Contacts of the helix formed by residues 261 - 277 (chain E) in PDB entry 4Q9U
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 ILE 261 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ASN* 4.2 5.2 - - + +
259E GLU 3.1 12.9 - - - +
260E ASP* 1.3 77.3 - - + +
262E PRO* 1.3 81.5 - - + +
263E GLU* 3.2 23.2 + - + +
264E VAL* 3.4 23.1 - - + -
265E SER* 3.4 11.1 + - - -
304E ILE* 3.6 25.1 - - + +
305E THR* 4.1 9.0 - - + -
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Residues in contact with PRO 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D GLN* 5.7 10.3 - - + +
260E ASP 3.5 6.7 - - - +
261E ILE* 1.3 89.5 - - + +
263E GLU* 1.3 55.0 + - + +
265E SER* 3.8 2.3 - - - -
266E ASP* 2.7 45.3 + - - +
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Residues in contact with GLU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E ILE* 3.1 14.8 - - + +
262E PRO* 1.3 76.4 - - + +
264E VAL* 1.3 61.7 + - - +
266E ASP* 2.8 31.0 + - - +
267E MET* 3.0 17.2 + - - +
304E ILE* 3.1 33.0 - - + +
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Residues in contact with VAL 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E VAL* 4.9 2.0 - - + -
258E ASN 3.2 30.5 - - - +
259E GLU* 4.1 7.4 - - - -
261E ILE* 3.4 22.2 - - + +
263E GLU* 1.3 75.7 - - - +
265E SER* 1.3 58.6 + - - +
267E MET* 3.3 10.4 + - - +
268E VAL* 2.9 26.2 + - + +
301E ALA* 3.5 26.2 - - + -
304E ILE* 3.4 31.8 - - + +
305E THR* 3.5 12.8 - - + -
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Residues in contact with SER 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D ILE* 6.1 1.3 - - - -
259E GLU* 3.1 45.5 + - - +
261E ILE 3.4 8.4 + - - -
262E PRO* 4.2 2.2 - - - -
263E GLU 3.2 0.4 - - - -
264E VAL* 1.3 74.6 - - - +
266E ASP* 1.3 64.7 + - - +
267E MET 3.2 1.3 - - - -
268E VAL* 3.2 15.2 - - - +
269E VAL* 3.0 28.6 + - - +
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Residues in contact with ASP 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607D GLU* 5.3 2.4 - - - +
608D ILE* 3.9 21.6 - - - +
611D GLU* 4.8 10.4 - - - +
262E PRO* 2.7 37.5 + - - +
263E GLU* 2.8 23.2 + - - +
265E SER* 1.3 78.1 - - - +
267E MET* 1.3 57.5 + - - +
269E VAL* 3.8 15.7 + - - +
270E LYS* 4.0 5.9 + - - +
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Residues in contact with MET 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E GLU* 3.0 13.4 + - - +
264E VAL* 3.5 12.8 - - - +
266E ASP* 1.3 75.0 - - - +
268E VAL* 1.3 59.5 + - - +
269E VAL 3.3 1.1 - - - -
270E LYS* 3.6 7.6 + - + +
271E ALA* 2.9 27.8 + - + +
297E HIS* 3.2 15.3 - - + +
298E ILE 5.5 0.2 - - - +
300E ASN* 3.1 39.0 - - + +
301E ALA* 3.3 29.6 - - + -
304E ILE* 3.6 30.1 - - + -
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Residues in contact with VAL 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E VAL* 6.0 2.7 - - + -
259E GLU* 3.9 24.5 - - + +
264E VAL* 2.9 24.3 + - + +
265E SER* 3.2 25.6 - - - +
267E MET* 1.3 76.9 - - - +
269E VAL* 1.3 69.1 + - + +
271E ALA* 3.1 10.0 - - - +
272E ILE* 2.9 28.0 + - + +
301E ALA* 5.2 6.5 - - + -
321E TYR* 6.3 2.2 - - + -
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Residues in contact with VAL 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D ILE* 3.4 35.2 - - + +
611D GLU* 4.7 5.6 - - - +
612D GLU* 3.3 44.6 - - + +
265E SER* 3.0 15.9 + - - +
266E ASP* 3.8 9.6 - - - +
267E MET 3.3 0.2 - - - -
268E VAL* 1.3 80.1 - - + +
270E LYS* 1.3 58.2 + - - +
272E ILE* 3.1 12.3 + - + +
273E THR* 3.0 27.5 + - - +
