Contacts of the helix formed by residues 402 - 420 (chain B) in PDB entry 4DUB
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 GLY 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PHE* 4.1 13.2 - - - -
400B CYS* 3.1 15.8 - - - -
401B ILE* 1.3 82.7 - - - +
403B GLN* 1.4 57.1 + - - +
404B GLN 3.3 2.5 - - - -
405B PHE* 3.2 5.3 + - - +
406B ALA* 2.8 31.5 + - - +
500B HEM 3.7 20.8 - - - -
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Residues in contact with GLN 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B PHE* 3.5 58.4 - - + +
399B ALA* 5.5 3.8 - - - +
400B CYS* 3.5 14.7 + - - +
401B ILE 3.3 4.0 + - - -
402B GLY* 1.4 75.9 - - - +
404B GLN* 1.3 81.7 + - - +
406B ALA* 3.4 0.7 + - - +
407B LEU* 3.0 40.0 + - + +
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE 3.3 23.8 + - - +
108B SER* 4.9 1.5 - - - +
109B GLN* 3.7 48.7 + - + +
112B MET* 4.1 5.5 - - + +
400B CYS 5.2 0.8 + - - -
401B ILE 4.1 9.5 + - - -
403B GLN* 1.3 100.0 + - + +
405B PHE* 1.3 56.2 + - - +
407B LEU* 3.8 4.1 - - - +
408B HIS* 2.8 32.2 + - - +
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Residues in contact with PHE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 4.4 12.1 + + + -
112B MET* 3.5 28.8 - - + +
115B TYR* 4.0 14.6 - + - -
119B MET* 3.4 27.0 - - + +
152B THR* 4.2 12.8 - - + -
153B ILE* 3.9 26.5 - - + -
156B CYS* 3.7 35.2 - - + -
233B LEU* 5.2 6.1 - - + -
269B THR* 6.3 0.7 - - + -
402B GLY* 3.2 15.7 + - - +
404B GLN* 1.3 77.5 - - - +
406B ALA* 1.4 65.0 + - - +
408B HIS* 3.3 0.7 + - - -
409B GLU* 3.0 32.4 + - + +
500B HEM 4.0 21.1 - - + -
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B THR* 3.7 29.5 - - + +
272B LEU* 5.5 0.4 - - - -
393B PHE* 4.3 6.1 - - + -
402B GLY 2.8 20.5 + - - +
403B GLN 3.8 3.4 - - - +
405B PHE* 1.4 76.4 - - - +
407B LEU* 1.3 57.6 + - - +
409B GLU* 3.5 2.6 + - - +
410B ALA* 2.9 31.4 + - - +
500B HEM 3.7 28.5 - - + -
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 4.1 20.9 - - + -
309B LYS* 5.8 0.4 - - - -
318B LEU* 4.7 14.1 - - + -
319B ASN* 4.8 11.2 - - - +
322B LEU* 4.1 9.2 - - + -
393B PHE* 3.8 22.4 - - + -
403B GLN* 3.0 45.9 + - + +
404B GLN* 4.2 4.0 - - - +
406B ALA* 1.3 74.5 - - - +
408B HIS* 1.3 60.0 + - - +
410B ALA* 4.5 1.1 - - - -
411B THR* 2.6 39.9 + - - +
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Residues in contact with HIS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET* 4.2 17.0 - - + -
116B HIS* 2.9 32.9 + - - +
119B MET* 3.7 24.5 - - + -
305B TYR* 3.4 28.0 - + - -
308B VAL* 3.7 20.3 - - + +
309B LYS* 2.8 36.1 + - - +
404B GLN 2.8 20.8 + - - +
405B PHE 3.8 3.1 - - - +
407B LEU* 1.3 78.1 - - - +
409B GLU* 1.3 57.0 + - - +
411B THR* 3.9 2.5 - - - -
412B LEU* 2.9 35.6 + - + +
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B MET* 3.8 25.7 - - + +
148B LEU* 3.6 25.8 - - + +
149B THR* 3.9 7.3 - - + -
152B THR* 3.1 39.7 + - - +
153B ILE* 6.1 0.2 - - - +
269B THR* 3.9 20.6 - - + -
273B LEU* 4.7 1.3 - - + -
405B PHE* 3.0 22.8 + - + +
406B ALA* 3.7 3.8 - - - +
408B HIS* 1.3 76.3 - - - +
410B ALA* 1.4 59.7 + - - +
412B LEU* 3.7 2.3 - - - +
413B VAL* 3.0 45.0 + - - +
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Residues in contact with ALA 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B THR* 5.0 2.5 - - + -
272B LEU* 4.0 14.4 - - + -
273B LEU* 3.6 24.4 - - + +
318B LEU* 3.7 29.4 - - + -
406B ALA 2.9 19.9 + - - +
407B LEU* 4.2 1.6 - - - +
409B GLU* 1.4 76.2 - - - +
411B THR* 1.3 56.2 + - - +
414B LEU* 2.9 35.2 + - - +
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B VAL* 3.7 33.7 - - + +
311B LEU* 3.7 25.8 - - + +
314B VAL* 4.0 11.3 - - + +
315B GLY* 4.6 6.7 - - - +
318B LEU* 3.3 18.2 - - - +
407B LEU* 2.6 24.7 + - - +
408B HIS* 4.7 0.2 - - - -
410B ALA* 1.3 74.1 - - - +
412B LEU* 1.4 57.4 + - - +
