Contacts of the helix formed by residues 253 - 268 (chain A) in PDB entry 5J2N
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 THR 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A SER 3.4 14.6 + - - +
252A TRP* 1.3 73.2 - - - +
254A VAL* 1.3 66.1 + - - +
255A ASN* 3.5 5.7 + - - +
256A ASP* 3.4 28.8 + - - +
257A ILE* 3.0 27.1 + - - +
289A LEU 3.6 8.3 + - - -
290A THR* 4.0 10.3 - - - +
291A GLU 3.5 12.8 - - - -
292A VAL* 3.8 18.2 - - + +
293A ILE* 4.8 3.1 - - - -
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Residues in contact with VAL 254 (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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253A THR* 1.3 75.7 - - - +
255A ASN* 1.3 58.2 + - - +
257A ILE* 3.2 1.4 + - - -
258A CYS* 2.8 44.3 + - - -
283A LEU* 3.8 23.5 - - + +
286A THR* 3.7 37.5 - - + +
288A ALA 3.5 25.8 - - - +
289A LEU* 3.5 11.2 + - + +
291A GLU* 3.0 22.8 + - + +
293A ILE* 4.6 6.1 - - + -
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Residues in contact with ASN 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.4 3.8 + - - +
254A VAL* 1.3 76.2 - - - +
256A ASP* 1.3 68.6 + - - +
258A CYS* 3.8 6.3 - - - +
259A LYS* 3.3 31.5 + - - +
289A LEU* 3.0 41.5 + - + +
818P C 3.4 35.7 + - - +
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Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PRO* 4.9 3.2 - - + +
249A LYS* 3.3 35.7 - - + +
251A SER 4.3 4.2 - - - +
252A TRP* 4.0 15.0 - - + -
253A THR* 3.4 32.5 + - - +
254A VAL 3.2 1.0 - - - -
255A ASN* 1.3 83.6 - - - +
257A ILE* 1.3 60.4 + - - +
259A LYS* 3.2 24.8 + - - +
260A LEU* 3.1 27.0 + - - +
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Residues in contact with ILE 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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252A TRP* 3.8 33.7 - - + -
253A THR 3.0 18.6 + - - +
256A ASP* 1.3 73.0 - - - +
258A CYS* 1.3 60.4 + - - +
260A LEU* 4.2 15.5 - - + -
261A VAL* 2.9 38.9 + - + +
279A LEU* 3.7 32.5 - - + +
282A LEU* 5.1 7.4 - - + -
283A LEU* 3.7 26.5 - - + -
293A ILE* 5.8 3.8 - - + +
295A LEU* 4.0 14.6 - - + -
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Residues in contact with CYS 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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254A VAL* 2.8 39.6 + - - +
255A ASN* 3.8 9.0 - - - +
256A ASP 3.3 0.4 - - - -
257A ILE* 1.3 78.1 - - - +
259A LYS* 1.3 57.0 + - - +
262A GLY* 3.3 16.5 + - - -
283A LEU* 4.0 3.8 - - - -
289A LEU* 5.1 2.7 - - - -
817P MRG 2.1 58.8 - - - +
818P C 3.3 32.6 + - - +
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Residues in contact with LYS 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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247A PRO* 4.0 27.6 - - + +
249A LYS* 4.9 10.8 - - - +
255A ASN* 3.3 17.5 + - - +
256A ASP* 3.2 34.3 + - - +
258A CYS* 1.3 76.9 - - - +
260A LEU* 1.3 60.6 + - - +
261A VAL 3.5 0.4 - - - -
262A GLY 3.7 0.7 - - - -
263A LYS* 3.1 35.9 + - + +
818P C 3.2 18.6 + - - +
819P G 3.5 24.0 - - - +
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Residues in contact with LEU 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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246A LEU* 4.0 23.1 - - + -
247A PRO* 3.9 31.0 - - + +
252A TRP* 4.5 9.6 - - - +
256A ASP 3.1 17.9 + - - +
257A ILE* 3.2 19.0 + - + +
259A LYS* 1.3 76.3 - - - +
261A VAL* 1.3 60.9 + - - +
263A LYS* 3.3 2.9 + - - +
264A LEU* 3.0 40.5 + - + +
279A LEU* 4.0 13.9 - - + -
303A LEU* 3.7 39.5 - - + -
307A ARG* 5.4 0.7 - - - +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 2.9 34.3 + - + +
258A CYS 4.5 2.9 - - - +
260A LEU* 1.3 75.9 - - + +
262A GLY* 1.3 56.7 + - - +
264A LEU* 3.2 7.4 + - - +
