Contacts of the helix formed by residues 257 - 272 (chain E) in PDB entry 6CP3
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 ASN 257 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E VAL* 3.4 11.5 + - - +
255E ILE* 4.4 2.0 - - - -
256E ASP* 1.3 87.2 + - - +
258E ILE* 1.3 58.4 + - - +
259E PHE* 3.1 2.0 - - - -
260E ARG* 2.8 60.0 + - - +
261E PHE* 3.4 3.3 + - - +
309E ALA* 3.1 24.6 - - - +
310E VAL 3.2 3.6 + - - -
311E TYR* 3.3 36.1 + - - +
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Residues in contact with ILE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ALA* 5.5 0.2 - - + -
255E ILE* 3.9 20.1 - - + +
256E ASP* 4.6 0.2 - - - +
257E ASN* 1.3 75.8 + - - +
259E PHE* 1.3 60.7 + - + +
261E PHE* 3.2 18.2 + - + +
262E THR* 3.0 28.6 + - - +
289E MET* 4.5 14.1 - - - -
292E LEU* 3.7 28.9 - - + -
293E GLN* 5.2 0.4 - - - +
308E GLN* 3.7 25.8 - - + +
309E ALA 3.3 20.0 + - - +
310E VAL* 4.1 13.7 - - + -
325E THR* 4.0 22.7 - - + +
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Residues in contact with PHE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 6.2 0.7 - - - -
342A THR* 5.1 11.9 - - + -
346A SER* 5.8 6.3 - - - -
257E ASN* 3.0 2.7 + - - +
258E ILE* 1.3 81.5 - - + +
260E ARG* 1.3 66.9 + - + +
262E THR* 3.1 6.0 + - - -
263E GLN* 2.9 48.0 + - + +
281E TYR* 3.2 34.3 - + - -
310E VAL* 5.4 1.6 - - + -
311E TYR* 3.5 56.1 - + + +
313E PRO* 3.5 25.4 - - + -
321E ALA* 4.0 15.0 - - + -
322E PRO* 5.3 0.7 - - + -
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Residues in contact with ARG 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 4.9 8.5 - - + -
346A SER* 3.4 36.3 + - - +
187E VAL* 3.5 13.0 + - - +
188E GLY* 2.7 39.7 + - - -
189E GLU* 4.3 5.5 + - - +
190E ARG* 5.0 17.1 - - - +
222E MET* 4.8 8.1 - - - -
229E ARG* 4.9 8.2 + - - +
256E ASP* 3.4 24.5 + - - -
257E ASN* 2.8 37.9 + - + +
259E PHE* 1.3 77.4 - - + +
261E PHE* 1.3 60.5 + - - +
263E GLN* 3.3 11.7 + - + +
264E ALA* 2.9 26.2 + - - +
311E TYR* 5.8 3.0 - - + +
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Residues in contact with PHE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E VAL* 3.9 17.5 - - + +
229E ARG 3.8 14.8 - - - -
230E ALA* 3.9 25.1 - - + -
233E ALA* 4.3 13.0 - - + -
234E LEU* 5.5 7.2 - - + -
257E ASN 3.4 3.0 + - - -
258E ILE* 3.2 28.1 + - + +
260E ARG* 1.3 79.3 - - - +
262E THR* 1.3 60.3 + - - +
264E ALA* 3.2 3.0 + - - +
265E GLY* 3.0 25.1 + - - -
288E ASP* 3.5 28.5 - - + -
289E MET* 4.3 13.2 - - + -
292E LEU* 3.6 33.7 - - + -
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Residues in contact with THR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ILE* 3.0 14.1 + - - +
259E PHE* 3.1 11.2 + - - -
261E PHE* 1.3 77.9 - - - +
263E GLN* 1.3 58.1 + - - +
265E GLY* 3.3 2.2 + - - +
266E SER* 2.9 25.3 + - - -
281E TYR* 4.5 13.5 - - + -
282E GLN* 3.6 6.2 - - - +
285E LEU* 3.8 26.9 - - + -
289E MET* 3.5 19.2 - - + +
321E ALA* 3.8 30.9 - - + +
325E THR* 5.2 1.4 + - - -
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Residues in contact with GLN 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 4.8 5.7 - - - +
301A PHE* 5.3 7.9 - - + -
339A TYR* 4.0 19.6 + - - -
342A THR* 5.9 2.8 - - - +
343A ASN* 4.1 13.5 + - - +
229E ARG* 5.2 7.4 - - - +
259E PHE* 2.9 44.3 + - + +
260E ARG* 3.5 15.5 - - + +
262E THR* 1.3 74.3 - - - +
264E ALA* 1.3 59.3 + - - +
266E SER* 3.2 9.8 + - - -
267E GLU* 2.9 55.8 + - - +
281E TYR* 4.1 17.0 - - - -
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Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E PRO* 3.9 10.0 - - - +
229E ARG* 3.6 24.0 - - + +
230E ALA* 3.5 33.0 - - + +
260E ARG 2.9 14.0 + - - +
261E PHE 3.2 8.9 + - - +
263E GLN* 1.3 75.7 - - - +
265E GLY* 1.3 57.2 + - - +
267E GLU* 3.9 0.5 - - - +
268E VAL* 2.9 35.3 + - - +