415B GLY* 2.9 31.7 + - - -
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 4.0 10.5 - - + +
119B MET* 3.7 44.9 - - + +
120B VAL* 3.8 12.6 - - + +
123B ALA* 4.2 4.5 - - + -
298B LEU* 5.4 0.5 - - - +
303B PRO* 3.6 35.2 - - + +
308B VAL* 3.6 23.3 - - + +
311B LEU* 5.1 1.3 - - - +
408B HIS* 2.9 19.9 + - + +
409B GLU* 3.7 3.4 - - - +
411B THR* 1.4 76.6 - - - +
413B VAL* 1.3 62.9 + - + +
415B GLY* 3.5 0.9 + - - -
416B MET* 3.0 38.7 + - - +
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.8 26.5 - - + -
126B LEU* 4.0 19.3 - - + -
145B MET* 4.7 1.6 - - - -
148B LEU* 3.9 18.6 - - + -
273B LEU* 4.0 15.3 - - + -
409B GLU* 3.0 36.6 + - - +
410B ALA 4.1 1.1 - - - +
412B LEU* 1.3 75.3 - - + +
414B LEU* 1.3 62.4 + - - +
416B MET* 3.3 7.0 + - - +
417B MET* 2.9 45.6 + - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 4.1 8.5 - - + +
276B ALA* 4.0 12.8 - - + -
277B LEU* 4.8 11.4 - - + +
280B LEU* 3.9 26.2 - - + -
314B VAL* 3.9 20.6 - - + -
317B VAL* 4.2 7.9 - - + -
318B LEU* 3.9 22.2 - - + -
410B ALA 2.9 19.1 + - - +
413B VAL* 1.3 76.5 - - - +
415B GLY* 1.3 56.1 + - - +
417B MET* 3.3 27.7 + - + +
418B LEU* 3.0 49.5 + - + +
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Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ALA* 3.6 13.5 - - - +
298B LEU* 3.7 7.6 - - - -
311B LEU* 4.0 17.5 - - - -
314B VAL* 4.4 7.5 - - - +
411B THR 2.9 19.3 + - - -
412B LEU 3.7 1.3 - - - -
414B LEU* 1.3 77.1 - - - +
416B MET* 1.3 55.3 + - - +
418B LEU* 3.3 1.6 + - - -
419B LYS* 3.0 28.8 + - - +
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B VAL* 5.4 1.8 - - - +
123B ALA* 3.8 21.5 - - - -
124B VAL* 4.0 21.3 - - + +
127B VAL* 3.9 22.7 - - + -
298B LEU* 4.0 3.1 - - + +
303B PRO* 3.6 37.9 - - + -
412B LEU* 3.0 26.4 + - - +
413B VAL* 3.3 4.7 + - - +
415B GLY* 1.3 72.0 - - - +
417B MET* 1.3 67.6 + - - +
419B LYS* 3.2 6.8 + - + -
420B HIS* 3.0 35.3 + - + +
455B LEU* 3.8 28.5 - - + -
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Residues in contact with MET 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 4.7 5.4 - - + -
127B VAL* 5.3 5.2 - - + -
130B TRP* 3.7 33.7 - - + -
145B MET* 4.6 11.0 - - + +
273B LEU* 4.9 3.8 - - - +
277B LEU* 3.8 42.8 - - + -
413B VAL* 2.9 44.6 + - + +
414B LEU* 3.6 20.9 - - + +
416B MET* 1.3 72.0 - - - +
418B LEU* 1.4 57.5 + - - +
420B HIS 3.2 0.2 + - - -
421B PHE* 3.0 42.1 + - + +
423B PHE* 3.6 12.0 - - + -
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 5.7 0.7 - - + -
280B LEU* 4.2 10.1 - - + -
287B LEU* 3.1 39.3 - - + +
290B ALA* 3.6 31.9 - - + +
291B ALA* 4.1 13.8 - - + +
294B ALA* 4.0 11.2 - - + -
314B VAL* 4.2 13.0 - - + -
414B LEU* 3.0 40.8 + - + +
415B GLY 3.8 3.6 - - - +
417B MET* 1.4 74.7 - - - +
419B LYS* 1.3 64.0 + - - +
421B PHE 4.0 4.6 - - - +
423B PHE* 4.8 9.0 - - + -
451B LYS* 3.2 22.7 + - - -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ALA* 4.0 13.6 - - + +
295B ALA* 5.1 7.6 - - - +
298B LEU* 2.9 41.1 + - + +
299B VAL 4.5 1.0 - - - -
300B ASP 2.8 31.3 + - - +
301B PRO* 4.6 4.9 + - - +
303B PRO* 6.2 1.9 - - + +
415B GLY 3.0 17.5 + - - +
416B MET* 3.2 7.4 + - + +
418B LEU* 1.3 77.0 - - - +
420B HIS* 1.4 83.1 + - + +
421B PHE 3.7 0.2 - - - -
451B LYS* 3.4 19.1 - - - +
453B ILE* 3.4 36.4 - - + +
454B PRO 4.9 0.6 + - - -
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Residues in contact with HIS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 4.0 15.0 - - + +
131B GLU* 3.9 8.8 + - - +
301B PRO 5.0 1.0 + - - -
416B MET* 3.0 35.3 + - + +
419B LYS* 1.4 110.1 + - + +
421B PHE* 1.3 84.9 + - + +
450B SER* 3.7 3.8 + - - -
451B LYS* 2.9 26.3 + - - +
452B LYS 4.4 0.7 + - - -
453B ILE* 3.1 34.7 + - + +
454B PRO 3.8 13.0 - - - -
455B LEU* 3.8 22.4 - - + +
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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