Contacts of the helix formed by residues 267 - 286 (chain E) in PDB entry 3EXG
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 267 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LYS* 3.5 22.3 + - - +
268E PRO* 1.4 65.4 - - - +
269E GLY* 2.4 7.2 + - - -
270E VAL* 2.4 50.0 + - + +
271E ALA* 3.3 8.7 + - - +
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Residues in contact with PRO 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E ASP* 1.4 83.5 - - - +
269E GLY* 1.3 62.6 + - - +
270E VAL 3.4 0.2 - - - -
271E ALA* 3.1 10.7 - - + +
272E TYR* 3.0 25.1 + - - +
275E ARG* 4.6 2.0 + - - +
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Residues in contact with GLY 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 3.8 23.6 - - - +
46D LYS* 3.9 22.6 - - - -
267E ASP 2.4 9.3 + - - -
268E PRO* 1.3 76.9 - - - +
270E VAL* 1.3 60.0 + - - -
272E TYR* 3.2 5.2 + - - +
273E ARG 3.2 16.6 + - - -
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Residues in contact with VAL 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 3.7 37.7 + - + +
267E ASP* 2.4 31.7 + - + +
269E GLY* 1.3 64.6 - - - -
271E ALA* 1.3 67.2 + - - +
273E ARG* 3.6 18.2 + - - +
274E THR* 3.0 32.7 + - + +
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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
----------------------------------------------------------
267E ASP 3.3 6.8 + - - +
268E PRO* 3.1 22.2 - - + +
270E VAL* 1.3 75.6 - - - +
272E TYR* 1.3 66.1 - - - +
273E ARG 2.8 2.6 + - - -
274E THR* 2.8 24.8 + - - -
275E ARG* 3.2 29.0 + - - +
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Residues in contact with TYR 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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18D GLU* 2.6 47.2 + - + +
46D LYS* 3.6 32.1 - - + -
47D TYR* 4.1 17.3 - + - -
51D ARG* 5.7 0.3 + - - -
268E PRO 3.0 9.3 + - - +
269E GLY* 3.6 9.0 - - - +
271E ALA* 1.3 79.1 - - - +
273E ARG* 1.3 64.1 + - - +
275E ARG* 3.5 28.7 - - - +
276E GLU* 2.5 48.4 + - + +
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Residues in contact with ARG 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D TRP* 3.6 33.9 + - - -
45D LYS* 3.3 27.2 + - - +
46D LYS 3.6 21.3 - - - +
47D TYR 4.4 6.1 - - - +
48D GLY* 4.0 18.7 - - - +
269E GLY 3.2 6.3 + - - -
270E VAL* 4.0 26.7 + - - +
271E ALA 2.8 6.1 + - - -
272E TYR* 1.3 72.8 - - - +
274E THR* 1.3 64.4 + - - +
276E GLU* 2.8 16.2 + - + +
277E GLU* 2.5 41.6 + - - +
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Residues in contact with THR 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 VAL* 3.0 27.5 + - + +
271E ALA* 2.8 22.2 + - - -
273E ARG* 1.3 76.2 - - + +
275E ARG* 1.3 51.9 + - - +
276E GLU 3.1 0.3 + - - -
277E GLU* 3.2 14.4 + - - +
278E ILE* 2.9 47.6 + - - +
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Residues in contact with ARG 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E PRO* 4.6 2.8 + - - +
271E ALA* 3.5 31.0 - - - +
272E TYR* 3.5 39.8 - - - +
274E THR* 1.3 77.8 + - - +
276E GLU* 1.3 58.8 + - + +
278E ILE* 3.8 9.3 - - - +
279E GLN* 3.1 26.9 + - - +
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Residues in contact with GLU 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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47D TYR* 5.1 3.8 - - - -
51D ARG* 5.2 7.0 + - - -
272E TYR* 2.5 55.5 + - + +
273E ARG* 2.8 19.3 + - + +
275E ARG* 1.3 75.9 - - + +
277E GLU* 1.3 58.2 + - - +
279E GLN* 2.9 10.1 - - - +
280E GLU* 2.7 26.7 + - - +
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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
----------------------------------------------------------
258E TYR* 3.8 16.2 - - + +
273E ARG* 2.5 50.6 + - - +
274E THR* 3.6 14.3 - - - +
276E GLU* 1.3 74.6 - - - +
