Contacts of the helix formed by residues 384 - 396 (chain B) in PDB entry 4D1Q
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 PHE 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B GLU* 4.3 11.9 - - + +
374B LEU* 4.7 8.1 - - + -
380B PRO 4.9 10.3 - - - -
381B SER* 2.7 21.0 + - - +
383B CYS* 1.3 92.6 - - - +
385B VAL* 1.3 61.0 + - - +
387B PRO* 3.2 11.6 - - + +
388B SER* 2.7 30.3 + - - +
433B PHE* 6.3 0.2 - + - -
436B TYR* 3.7 37.9 - + - -
540B VAL* 5.7 1.1 - - + -
500G THR* 3.3 28.9 - - + -
501G THR* 6.1 1.6 - - + -
504G PHE* 3.5 32.0 - + + -
505G PHE* 5.2 5.2 - + - -
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 3.4 27.1 - - - +
374B LEU* 4.3 12.1 - - + -
381B SER 3.7 0.4 + - - -
382B LEU* 3.6 20.2 - - + +
383B CYS 3.0 2.4 + - - -
384B PHE* 1.3 74.0 - - - +
386B VAL* 1.3 73.0 + - + +
388B SER* 2.8 18.6 + - - -
389B ILE* 3.0 12.4 + - + +
421B TRP* 4.2 9.0 - - + +
425B LEU* 3.8 26.2 - - + -
429B HIS* 3.7 25.6 - - + +
566B ALA* 4.4 5.8 - - + -
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B CYS 3.8 1.0 + - - -
385B VAL* 1.3 82.9 - - + +
387B PRO* 1.3 72.3 - - + +
389B ILE* 3.1 11.7 + - + +
390B LEU* 3.0 33.4 + - + +
425B LEU* 4.7 5.8 - - + -
429B HIS* 4.2 16.6 - - + +
430B TYR* 3.9 30.5 - - + -
433B PHE* 3.6 26.5 - - + -
442B MET* 4.4 9.9 - - + -
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Residues in contact with PRO 387 (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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383B CYS 3.0 13.5 - - - +
384B PHE* 3.2 30.1 - - + +
386B VAL* 1.3 93.6 - - + +
388B SER* 1.3 55.4 + - - +
390B LEU* 3.2 12.6 + - + +
391B LYS* 2.8 27.5 + - - +
433B PHE* 3.5 21.5 - - + -
504G PHE* 3.5 24.5 - - + +
505G PHE* 3.9 26.5 - - + -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 3.4 30.2 - - - +
374B LEU* 4.3 5.6 - - - +
384B PHE 2.7 18.5 + - - -
385B VAL* 2.8 18.1 + - - -
387B PRO* 1.3 67.9 - - - +
389B ILE* 1.3 59.6 + - - -
391B LYS* 2.9 8.3 + - - +
392B VAL* 2.8 33.6 + - - +
421B TRP* 3.9 9.4 - - - -
504G PHE* 2.9 21.2 - - - -
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Residues in contact with ILE 389 (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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385B VAL 3.0 12.9 + - - +
386B VAL* 3.4 13.5 - - + +
388B SER* 1.3 75.1 - - - +
390B LEU* 1.3 70.7 + - + +
392B VAL* 3.1 4.7 + - - +
393B LYS* 3.0 35.6 + - - +
417B VAL* 4.2 4.2 - - + +
421B TRP* 3.6 44.9 - - + -
422B GLU* 3.2 40.4 - - + +
425B LEU* 3.6 29.2 - - + -
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Residues in contact with LEU 390 (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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386B VAL* 3.0 31.3 + - + +
387B PRO* 3.3 13.9 - - + +
389B ILE* 1.3 84.2 - - + +
391B LYS* 1.3 58.2 + - - +
393B LYS* 3.3 13.1 + - + +
394B GLU* 3.0 29.5 + - - +
422B GLU* 5.5 1.3 - - - +
433B PHE* 5.2 3.6 - - + -
441B HIS* 4.8 22.0 - - + +
504G PHE 5.7 2.2 - - - +
507G GLN* 5.8 3.1 - - - +
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Residues in contact with LYS 391 (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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370B ILE* 4.2 6.7 - - + -
387B PRO 2.8 13.6 + - - +
388B SER* 2.9 13.2 + - - +
390B LEU* 1.3 73.8 - - - +
392B VAL* 1.3 66.0 + - - +
394B GLU* 3.1 37.7 + - - +
395B ILE* 2.9 45.8 + - + +
502G SER 5.0 0.8 + - - -
503G PHE* 3.0 70.2 + - + +
504G PHE* 5.0 6.3 + - + +
506G PRO* 4.9 5.5 - - - +
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Residues in contact with VAL 392 (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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270B LEU* 5.2 0.9 - - + -
367B PHE* 3.5 36.3 - - + -
370B ILE* 3.5 20.9 - - + -
388B SER 2.8 21.7 + - - +
389B ILE 3.1 4.7 + - - +
391B LYS* 1.3 71.3 - - - +
393B LYS* 1.3 57.7 + - - +
395B ILE* 2.7 30.5 + - - +
396B CYS* 3.0 11.0 + - - -
413B ILE* 3.7 19.1 - - + -
414B ILE* 5.7 0.7 - - + -
417B VAL* 3.8 16.8 - - + -
421B TRP* 4.1 19.5 - - + -
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Residues in contact with LYS 393 (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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389B ILE* 3.0 20.1 + - + +
390B LEU* 3.6 14.4 - - + +
392B VAL* 1.3 76.1 - - - +
394B GLU* 1.3 58.7 + - - +
396B CYS 3.4 3.2 + - - -
397B SER* 3.4 17.8 + - - -
414B ILE* 3.5 30.6 - - + +
417B VAL* 4.4 13.7 - - + -
418B ARG* 3.8 18.5 - - - +
422B GLU* 3.0 39.7 + - - -
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Residues in contact with GLU 394 (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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390B LEU 3.0 14.3 + - - +
391B LYS* 3.2 44.9 + - - +
392B VAL 3.0 0.4 - - - -
393B LYS* 1.3 75.8 - - - +
395B ILE* 1.3 62.9 + - - +
397B SER* 3.0 25.7 + - - -
504G PHE 5.6 0.7 - - - +
506G PRO* 4.1 21.1 - - - +
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Residues in contact with ILE 395 (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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362B ASN 4.9 3.6 - - - +
363B ILE* 4.2 34.2 - - + +
366B GLY* 4.1 27.4 - - - -
367B PHE* 5.3 4.9 - - + +
370B ILE* 5.7 0.9 - - + -
391B LYS* 3.0 40.6 - - + +
392B VAL* 2.7 16.7 + - - +
394B GLU* 1.3 77.6 - - + +
396B CYS* 1.3 59.6 + - - +
397B SER* 3.2 6.6 + - - -
399B ASP* 5.1 0.9 - - - +
410B LYS* 3.6 18.0 + - - -
503G PHE* 5.7 0.2 - - + -
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Residues in contact with CYS 396 (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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363B ILE* 4.8 8.7 - - - -
367B PHE* 5.1 0.7 - - - -
392B VAL* 3.0 16.5 + - - +
393B LYS 3.4 3.6 + - - -
394B GLU 3.3 0.2 - - - -
395B ILE* 1.3 78.2 - - - +
397B SER* 1.3 64.7 + - - +
398B PRO* 3.2 9.9 - - - +
410B LYS* 3.8 33.5 - - + +
413B ILE* 3.5 41.3 - - - -
414B ILE* 3.5 32.8 - - + +
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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