Contacts of the helix formed by residues 391 - 405 (chain O) in PDB entry 6FF7
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 TYR 391 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385O PHE* 3.6 34.5 - - + +
389O HIS* 3.2 12.9 + - + +
390O ALA* 1.3 69.9 - - - +
392O PHE* 1.3 53.5 + - - +
393O ALA 3.6 0.9 - - - -
394O HIS* 3.0 14.4 + - + +
395O ALA* 2.4 42.7 + - + +
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Residues in contact with PHE 392 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390O ALA 2.8 12.8 + - - +
391O TYR* 1.3 69.4 - - - +
393O ALA* 1.3 59.2 + - - +
395O ALA* 3.1 5.5 + - - +
396O ARG* 3.0 26.7 + - - +
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Residues in contact with ALA 393 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391O TYR 3.6 0.2 - - - -
392O PHE* 1.3 77.7 - - - +
394O HIS* 1.3 59.3 + - - +
396O ARG* 3.2 10.6 + - - +
397O LYS* 3.0 22.9 + - - +
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Residues in contact with HIS 394 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391O TYR* 3.0 11.1 + - + +
393O ALA* 1.3 75.8 - - - +
395O ALA* 1.3 59.7 + - - +
396O ARG 3.3 0.2 - - - -
397O LYS* 3.6 10.6 - - + +
398O VAL* 2.8 28.9 + - - +
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Residues in contact with ALA 395 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386O GLU* 5.0 13.5 - - + -
390O ALA 4.2 5.8 - - - +
391O TYR* 2.4 40.2 + - + +
392O PHE* 3.1 10.7 + - - +
394O HIS* 1.3 69.3 - - - +
396O ARG* 1.3 59.3 + - - +
398O VAL* 3.7 6.4 - - - +
399O TYR* 2.9 29.6 + - - +
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Residues in contact with ARG 396 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392O PHE 3.0 12.8 + - - +
393O ALA* 3.2 11.9 + - - +
395O ALA* 1.3 76.4 - - - +
397O LYS* 1.3 56.7 + - - +
399O TYR* 3.4 6.7 + - - +
400O GLU* 2.9 27.0 + - - +
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Residues in contact with LYS 397 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393O ALA 3.0 13.3 + - - +
394O HIS* 3.6 13.2 - - + +
395O ALA 3.3 0.2 - - - -
396O ARG* 1.3 77.8 - - - +
398O VAL* 1.3 56.1 + - - +
400O GLU* 3.2 9.8 + - - +
401O ARG* 2.9 26.0 + - - +
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Residues in contact with VAL 398 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382O TYR 4.9 12.6 - - - +
383O ALA* 5.4 10.3 - - + +
394O HIS 2.8 20.2 + - - +
395O ALA* 3.8 8.1 - - - +
396O ARG 3.4 0.2 - - - -
397O LYS* 1.3 72.6 - - - +
399O TYR* 1.3 57.7 + - - +
401O ARG* 3.2 9.6 + - - +
402O ALA* 2.8 26.3 + - - +
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Residues in contact with TYR 399 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395O ALA 2.9 18.3 + - - +
396O ARG* 3.7 7.4 - - - +
397O LYS 3.3 0.2 - - - -
398O VAL* 1.3 74.6 - - - +
400O GLU* 1.3 59.6 + - - +
402O ALA* 3.2 10.4 + - + +
403O VAL* 3.0 29.5 + - - +
419O PHE* 6.4 2.5 - - + -
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Residues in contact with GLU 400 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396O ARG 2.9 14.8 + - - +
397O LYS* 3.2 12.5 + - - +
399O TYR* 1.3 76.7 - - - +
401O ARG* 1.3 57.5 + - - +
403O VAL* 3.1 5.3 + - - +
404O GLU* 2.9 32.1 + - - +
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Residues in contact with ARG 401 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397O LYS 2.9 12.7 + - - +
398O VAL* 3.2 13.2 + - - +
400O GLU* 1.3 76.8 - - - +
402O ALA* 1.3 60.5 + - - +
403O VAL 3.5 0.2 + - - -
404O GLU* 4.7 2.5 - - - +
405O PHE* 3.8 23.0 + - - +
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Residues in contact with ALA 402 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379O TRP* 5.4 9.4 - - + +
383O ALA* 6.2 4.7 - - + -
398O VAL 2.8 13.8 + - - +
399O TYR* 3.2 14.5 + - - +
401O ARG* 1.3 77.0 - - - +
403O VAL* 1.3 58.7 + - - +
404O GLU 3.6 0.2 - - - -
405O PHE* 4.7 5.2 + - - +
406O PHE 5.6 1.2 - - - +
415O LEU* 5.3 13.2 - - + +
419O PHE* 6.5 0.9 - - + -
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Residues in contact with VAL 403 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399O TYR 3.0 15.7 + - - +
400O GLU* 3.1 4.9 + - - +
402O ALA* 1.3 80.1 - - - +
404O GLU* 1.3 62.0 + - - +
405O PHE 3.8 4.1 + - - +
407O GLY 5.5 1.9 - - - +
408O ASP* 6.0 1.2 - - - -
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Residues in contact with GLU 404 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400O GLU 2.9 15.1 + - - +
401O ARG* 3.9 3.3 + - - +
402O ALA 3.6 0.2 - - - -
403O VAL* 1.3 76.6 - - - +
405O PHE* 1.3 65.3 + - - +
408O ASP* 5.6 3.3 - - - +
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Residues in contact with PHE 405 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401O ARG 3.8 16.4 + - - +
402O ALA 4.7 4.0 + - - +
403O VAL 3.5 6.3 - - - +
404O GLU* 1.3 83.6 - - - +
406O PHE* 1.3 69.7 + - + +
407O GLY 3.6 8.1 + - - -
408O ASP* 4.1 5.0 + - - +
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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