Contacts of the helix formed by residues 416 - 436 (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 VAL 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with GLY 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A MET 3.1 10.1 + - - -
413A ILE 3.1 10.0 + - - -
416A VAL* 1.3 76.5 - - - +
418A ILE* 1.3 56.4 + - - +
420A GLU* 3.9 2.1 - - - +
421A VAL* 2.9 36.0 + - - +
502A 2OB 3.4 37.6 - - - +
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Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 4.3 14.8 - - + -
369A THR* 4.0 14.6 - - + -
384A LEU* 3.7 26.5 - - + -
387A PHE* 4.0 19.5 - - + -
389A ILE* 3.8 29.4 - - + -
413A ILE 3.1 8.7 + - - +
414A THR* 3.5 19.7 - - - +
417A GLY* 1.3 73.9 - - - +
419A PRO* 1.4 64.8 - - + +
421A VAL* 3.9 1.0 - - - +
422A MET* 3.1 30.8 + - - +
502A 2OB 4.2 22.8 - - + +
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Residues in contact with PRO 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TRP* 3.5 36.8 - - + -
414A THR 3.5 16.2 - - - +
415A ALA* 3.3 21.1 - - - +
416A VAL* 3.4 12.8 - - - +
418A ILE* 1.4 90.8 - - + +
420A GLU* 1.4 52.6 + - - +
422A MET* 3.6 8.5 + - + +
423A SER* 2.9 29.1 + - - -
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Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 5.0 7.2 - - + -
287A LEU* 5.5 2.0 - - + -
295A VAL* 3.8 29.7 - - + +
298A THR* 4.8 7.6 - - - +
299A TRP* 3.0 27.3 + - - +
416A VAL 3.0 21.3 + - - +
417A GLY* 4.0 3.1 - - - +
419A PRO* 1.4 73.2 - - - +
421A VAL* 1.4 57.3 + - + +
423A SER* 3.0 8.8 + - - -
424A ARG* 2.8 75.1 + - - +
502A 2OB 5.7 0.9 - - + -
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Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.0 24.0 - - + -
323A VAL* 5.7 0.2 - - + -
417A GLY 2.9 21.7 + - - +
418A ILE 4.1 0.2 - - - +
420A GLU* 1.4 72.9 - - + +
422A MET* 1.3 56.8 + - - +
424A ARG* 3.7 6.3 - - - +
425A LEU* 2.8 42.5 + - + +
502A 2OB 3.6 48.2 - - + -
503A DLP 3.7 35.7 - - + -
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Residues in contact with MET 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 3.8 22.2 - - + -
382A LEU* 3.7 26.3 - - + +
383A SER 3.6 29.6 - - - +
384A LEU* 3.6 28.7 - - - +
418A ILE* 3.1 24.1 + - - +
419A PRO* 3.7 7.0 - - + +
421A VAL* 1.3 75.0 - - - +
423A SER* 1.4 56.1 + - - +
425A LEU* 3.4 7.8 - - - +
426A GLU* 3.0 33.2 + - - +
502A 2OB 3.5 25.6 - - + +
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Residues in contact with SER 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TRP* 4.0 18.4 - - - -
419A PRO 2.9 15.9 + - - -
420A GLU* 3.0 15.3 + - - -
422A MET* 1.4 72.8 - - - +
424A ARG* 1.4 64.3 + - - +
426A GLU* 3.2 34.5 + - - +
427A VAL* 3.2 16.3 + - - +
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Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.5 42.5 - - - +
287A LEU* 3.3 24.2 - - - +
291A GLU* 3.4 19.8 + - - +
295A VAL* 4.3 3.6 - - - +
420A GLU* 2.8 49.7 + - - +
421A VAL* 3.8 4.3 - - - +
423A SER* 1.4 71.2 - - - +
425A LEU* 1.3 61.1 + - - +
427A VAL* 3.4 10.2 + - - +
428A VAL* 3.1 26.7 + - - +
503A DLP 3.9 39.1 + - + +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.6 0.2 - - + -
382A LEU* 4.0 7.4 - - + -
421A VAL* 2.8 28.1 + - + +
422A MET* 3.4 7.4 - - - +
423A SER 3.3 0.2 - - - -
424A ARG* 1.3 74.8 - - - +
426A GLU* 1.4 61.1 + - - +
428A VAL* 3.2 5.2 + - - +
429A PHE* 3.2 37.2 + - + -
502A 2OB 3.7 56.8 - - + +
503A DLP 3.6 58.1 - - + +
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Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.3 38.3 - - + +
381A PHE* 3.5 10.3 - - - +
382A LEU* 2.7 43.8 + - + +
422A MET 3.0 15.4 + - - +
423A SER* 3.2 30.0 + - - +
425A LEU* 1.4 73.2 - - - +
427A VAL* 1.4 57.6 + - + +
429A PHE* 3.4 2.1 + - - -
430A THR* 2.7 36.9 + - - -
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A SER* 3.2 20.5 + - - +
424A ARG* 3.5 12.1 - - - +