278E ILE* 1.3 70.5 + - - +
279E GLN 2.7 0.4 - - - -
280E GLU* 3.4 11.2 - - + +
281E VAL* 2.8 37.6 + - + +
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Residues in contact with ILE 278 (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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258E TYR* 3.3 37.2 - - + +
259E ARG 4.2 4.5 - - - +
260E TYR* 3.7 35.9 - - + +
274E THR* 2.9 36.7 + - - +
275E ARG* 3.8 8.5 - - - +
277E GLU* 1.3 79.4 - - + +
279E GLN* 1.3 58.4 + - - +
281E VAL* 4.3 1.8 - - - +
282E ARG* 3.4 39.5 + - - +
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Residues in contact with GLN 279 (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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275E ARG 3.1 15.3 + - - +
276E GLU* 2.9 18.4 - - - +
277E GLU 2.7 0.4 - - - -
278E ILE* 1.3 78.0 - - - +
280E GLU* 1.3 57.2 + - - -
282E ARG* 3.1 24.4 + - - +
283E SER* 2.9 33.6 + - - -
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Residues in contact with GLU 280 (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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50D LYS* 6.3 2.0 - - - -
276E GLU 2.7 19.6 + - - +
277E GLU* 3.1 9.5 + - + +
279E GLN* 1.3 72.8 - - + +
281E VAL* 1.3 68.1 + - - +
283E SER* 3.6 9.6 + - - +
284E LYS* 3.2 51.8 + - - +
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Residues in contact with VAL 281 (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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228E MET* 4.5 6.3 - - + -
258E TYR* 3.9 51.1 - - + -
260E TYR* 4.4 9.0 - - + -
277E GLU* 2.8 27.5 + - + +
278E ILE 4.3 2.0 - - - +
280E GLU* 1.3 78.7 + - - +
282E ARG* 1.3 56.0 + - - +
284E LYS* 3.3 2.1 + - - +
285E SER* 2.9 41.3 + - - +
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Residues in contact with ARG 282 (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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43E ARG* 4.5 9.7 - - - +
260E TYR* 3.3 56.5 + - - +
278E ILE* 3.4 33.3 + - - +
279E GLN* 3.1 31.1 + - - +
281E VAL* 1.3 76.9 - - - +
283E SER* 1.3 65.3 + - - +
284E LYS 2.9 1.4 + - - -
286E ASP* 2.9 35.9 + - + +
289E MET* 4.6 1.4 - - - +
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Residues in contact with SER 283 (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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279E GLN* 2.9 19.6 + - - -
280E GLU* 3.6 14.9 + - - +
282E ARG* 1.3 78.4 - - - +
284E LYS* 1.3 62.8 + - - +
289E MET* 3.5 20.3 - - - +
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Residues in contact with LYS 284 (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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156C GLY 6.1 1.1 - - - +
280E GLU* 3.2 38.2 + - - +
281E VAL* 4.2 2.0 - - - +
282E ARG 3.1 1.0 - - - -
283E SER* 1.3 83.9 + - - +
285E SER* 1.3 70.3 + - - +
289E MET* 4.5 4.6 - - - +
290E LEU* 4.1 7.6 - - - +
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Residues in contact with SER 285 (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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228E MET* 3.2 33.9 - - - +
281E VAL* 2.9 24.2 + - - +
282E ARG 3.1 0.4 + - - -
284E LYS* 1.3 90.3 + - - +
286E ASP* 1.3 67.6 + - - +
287E PRO 3.3 0.9 - - - -
289E MET* 4.9 0.2 - - - +
290E LEU* 3.8 21.0 - - - +
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Residues in contact with ASP 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ARG* 2.7 34.6 + - - -
260E TYR* 3.3 17.9 + - - +
281E VAL 3.8 0.6 + - - -
282E ARG* 2.9 25.8 + - + +
285E SER* 1.3 75.9 - - - +
287E PRO* 1.3 73.0 - - - +
288E ILE* 2.7 34.8 + - - +
289E MET* 3.1 21.7 + - + +
290E LEU* 3.0 21.1 + - - +
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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