Contacts of the helix formed by residues 262 - 274 (chain A) in PDB entry 5A5J
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 ASP 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A MET* 3.6 13.5 - - - +
144A ARG* 4.8 0.4 - - - +
180A SER 4.6 0.9 - - - +
181A ILE 3.4 14.1 - - - +
182A ILE 3.0 12.7 - - - +
183A PHE 3.1 17.0 - - - +
184A HIS* 3.5 13.1 - - + +
251A HIS* 2.8 26.8 + - - -
260A PRO 4.0 0.4 - - - -
261A GLN* 1.3 80.5 - - - +
263A PHE* 1.3 66.3 + - - +
264A ILE 3.1 3.5 + - - -
265A ASP* 3.1 24.5 + - - +
266A CYS* 3.0 18.9 + - - +
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Residues in contact with PHE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 4.3 7.1 - + - -
127A SER* 3.2 34.8 - - - -
130A THR* 3.3 35.7 - - + -
131A LEU* 4.5 5.2 - - + -
136A MET* 3.4 5.1 - - - -
181A ILE* 2.8 29.2 + - + +
182A ILE* 3.9 17.9 - - + -
262A ASP* 1.3 72.1 - - - +
264A ILE* 1.3 57.4 + - + +
266A CYS* 3.3 4.0 + - - +
267A PHE* 2.8 46.4 + + + +
287A LEU* 4.5 11.4 - - + -
290A THR* 3.7 24.0 - - + -
291A ALA* 5.7 4.0 - - + -
294A LEU* 4.1 22.0 - - + -
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Residues in contact with ILE 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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182A ILE* 3.4 25.6 - - + +
183A PHE* 3.8 25.1 - - + -
244A ILE* 4.6 4.0 - - + +
247A LYS* 4.5 7.2 - - + -
248A VAL* 4.1 31.2 - - + -
251A HIS* 3.2 40.6 - - + +
262A ASP* 3.1 1.6 + - - -
263A PHE* 1.3 75.2 - - + +
265A ASP* 1.3 62.8 + - - +
267A PHE* 3.2 7.8 + - - +
268A LEU* 2.9 35.3 + - + +
287A LEU* 4.2 15.4 - - + +
291A ALA* 6.2 1.1 - - + -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A HIS* 3.7 27.8 + - - +
254A SER* 5.1 4.3 + - - +
255A MET* 5.4 4.7 - - - +
259A ASN 5.0 2.4 - - - +
260A PRO* 4.0 9.4 - - + -
261A GLN* 3.7 30.2 + - - +
262A ASP* 3.1 27.6 + - - +
264A ILE* 1.3 73.4 - - - +
266A CYS* 1.3 65.1 + - - +
268A LEU* 3.2 11.7 + - - +
269A MET* 3.0 23.4 + - - +
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Residues in contact with CYS 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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126A PHE* 3.4 25.8 - - - -
130A THR* 3.7 21.8 - - + -
134A PHE 3.9 8.3 - - - -
135A GLY* 3.0 30.3 - - - +
136A MET* 4.2 0.9 - - + -
260A PRO* 4.2 6.1 - - + -
262A ASP 3.0 13.7 + - - +
263A PHE 3.5 3.8 - - - +
265A ASP* 1.3 78.8 - - - +
267A PHE* 1.3 62.0 + - - +
269A MET* 3.2 9.8 + - - +
270A LYS* 3.1 17.3 + - - +
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Residues in contact with PHE 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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123A ILE* 5.4 5.8 - - + -
126A PHE* 3.4 33.4 - + + -
263A PHE* 2.8 23.9 + + - +
264A ILE 3.4 4.7 - - - +
266A CYS* 1.3 74.8 - - - +
268A LEU* 1.3 64.6 + - - +
270A LYS* 3.1 6.6 + - - +
271A MET* 3.0 28.8 + - - +
282A PHE* 4.3 24.7 - + + -
283A THR 3.3 20.0 - - - -
286A SER* 3.3 24.9 - - - -
287A LEU* 3.3 45.8 - - + -
290A THR* 4.8 10.8 - - + -
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Residues in contact with LEU 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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248A VAL* 4.8 6.5 - - + +
251A HIS* 4.2 16.6 - - + +
252A GLN* 4.0 42.2 - - + +
255A MET* 4.3 24.3 - - + +
264A ILE* 2.9 35.1 + - + +
265A ASP* 3.4 10.3 - - - +
267A PHE* 1.3 76.4 - - - +
269A MET* 1.3 62.0 + - - +
271A MET* 3.2 23.3 + - + +
272A GLU* 3.1 19.6 + - - +
284A ILE* 5.5 2.0 - - + -
287A LEU* 4.4 15.9 - - + -
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Residues in contact with MET 269 (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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135A GLY* 5.0 8.5 - - - +
255A MET* 5.0 4.9 - - - +
256A ASP 4.4 2.7 - - - +
257A MET* 3.0 50.7 - - + +
260A PRO* 3.6 35.4 - - + -
265A ASP 3.0 11.5 + - - +
266A CYS* 3.2 12.3 - - - +
267A PHE 3.2 0.2 - - - -
268A LEU* 1.3 76.3 - - - +
270A LYS* 1.3 56.9 + - - +
272A GLU* 3.0 12.0 + - + +
273A LYS* 3.0 51.5 + - + +
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Residues in contact with LYS 270 (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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126A PHE* 3.7 33.8 - - + -
266A CYS 3.1 5.7 + - - -
267A PHE 3.1 9.6 + - - +
269A MET* 1.3 75.1 - - - +
271A MET* 1.3 61.4 + - - +
273A LYS* 4.4 21.4 - - + +
274A GLU* 3.1 48.4 + - - +
282A PHE* 4.0 40.2 - - + +
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Residues in contact with MET 271 (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 GLN* 5.5 3.8 - - - +
267A PHE* 3.0 23.9 + - + +
268A LEU* 3.3 28.0 - - + +
269A MET 3.2 0.4 - - - -
270A LYS* 1.3 75.7 - - - +
272A GLU* 1.3 62.5 + - - +
274A GLU 3.6 15.3 - - - +
275A LYS* 3.7 8.8 + - - +
282A PHE* 3.3 32.1 - - + +
283A THR* 4.0 19.1 - - - +
284A ILE* 4.1 28.0 - - + +
287A LEU* 5.3 0.9 - - - -
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Residues in contact with GLU 272 (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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255A MET* 3.6 24.5 - - + +
257A MET* 5.5 13.9 - - + -
268A LEU 3.1 9.1 + - - +
269A MET* 3.0 15.0 + - + +
271A MET* 1.3 74.0 - - - +
273A LYS* 1.3 69.4 + - + +
274A GLU 2.9 3.2 + - - -
275A LYS* 2.7 59.2 + - + +
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Residues in contact with LYS 273 (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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257A MET* 5.5 9.9 - - - -
269A MET* 3.0 52.3 + - + +
270A LYS* 3.4 20.4 + - + +
272A GLU* 1.3 73.3 - - + +
274A GLU* 1.3 59.2 + - + +
275A LYS 3.7 4.9 + - - +
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Residues in contact with GLU 274 (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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122A GLU* 5.4 5.5 - - - +
270A LYS* 3.1 43.9 + - + +
271A MET* 3.6 10.3 - - - +
272A GLU 3.0 0.6 - - - -
273A LYS* 1.3 77.2 - - - +
275A LYS* 1.3 58.9 + - - +
277A ASN* 3.9 33.8 + - + +
278A GLN* 6.1 0.2 - - - +
280A SER* 4.0 26.4 + - - +
282A PHE* 5.3 9.4 - - + +
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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