425A LEU 3.3 0.2 - - - -
426A GLU* 1.4 79.1 - - + +
428A VAL* 1.3 55.2 + - + +
430A THR* 3.2 7.0 + - - -
431A ALA* 2.8 36.9 + - + +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ARG 3.1 15.2 + - - +
425A LEU* 3.2 8.7 + - - +
427A VAL* 1.3 76.2 - - + +
429A PHE* 1.3 60.6 + - + +
431A ALA* 3.3 7.5 + - - +
432A LEU* 3.0 39.8 + - + +
503A DLP 3.4 73.1 - - + +
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Residues in contact with PHE 429 (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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273A LEU* 4.5 8.1 - - + -
380A LEU* 4.1 17.0 - - + -
425A LEU* 3.2 32.7 + - + +
426A GLU 4.1 2.9 - - - +
428A VAL* 1.3 75.8 - - + +
430A THR* 1.3 63.9 + - - +
432A LEU* 3.6 6.9 - - + +
433A MET* 3.1 32.1 + - - +
502A 2OB 3.8 58.6 - - + -
503A DLP 3.8 83.7 - - + -
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Residues in contact with THR 430 (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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375A TYR* 6.0 0.9 - - + -
378A LYS 3.7 23.6 - - - +
379A LYS* 3.8 15.7 - - + +
380A LEU* 3.1 25.2 + - - +
426A GLU 2.7 24.1 + - - -
427A VAL* 3.6 7.6 - - - -
429A PHE* 1.3 76.8 - - - +
431A ALA* 1.4 55.3 + - - +
433A MET* 3.8 6.5 - - - +
434A ASN* 2.9 44.2 + - - +
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Residues in contact with ALA 431 (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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427A VAL* 2.8 23.3 + - + +
428A VAL* 3.3 8.3 + - - +
430A THR* 1.4 67.6 - - - +
432A LEU* 1.4 60.2 + - + +
434A ASN* 3.6 8.8 - - - +
435A SER* 2.9 34.4 + - - -
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Residues in contact with LEU 432 (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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207A SER 5.3 0.4 - - - +
208A ASP* 3.4 33.2 - - + +
282A ARG* 6.0 0.2 - - - +
428A VAL* 3.0 30.3 + - + +
429A PHE* 3.6 14.6 - - + +
430A THR 3.3 0.2 - - - -
431A ALA* 1.4 75.6 - - + +
433A MET* 1.3 61.9 + - - +
435A SER* 3.1 10.1 + - - +
436A LYS* 3.1 35.8 + - + +
503A DLP 3.8 57.4 - - + -
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Residues in contact with MET 433 (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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205A ILE* 5.7 1.3 - - + -
375A TYR* 3.9 22.0 - - + +
380A LEU* 5.1 3.8 - - - -
429A PHE 3.1 20.2 + - - +
430A THR* 3.8 5.6 - - - +
432A LEU* 1.3 73.9 - - - +
434A ASN* 1.3 61.4 + - - +
436A LYS* 3.3 2.0 + - - -
437A GLY 3.1 5.4 + - - -
438A VAL* 2.8 57.5 + - + +
439A SER* 4.7 0.2 - - - -
501A 2OB 5.5 2.7 - - + -
502A 2OB 3.3 66.4 - - + -
503A DLP 4.1 22.4 - - + -
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Residues in contact with ASN 434 (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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375A TYR* 5.1 1.2 + - - -
378A LYS* 3.9 11.1 + - - +
430A THR* 2.9 37.5 + - - +
431A ALA* 3.6 7.9 - - - +
433A MET* 1.3 75.8 - - - +
435A SER* 1.4 55.0 + - - +
437A GLY* 2.8 26.5 + - - -
439A SER* 2.7 37.1 + - - +
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA 2.9 18.4 + - - -
432A LEU* 3.1 18.0 + - - +
434A ASN* 1.4 71.1 - - - +
436A LYS* 1.3 67.9 + - - +
437A GLY 3.3 1.3 + - - -
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Residues in contact with LYS 436 (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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201A ARG* 4.3 15.9 + - - +
204A SER* 2.8 46.7 + - - +
205A ILE* 3.8 38.6 - - + +
207A SER* 3.1 23.7 + - - +
208A ASP* 5.1 8.7 - - - +
432A LEU* 3.1 31.3 + - + +
433A MET* 3.3 6.0 + - - +
434A ASN 3.1 0.4 - - - -
435A SER* 1.3 85.8 - - - +
437A GLY* 1.3 60.8 + - - +
438A VAL 3.6 0.4 - - - -
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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