Contacts of the helix formed by residues 275 - 288 (chain A) in PDB entry 4E70
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A PRO* 1.3 74.7 - - - +
276A GLU* 1.3 54.7 + - - +
278A VAL* 4.4 2.2 - - - -
279A LEU* 2.7 38.0 + - + +
335A ARG* 2.8 33.5 + - - +
339A GLN* 5.6 7.6 + - - +
342A LYS* 5.7 2.6 + - - -
343A LEU* 3.9 20.1 - - + +
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Residues in contact with GLU 276 (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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274A PRO* 4.6 1.0 - - + +
275A ASP* 1.3 77.2 - - - +
277A PRO* 1.3 72.7 - - + +
279A LEU* 3.9 4.9 - - - +
280A LYS* 3.2 22.6 + - + +
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Residues in contact with PRO 277 (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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254A PHE* 3.9 26.8 - - + -
273A TRP* 4.6 7.4 - - + -
274A PRO* 3.2 39.7 - - + +
276A GLU* 1.3 97.4 - - + +
278A VAL* 1.3 63.0 + - - +
280A LYS* 3.5 9.1 + - + +
281A MET* 3.1 24.4 + - - +
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Residues in contact with VAL 278 (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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254A PHE* 5.8 0.2 - - + -
270A LEU* 4.0 33.4 - - + +
273A TRP* 3.7 30.1 - - + +
274A PRO 3.2 18.2 + - - +
275A ASP* 3.8 2.9 - - - +
277A PRO* 1.3 76.7 - - - +
279A LEU* 1.3 58.1 + - - +
281A MET* 3.2 11.6 + - + +
282A LEU* 2.8 53.1 + - + +
335A ARG* 3.8 8.5 - - - +
340A TRP* 5.3 0.7 - - + -
343A LEU* 4.3 15.3 - - + -
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Residues in contact with LEU 279 (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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275A ASP 2.7 22.3 + - - +
276A GLU* 3.9 4.9 - - - +
278A VAL* 1.3 73.7 - - - +
280A LYS* 1.3 58.2 + - - +
282A LEU* 3.1 4.5 + - + -
283A LYS* 2.8 52.6 + - + +
343A LEU* 3.8 25.3 - - + +
346A GLU* 3.5 28.7 - - + +
347A ALA* 3.7 32.1 - - + +
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Residues in contact with LYS 280 (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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254A PHE 5.1 8.8 + - - +
276A GLU* 3.2 15.5 + - + +
277A PRO* 3.7 8.1 - - + +
278A VAL 3.3 0.2 - - - -
279A LEU* 1.3 79.7 - - - +
281A MET* 1.3 62.1 + - - +
283A LYS* 3.4 10.6 + - - +
284A GLN* 3.1 43.8 + - + +
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Residues in contact with MET 281 (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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253A MET* 3.7 51.8 - - + +
254A PHE* 4.2 19.5 - - + -
258A ILE* 3.9 17.7 - - + -
266A PHE* 3.8 17.3 - - + -
270A LEU* 3.6 31.6 - - + -
273A TRP* 5.8 0.9 - - + -
277A PRO 3.1 11.5 + - - +
278A VAL* 3.6 9.4 - - + +
280A LYS* 1.3 78.2 - - - +
282A LEU* 1.3 60.2 + - + +
284A GLN* 3.1 15.7 + - - +
285A CYS* 3.0 26.2 + - - -
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Residues in contact with LEU 282 (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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266A PHE* 4.3 22.4 - - + -
270A LEU* 4.4 14.8 - - + -
278A VAL* 2.8 36.3 + - + +
279A LEU* 3.6 5.2 - - - +
281A MET* 1.3 78.1 - - + +
283A LYS* 1.3 58.3 + - - +
285A CYS* 3.2 5.9 + - - +
286A LYS 2.8 24.3 + - - -
298A LEU* 3.9 23.1 - - + -
340A TRP* 5.5 0.7 - - + -
343A LEU* 4.5 13.9 - - + -
344A PHE* 4.4 27.6 - - + -
347A ALA* 3.8 18.2 - - + -
349A PHE* 3.6 10.6 - - + -
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Residues in contact with LYS 283 (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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279A LEU* 2.8 39.7 + - + +
280A LYS* 3.6 11.9 - - - +
281A MET 3.3 0.2 - - - -
282A LEU* 1.3 73.2 - - - +
284A GLN* 1.3 66.3 + - + +
286A LYS* 3.3 3.1 + - - +
287A LYS* 3.1 23.6 + - - +
346A GLU* 3.4 21.7 + - - -
347A ALA* 3.8 22.9 - - - +
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Residues in contact with GLN 284 (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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253A MET 4.5 7.6 - - - +
254A PHE* 4.6 10.3 + - - +
256A ASP 5.5 2.1 - - - +
258A ILE* 5.3 4.8 - - + +
280A LYS* 3.1 35.3 + - + +
281A MET* 3.1 24.3 + - + +
283A LYS* 1.3 76.7 - - + +
285A CYS* 1.3 58.7 + - - +
287A LYS* 3.4 7.0 + - - +
288A ALA* 3.1 27.4 + - - +
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Residues in contact with CYS 285 (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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258A ILE* 4.1 20.0 - - - -
264A VAL* 4.0 28.9 - - + -
266A PHE* 4.2 13.7 - - - -
281A MET 3.0 18.0 + - - -
282A LEU* 3.2 11.2 + - - +
284A GLN* 1.3 76.4 - - - +
286A LYS* 1.3 59.6 + - - +
288A ALA* 3.1 6.1 + - - +
289A LEU* 2.8 48.6 + - + +
298A LEU* 4.9 5.2 - - + -
349A PHE* 4.6 4.3 - - + -
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Residues in contact with LYS 286 (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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282A LEU 2.8 15.0 + - - +
283A LYS 3.3 5.1 + - - +
285A CYS* 1.3 77.1 - - - +
287A LYS* 1.3 63.5 + - + +
289A LEU* 3.4 2.1 + - - +
290A THR* 2.9 44.5 + - - +
347A ALA 3.5 24.2 - - - +
348A GLY* 2.4 42.3 + - - +
349A PHE* 3.7 24.4 - - + -
350A LYS* 4.6 9.5 - - - +
368A PRO* 4.5 9.8 + - + -
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Residues in contact with LYS 287 (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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283A LYS 3.1 16.1 + - - +
284A GLN* 3.7 6.7 - - - +
286A LYS* 1.3 82.2 - - + +
288A ALA* 1.3 61.3 + - - +
290A THR* 3.3 16.3 + - - -
291A LYS* 3.4 12.8 + - - +
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Residues in contact with ALA 288 (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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258A ILE 5.8 1.1 - - - +
260A HIS* 4.9 20.1 - - + +
284A GLN 3.1 16.6 + - - +
285A CYS* 3.1 7.6 + - - +
287A LYS* 1.3 76.3 - - - +
289A LEU* 1.3 62.6 + - + +
290A THR 3.1 4.6 + - - -
291A LYS* 3.3 20.0 + - - +
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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