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Residues in contact with LYS 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D GLU* 6.6 0.2 - - - +
615D GLN* 5.4 18.2 - - - +
619D GLN* 5.5 5.5 - - - +
266E ASP 4.0 6.2 + - - +
267E MET* 3.6 9.0 + - - +
268E VAL 3.4 0.2 - - - -
269E VAL* 1.3 75.5 - - - +
271E ALA* 1.3 62.6 + - - +
272E ILE 3.1 0.2 - - - -
273E THR* 4.0 18.6 - - - +
274E ASP* 2.9 39.4 + - - +
297E HIS* 2.8 34.6 + - + -
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Residues in contact with ALA 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E MET* 2.9 17.8 + - + +
268E VAL* 3.1 15.7 - - - +
270E LYS* 1.3 77.5 - - - +
272E ILE* 1.3 63.6 + - - +
274E ASP 3.9 0.9 + - - -
275E ILE* 3.6 6.1 - - - +
294E CYS* 3.6 1.2 - - - -
297E HIS* 3.1 30.3 + - + +
298E ILE* 4.1 9.9 - - + -
322E ILE* 3.2 33.2 - - + +
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Residues in contact with ILE 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D GLU* 4.5 10.1 - - - +
268E VAL* 2.9 19.0 + - + +
269E VAL* 3.2 13.0 - - - +
270E LYS 3.1 0.2 - - - -
271E ALA* 1.3 77.0 - - - +
273E THR* 1.3 63.0 + - - +
275E ILE* 3.0 10.7 - - + +
276E ILE* 3.0 31.8 - - + +
322E ILE* 3.2 41.3 - - + +
325E LYS* 4.1 8.7 - - + -
326E GLY* 3.4 28.3 - - - +
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Residues in contact with THR 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D GLU* 3.8 27.1 + - + +
616D GLY* 6.1 3.6 - - - -
619D GLN* 5.1 14.4 - - - +
269E VAL* 3.0 15.3 + - - +
270E LYS* 2.9 26.2 + - - +
272E ILE* 1.3 77.7 - - - +
274E ASP* 1.3 58.0 + - - +
275E ILE 3.3 0.2 - - - -
276E ILE* 3.1 16.8 + - + +
277E GLU* 3.0 27.4 + - + +
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Residues in contact with ASP 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E LYS* 2.9 34.2 + - - +
273E THR* 1.3 73.9 - - - +
275E ILE* 1.3 61.8 + - - +
276E ILE 3.4 0.3 + - - -
277E GLU* 3.7 15.2 + - - +
278E MET 3.9 0.2 + - - -
290E CYS* 3.5 31.1 - - - +
293E LYS* 4.5 15.8 - - + +
294E CYS* 4.1 8.7 - - + +
297E HIS* 2.7 41.5 + - + +
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Residues in contact with ILE 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E ALA 3.6 12.1 + - - +
272E ILE* 3.0 22.9 - - + +
274E ASP* 1.3 78.4 - - - +
276E ILE* 1.3 65.0 + - + +
278E MET* 3.0 43.6 - - + +
290E CYS 4.8 0.9 - - - -
291E ILE* 5.2 14.4 - - + -
294E CYS* 3.7 18.0 - - - -
322E ILE* 3.7 15.7 - - + -
323E VAL* 6.0 6.1 - - + -
326E GLY* 6.0 0.4 - - - -
328E PRO* 4.4 22.7 - - + +
331E LEU* 5.8 2.0 - - + -
359E LEU* 5.5 8.5 - - + -
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Residues in contact with ILE 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621C LYS* 6.1 3.4 - - - +
272E ILE* 3.0 29.2 - - + +
273E THR* 3.1 22.6 + - + +
275E ILE* 1.3 86.3 - - + +
277E GLU* 1.3 63.5 + - + +
278E MET* 2.8 14.1 + - - +
279E ASP* 3.3 16.5 + - - +
280E SER* 4.5 0.5 + - - -
326E GLY* 4.2 21.1 - - - +
327E ASN 5.8 0.2 - - - +
328E PRO* 4.4 13.2 - - + -
329E PRO* 4.2 22.7 - - + +
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Residues in contact with GLU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D GLN* 2.9 47.6 + - - +
622D ARG* 5.1 6.6 - - - -
623D ASP* 3.4 14.7 - - - +
273E THR* 3.0 15.3 + - + +
274E ASP* 3.7 13.5 + - - +
275E ILE 3.6 0.4 - - - -
276E ILE* 1.3 79.1 - - + +
278E MET* 1.3 63.7 + - - +
279E ASP 3.1 0.9 - - - -
280E SER* 2.8 32.3 + - - +
281E LYS* 3.6 3.5 + - - +
290E CYS* 4.0 11.8 - - - -
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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