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Residues in contact with GLY 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ALA* 4.5 6.1 - - - +
261E PHE* 3.0 15.5 + - - -
262E THR 3.3 1.8 + - - -
263E GLN 3.2 0.2 - - - -
264E ALA* 1.3 77.1 - - - +
266E SER* 1.3 61.0 + - - +
268E VAL* 4.1 3.0 - - - +
269E SER* 3.0 21.3 + - - -
282E GLN* 3.2 31.7 - - - +
288E ASP* 6.3 0.2 - - - -
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Residues in contact with SER 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A TYR* 5.4 2.9 + - - -
262E THR 2.9 13.8 + - - -
263E GLN* 3.2 17.3 + - - -
265E GLY* 1.3 74.1 - - - +
267E GLU* 1.3 64.8 + - - +
269E SER 3.6 0.9 - - - -
270E ALA* 2.9 31.9 + - - +
280E GLY 3.2 23.2 + - - -
281E TYR* 4.3 11.3 - - - -
282E GLN* 2.9 18.3 + - - +
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Residues in contact with GLU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLY* 3.1 25.3 - - - +
299A ASP* 4.1 2.6 - - - -
301A PHE* 3.2 32.0 + - - +
302A TYR 4.4 0.3 + - - -
339A TYR* 3.1 24.1 + - - +
226E PRO* 3.7 28.3 - - + +
229E ARG* 3.9 7.7 + - - -
263E GLN* 2.9 28.1 + - - +
266E SER* 1.3 78.6 - - - +
268E VAL* 1.3 61.4 + - - +
270E ALA* 4.2 4.7 - - - +
271E LEU* 2.9 35.6 + - + +
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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
----------------------------------------------------------
51E ALA* 6.3 0.2 - - + -
62E ILE* 3.8 30.9 - - + +
226E PRO* 3.5 32.3 - - + +
227E GLY* 3.7 10.8 - - - +
230E ALA* 4.0 8.1 - - + -
231E ARG* 5.0 6.1 - - - +
264E ALA 2.9 21.0 + - - +
265E GLY* 4.1 4.3 - - - +
267E GLU* 1.3 75.7 - - - +
269E SER* 1.3 60.0 + - - +
271E LEU* 3.2 8.5 + - + +
272E LEU* 3.1 35.9 + - + +
274E ARG* 6.2 0.2 - - - +
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Residues in contact with SER 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E GLY 3.0 9.8 + - - -
266E SER 3.6 2.5 - - - -
268E VAL* 1.3 78.0 - - - +
270E ALA* 1.3 57.2 + - - +
272E LEU* 4.2 9.9 - - - +
274E ARG* 3.2 54.8 + - - +
276E PRO* 5.7 1.0 - - - +
282E GLN* 3.6 31.0 - - - +
283E PRO* 4.0 8.1 - - - +
284E THR* 4.6 4.0 + - - +
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Residues in contact with ALA 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PRO* 3.9 20.0 - - - +
291A PRO 5.3 2.2 - - - +
292A GLY* 5.0 11.7 - - - +
298A GLY* 4.7 12.4 - - - -
266E SER* 2.9 20.1 + - - +
267E GLU* 4.2 4.7 - - - +
268E VAL 3.1 0.2 - - - -
269E SER* 1.3 76.3 - - - +
271E LEU* 1.3 64.4 + - - +
272E LEU 3.2 1.8 - - - -
273E GLY* 3.5 8.4 + - - -
274E ARG 4.6 5.9 - - - +
276E PRO* 5.0 14.8 - - + -
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Residues in contact with LEU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 5.9 9.0 - - + -
290A PRO* 4.5 13.6 - - + +
298A GLY* 4.3 13.0 - - - +
299A ASP* 4.0 37.9 - - + +
17E ILE* 5.7 2.9 - - + +
18E GLY* 6.3 0.7 - - - -
19E ALA* 4.1 24.7 - - + +
20E ILE* 3.7 33.1 - - + +
60E ARG* 5.7 0.9 + - - -
62E ILE* 6.4 0.2 - - + -
226E PRO* 4.5 8.3 - - + -
267E GLU 2.9 24.8 + - - +
268E VAL* 3.7 7.0 - - + +
270E ALA* 1.3 76.3 - - - +
272E LEU* 1.3 59.6 + - - +
273E GLY 3.1 3.5 + - - -
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Residues in contact with LEU 272 (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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38B ASP* 5.1 1.2 - - - +
20E ILE* 3.8 22.0 - - + -
51E ALA* 4.4 18.8 - - + -
52E GLN* 4.1 19.6 + - + +
60E ARG* 4.1 34.0 + - + +
61E THR 5.3 0.7 - - - +
62E ILE* 3.8 10.8 - - + -
268E VAL* 3.1 29.4 + - + +
269E SER* 4.6 1.1 - - - -
270E ALA 3.2 0.8 - - - +
271E LEU* 1.3 76.0 - - - +
273E GLY* 1.3 60.4 + - - +
274E ARG* 3.5 46.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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