265A ASN* 2.9 54.6 + - - +
276A VAL* 4.3 9.2 - - + -
279A LEU* 4.0 24.9 - - + -
280A SER* 3.6 24.2 - - - +
283A LEU* 4.9 2.2 - - + -
817P MRG 5.0 13.0 - - + -
711T C 5.8 0.2 - - + -
712T C 5.3 5.2 - - - +
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Residues in contact with GLY 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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258A CYS 3.3 14.3 + - - -
259A LYS 3.6 0.2 + - - -
260A LEU 3.2 0.6 - - - -
261A VAL* 1.3 80.9 - - - +
263A LYS* 1.3 59.7 + - - +
265A ASN* 3.7 10.0 + - - +
266A TRP* 3.2 17.8 + - - +
817P MRG 5.6 1.5 - - - +
818P C 4.9 1.3 - - - -
819P G 3.2 35.8 + - - -
710T G 4.7 5.6 + - - -
711T C 6.1 0.2 - - - -
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.4 18.0 - - + +
245A VAL* 2.8 35.2 + - - +
246A LEU* 4.2 11.2 - - + -
247A PRO* 4.4 14.9 - - + +
259A LYS* 3.1 23.5 + - - +
260A LEU* 3.8 3.6 - - - +
261A VAL 3.3 0.2 - - - -
262A GLY* 1.3 74.5 - - - +
264A LEU* 1.3 61.5 + - - +
266A TRP* 3.2 9.2 + - + +
267A ALA* 2.8 28.2 + - - +
819P G 3.5 20.0 - - - +
820P C 3.4 22.1 + - - +
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Residues in contact with LEU 264 (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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246A LEU* 4.0 30.1 - - + -
260A LEU* 3.0 28.0 + - + +
261A VAL* 3.2 4.7 + - - +
263A LYS* 1.3 73.9 - - - +
265A ASN* 1.3 60.5 + - - +
267A ALA* 3.0 4.1 + - + +
268A SER* 2.9 30.0 + - - -
274A ILE* 3.7 16.6 - - + +
276A VAL* 3.8 21.1 - - + -
279A LEU* 3.9 19.5 - - + -
303A LEU* 4.9 2.2 - - + -
306A ASN* 3.5 38.4 - - + +
310A LEU* 4.5 8.1 - - + -
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Residues in contact with ASN 265 (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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261A VAL* 2.9 37.5 + - - +
262A GLY* 3.8 8.9 - - - +
264A LEU* 1.3 74.1 - - - +
266A TRP* 1.3 59.7 + - - +
268A SER* 2.8 23.8 + - - -
269A GLN* 4.3 2.6 + - - +
276A VAL* 3.8 9.4 - - - +
353A LYS* 3.2 25.8 + - - +
817P MRG 6.0 0.6 - - - +
710T G 5.1 7.2 - - + +
711T C 3.6 44.6 + - - +
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Residues in contact with TRP 266 (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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94A ILE* 6.4 2.7 - - + -
230A MET 4.6 7.4 - - - -
231A GLY 4.8 4.5 + - - -
232A TYR* 3.3 26.0 - + - -
241A VAL* 3.6 21.2 - - + +
244A ILE* 3.7 23.0 - - + +
262A GLY 3.2 13.0 + - - +
263A LYS* 3.2 10.5 + - + +
265A ASN* 1.3 78.9 - - - +
267A ALA* 1.3 60.9 + - - +
269A GLN* 3.1 59.4 + - - +
819P G 4.7 6.3 - - + +
820P C 3.5 65.5 + - + +
821P C 5.2 0.4 - - - -
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Residues in contact with ALA 267 (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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244A ILE* 3.6 26.2 - - + -
263A LYS 2.8 15.4 + - - +
264A LEU* 3.0 11.4 + - + +
266A TRP* 1.3 75.0 - - - +
268A SER* 1.3 56.6 + - - +
269A GLN* 3.0 11.7 + - - -
270A ILE* 3.3 3.3 + - - +
271A TYR* 3.1 27.5 + - + +
274A ILE* 4.6 3.4 - - + -
310A LEU* 4.0 24.2 - - + -
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Residues in contact with SER 268 (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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264A LEU 2.9 11.5 + - - -
265A ASN* 2.8 24.3 + - - -
266A TRP 3.4 0.2 - - - -
267A ALA* 1.3 74.9 - - - +
269A GLN* 1.3 56.4 + - - +
270A ILE 3.2 0.9 - - - -
271A TYR 3.7 12.2 - - - +
274A ILE* 3.8 20.4 - - - -
351A THR* 2.9 16.5 + - - -
352A GLY* 3.2 16.0 + - - +
353A LYS* 4.1 28.3 + - - +
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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