Contacts of the helix formed by residues 402 - 416 (chain A) in PDB entry 4EWS
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 SER 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A TYR* 3.2 14.7 + - - -
401A SER* 1.3 75.5 - - - +
403A GLU* 1.3 62.6 + - - +
404A SER* 3.0 23.4 + - - -
405A ILE* 3.3 20.9 + - - +
406A GLN* 3.2 12.3 + - - +
4B FUC 3.8 15.9 - - - -
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Residues in contact with GLU 403 (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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402A SER* 1.3 71.2 - - - +
404A SER* 1.4 59.5 + - - +
406A GLN* 3.5 22.1 + - - +
407A SER* 3.0 28.2 + - - -
4B FUC 2.7 39.3 + - - +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLU* 5.7 0.6 - - - +
402A SER* 3.0 15.6 + - - -
403A GLU* 1.4 74.6 - - - +
405A ILE* 1.4 61.3 + - - +
407A SER* 3.5 7.6 + - - -
408A PHE* 3.1 27.4 + - - +
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Residues in contact with ILE 405 (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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310A GLU* 4.9 8.1 - - - +
311A VAL* 4.3 20.2 - - + -
359A VAL* 3.8 23.3 - - + -
361A TYR* 3.5 22.7 - - + -
400A SER* 4.6 0.9 - - - +
401A SER* 3.8 13.2 - - - +
402A SER* 3.3 34.9 + - - +
404A SER* 1.4 81.3 + - - +
406A GLN* 1.4 59.5 + - - +
408A PHE* 3.1 7.2 + - - +
409A LEU* 2.9 44.9 + - + +
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Residues in contact with GLN 406 (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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361A TYR* 4.0 12.3 + - + -
363A PHE* 3.4 25.8 - - + -
391A PRO* 5.9 1.2 - - - +
394A VAL* 3.7 33.6 - - + +
402A SER 3.2 10.3 + - - +
403A GLU* 3.7 23.7 + - - +
404A SER 3.5 0.2 - - - -
405A ILE* 1.4 78.3 - - - +
407A SER* 1.4 56.3 + - - +
409A LEU* 4.6 0.2 - - - -
410A GLN* 3.0 30.5 + - + +
4B FUC 4.0 15.2 + - - -
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLU 3.0 17.7 + - - -
404A SER* 3.7 8.3 - - - -
405A ILE 3.2 0.2 - - - -
406A GLN* 1.4 73.9 - - - +
408A PHE* 1.4 56.8 + - - +
410A GLN* 3.3 4.8 + - - +
411A SER* 2.7 41.2 + - - -
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Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 5.8 0.7 - - + -
307A ILE* 3.7 60.8 - - + -
308A PHE* 4.3 14.8 - + - -
310A GLU* 4.9 10.1 - - - +
311A VAL* 4.8 8.7 - - + -
312A VAL* 4.4 13.7 - - + -
404A SER 3.1 17.2 + - - +
405A ILE* 3.1 6.5 + - - +
407A SER* 1.4 75.2 - - - +
409A LEU* 1.3 64.9 + - + +
411A SER* 3.5 6.6 + - - -
412A MET* 3.1 55.0 + - + +
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Residues in contact with LEU 409 (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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311A VAL* 4.4 7.6 - - + -
348A PHE* 3.8 17.1 - - + -
350A PHE* 3.9 24.5 - - + -
359A VAL* 4.5 1.8 - - + -
361A TYR* 3.8 30.5 - - + -
363A PHE* 3.6 15.7 - - + -
405A ILE* 2.9 38.2 + - + +
408A PHE* 1.3 84.3 - - + +
410A GLN* 1.4 62.2 + - - +
412A MET* 3.2 27.8 - - + +
413A ILE* 3.2 27.9 + - - +
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Residues in contact with GLN 410 (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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363A PHE* 3.3 19.0 - - + -
365A GLU* 2.9 41.5 + - - +
389A ILE* 3.7 12.0 - - + +
391A PRO* 3.3 19.9 - - + +
394A VAL* 4.6 0.3 - - - +
406A GLN* 3.0 21.9 + - + +
407A SER* 3.3 5.6 + - - +
409A LEU* 1.4 73.8 - - - +
411A SER* 1.3 61.6 + - - +
413A ILE* 3.3 11.4 + - - +
414A THR* 3.0 30.9 + - - +
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Residues in contact with SER 411 (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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407A SER* 2.7 30.3 + - - -
408A PHE* 3.9 7.4 - - - -
410A GLN* 1.3 71.0 - - - +
412A MET* 1.3 54.9 + - - +
414A THR* 3.5 5.5 + - - -
415A ALA* 2.9 41.6 + - - +
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Residues in contact with MET 412 (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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292A PHE* 3.9 21.5 - - + -
296A LEU* 3.7 27.6 - - + -
312A VAL* 4.4 6.5 - - + -
348A PHE* 3.7 23.1 - - + -
408A PHE* 3.1 30.0 + - + +
409A LEU* 3.2 37.2 - - + +
411A SER* 1.3 75.1 - - - +
413A ILE* 1.4 59.6 + - - +
415A ALA* 5.2 0.2 - - - -
416A VAL* 3.0 38.1 + - + +
417A GLY 3.1 6.8 + - - -
502A 2OB 3.9 15.7 - - + +
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Residues in contact with ILE 413 (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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346A VAL* 4.0 13.5 - - + -
348A PHE* 3.9 18.6 - - + -
363A PHE* 3.8 36.1 - - + -
365A GLU* 3.4 18.8 - - - +
367A ILE* 4.2 8.3 - - + -
389A ILE* 5.8 0.9 - - + -
409A LEU 3.2 17.3 + - - +
410A GLN* 3.3 21.3 + - - +
412A MET* 1.4 73.3 - - - +
414A THR* 1.3 56.5 + - - +
417A GLY* 3.1 7.2 - - - +
418A ILE* 3.1 27.1 + - + +
502A 2OB 3.8 30.0 - - + +
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Residues in contact with THR 414 (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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387A PHE* 3.6 38.2 - - + -
389A ILE* 3.2 16.1 - - + +
410A GLN* 3.0 22.7 + - - +
411A SER* 3.7 6.5 - - - -
413A ILE* 1.3 75.5 - - - +
415A ALA* 1.3 63.6 + - + +
418A ILE* 3.5 20.7 - - + +
419A PRO* 3.5 15.4 - - - +
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Residues in contact with ALA 415 (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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299A TRP* 4.3 8.3 - - - +
301A PHE* 6.2 4.3 - - + -
411A SER* 2.9 22.0 + - - +
414A THR* 1.3 74.6 - - + +
416A VAL* 1.4 65.1 + - + +
419A PRO* 3.3 16.6 - - - +
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 3.7 13.9 - - + +
296A LEU* 4.3 20.4 - - + +
299A TRP* 3.5 30.2 - - + -
301A PHE* 6.4 1.8 - - + -
412A MET* 3.0 23.1 + - - +
414A THR 3.4 0.2 - - - -
415A ALA* 1.4 83.0 - - + +
417A GLY* 1.3 62.9 - - - +
418A ILE 3.5 0.9 - - - -
419A PRO* 3.4 4.4 - - - +
420A GLU* 3.0 34.4 + - - +
502A 2OB 3.6 23.3 - - + -
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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