Contacts of the helix formed by residues 268 - 286 (chain U) 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 PRO 268 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269U GLY* 1.3 65.9 + - - +
270U VAL* 3.1 17.6 - - + +
271U ALA* 3.7 20.4 - - + +
272U TYR* 3.5 17.7 + - - +
275U ARG* 4.5 3.8 + - - -
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Residues in contact with GLY 269 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U PRO* 1.3 78.4 - - - +
270U VAL* 1.3 61.6 + - - +
272U TYR* 3.4 8.2 + - - +
273U ARG* 3.2 20.4 + - - +
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Residues in contact with VAL 270 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U PRO* 3.1 10.5 - - + -
269U GLY* 1.3 75.3 - - - +
271U ALA* 1.3 59.8 + - - +
273U ARG* 3.2 14.4 + - + +
274U THR* 2.4 42.1 + - - +
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Residues in contact with ALA 271 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U PRO* 3.7 18.3 - - + +
270U VAL* 1.3 76.4 - - - +
272U TYR* 1.3 56.1 + - - +
274U THR* 2.8 28.2 + - - -
275U ARG* 2.9 39.0 + - - +
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Residues in contact with TYR 272 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U PRO 3.5 9.9 + - - +
269U GLY* 3.4 12.7 + - - +
270U VAL 3.3 0.4 - - - -
271U ALA* 1.3 79.3 - - - +
273U ARG* 1.3 65.6 + - - +
274U THR 3.1 0.5 + - - -
275U ARG* 3.4 28.9 + - - +
276U GLU* 3.2 45.1 + - + +
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Residues in contact with ARG 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269U GLY 3.2 10.7 + - - +
270U VAL* 3.2 18.1 + - - +
272U TYR* 1.3 83.7 - - - +
274U THR* 1.3 58.5 + - - +
276U GLU* 3.4 6.7 + - - +
277U GLU* 3.0 54.2 + - + +
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Residues in contact with THR 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258U TYR* 5.7 1.8 - - - +
270U VAL* 2.4 29.2 + - - +
271U ALA* 2.8 14.3 + - - -
273U ARG* 1.3 75.2 - - - +
275U ARG* 1.3 64.4 + - - +
276U GLU 3.0 1.1 - - - -
277U GLU* 3.1 10.7 + - - +
278U ILE* 2.8 42.3 + - + +
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Residues in contact with ARG 275 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U PRO 4.5 4.9 + - - -
271U ALA* 2.9 36.2 + - - +
272U TYR* 3.8 31.9 - - - +
274U THR* 1.3 74.7 - - - +
276U GLU* 1.3 58.7 + - - +
278U ILE* 3.3 9.3 + - - +
279U GLN* 2.8 29.4 + - - +
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Residues in contact with GLU 276 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272U TYR* 3.2 41.0 + - + +
273U ARG* 3.7 5.8 - - - +
274U THR 3.0 0.8 - - - -
275U ARG* 1.3 79.3 - - - +
277U GLU* 1.3 60.4 + - - +
279U GLN* 3.1 8.9 + - + +
280U GLU* 2.7 34.7 + - + +
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Residues in contact with GLU 277 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258U TYR* 3.9 17.2 + - + +
273U ARG* 3.0 51.8 + - + +
274U THR* 3.7 8.5 + - + +
276U GLU* 1.3 73.0 - - - +
278U ILE* 1.3 62.0 + - - +
280U GLU* 3.7 6.8 - - - +
281U VAL* 2.9 36.1 + - + +
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Residues in contact with ILE 278 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258U TYR* 4.0 26.9 - - + +
259U ARG 4.4 1.8 - - - +
260U TYR* 3.3 39.4 - - + +
261U HIS 5.3 2.7 - - - +
274U THR* 2.8 36.0 + - + +
275U ARG* 3.6 7.9 - - - +
277U GLU* 1.3 77.4 - - - +
279U GLN* 1.3 58.0 + - - +
281U VAL* 4.0 5.6 - - - +
282U ARG* 3.1 45.6 + - - +
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Residues in contact with GLN 279 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275U ARG 2.8 18.4 + - - +
276U GLU* 3.4 11.4 - - + +
277U GLU 3.0 0.2 - - - -
278U ILE* 1.3 78.5 - - - +
280U GLU* 1.3 58.7 + - - +
282U ARG* 3.2 26.4 + - - +
283U SER* 2.9 37.1 + - - -
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Residues in contact with GLU 280 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276U GLU* 2.7 23.3 + - + +
277U GLU* 3.7 7.6 - - - +
279U GLN* 1.3 73.6 - - - +
281U VAL* 1.3 66.8 + - + +
283U SER* 3.7 10.3 + - - -
284U LYS* 3.2 40.8 + - - +
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Residues in contact with VAL 281 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197U ARG* 6.1 1.1 - - - +
228U MET* 4.2 19.3 - - + -
258U TYR* 4.1 41.5 - - + -
260U TYR* 4.5 6.1 - - + -
277U GLU* 2.9 20.9 + - + +
278U ILE* 4.0 5.4 - - - +
280U GLU* 1.3 78.8 - - + +
282U ARG* 1.3 65.3 + - - +
284U LYS* 3.2 1.2 + - - -
285U SER* 2.9 34.8 + - - +
286U ASP 3.8 0.3 + - - -
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Residues in contact with ARG 282 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43U ARG* 4.5 9.8 - - - +
260U TYR* 3.3 54.0 + - + +
278U ILE* 3.1 35.5 + - - +
279U GLN* 3.2 29.3 + - - +
281U VAL* 1.3 80.5 - - - +
283U SER* 1.3 64.6 + - - +
284U LYS 3.1 0.2 + - - -
286U ASP* 3.1 31.2 + - + +
289U MET* 4.7 2.6 - - - +
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Residues in contact with SER 283 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279U GLN* 2.9 25.4 + - - -
280U GLU* 3.7 14.1 + - - -
282U ARG* 1.3 74.6 - - - +
284U LYS* 1.3 66.8 + - - +
289U MET* 3.8 16.4 - - - +
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Residues in contact with LYS 284 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280U GLU* 3.2 31.0 + - - +
281U VAL* 3.2 3.1 + - - +
282U ARG 3.1 1.0 - - - -
283U SER* 1.3 84.6 + - - +
285U SER* 1.3 66.5 + - - +
289U MET* 4.9 2.0 - - - +
290U LEU* 4.3 8.9 - - - +
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Residues in contact with SER 285 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228U MET* 3.5 28.1 - - - +
281U VAL* 2.9 23.1 + - - +
282U ARG 3.4 0.6 + - - -
283U SER 3.8 0.2 + - - -
284U LYS* 1.3 83.8 - - - +
286U ASP* 1.3 68.0 + - - +
287U PRO 3.3 2.1 - - - -
289U MET* 5.0 0.2 - - - -
290U LEU* 3.7 26.8 - - - +
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Residues in contact with ASP 286 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43U ARG* 2.7 37.1 + - - -
260U TYR* 3.2 20.4 + - - +
281U VAL 3.8 1.6 + - - -
282U ARG* 3.1 25.5 + - + +
285U SER* 1.3 77.5 - - - +
287U PRO* 1.3 70.0 - - - +
288U ILE* 2.8 29.8 + - - +
289U MET* 2.9 23.4 + - + +
290U LEU* 3.1 20.3 + - - +
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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