEU* 3.8 15.3 - - + -
297A VAL* 4.0 20.6 - - + +
300A ARG* 2.9 59.2 + - + +
301A LEU* 3.8 21.3 - - + -
304A LEU* 3.9 19.7 - - + -
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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