Contacts of the helix formed by residues 405 - 416 (chain q) 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 PHE 405 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402q VAL* 3.3 15.2 - - - +
403q PHE 3.0 0.4 - - - -
404q PRO* 1.3 78.3 - - - +
406q ARG* 1.3 63.0 + - - +
407q GLU 3.2 2.7 - - - -
408q GLU* 2.8 23.8 + - + +
409q LEU* 2.9 15.7 + - + +
573q ILE* 5.9 7.6 - - + -
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Residues in contact with ARG 406 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402q VAL 3.3 7.5 + - - +
403q PHE* 3.0 20.1 + - - +
404q PRO 3.4 0.6 - - - -
405q PHE* 1.3 75.4 - - - +
407q GLU* 1.3 62.4 + - - +
409q LEU* 3.2 8.2 + - - +
410q LEU* 2.9 23.0 + - - +
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Residues in contact with GLU 407 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404q PRO 5.1 0.8 + - - -
405q PHE 3.2 0.8 - - - -
406q ARG* 1.3 77.0 - - - +
408q GLU* 1.3 63.8 + - - +
410q LEU* 3.1 9.5 + - - +
411q ALA* 3.0 22.5 + - - +
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Residues in contact with GLU 408 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405q PHE* 2.8 17.9 + - + +
407q GLU* 1.3 79.6 - - - +
409q LEU* 1.3 62.2 - - - +
411q ALA* 3.4 8.5 + - - +
412q ALA* 3.2 19.9 + - - +
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Residues in contact with LEU 409 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405q PHE* 2.9 14.1 + - + +
406q ARG* 3.5 12.3 - - - +
408q GLU* 1.3 75.5 - - - +
410q LEU* 1.3 64.6 + - - +
412q ALA* 3.1 8.1 + - - +
413q ILE* 2.9 24.1 + - - +
571q PHE* 5.6 9.2 - - + -
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Residues in contact with LEU 410 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406q ARG 2.9 13.3 + - - +
407q GLU* 3.1 11.2 + - - +
409q LEU* 1.3 75.8 - - - +
411q ALA* 1.3 53.3 + - - +
413q ILE* 3.1 7.3 + - - +
414q ALA* 2.8 37.2 + - - +
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Residues in contact with ALA 411 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407q GLU 3.0 12.0 + - - +
408q GLU* 3.6 11.4 - - - +
410q LEU* 1.3 76.2 - - - +
412q ALA* 1.3 63.4 + - - +
414q ALA* 3.2 6.8 + - - +
415q ASN* 3.0 25.8 + - - +
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Residues in contact with ALA 412 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408q GLU 3.2 9.0 + - - +
409q LEU* 3.1 10.2 + - - +
411q ALA* 1.3 79.0 - - - +
413q ILE* 1.3 63.8 + - - +
415q ASN* 3.3 5.4 + - - +
416q HIS* 3.0 27.4 + - - +
419q LEU* 5.1 15.1 - - + +
569q PRO* 5.5 10.1 - - + -
570q VAL 6.5 0.9 - - - -
571q PHE* 5.5 10.1 - - + -
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Residues in contact with ILE 413 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409q LEU 2.9 13.6 + - - +
410q LEU* 3.5 10.3 - - - +
412q ALA* 1.3 78.4 - - - +
414q ALA* 1.3 62.5 + - - +
416q HIS 3.2 18.5 - - - +
419q LEU* 5.6 5.4 - - - -
436q TYR* 6.5 1.6 - - + -
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Residues in contact with ALA 414 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410q LEU 2.8 17.9 + - - +
411q ALA* 3.6 6.7 - - - +
413q ILE* 1.3 78.4 - - - +
415q ASN* 1.3 61.5 - - - +
416q HIS 4.9 0.3 - - - +
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Residues in contact with ASN 415 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411q ALA 3.0 16.7 + - - +
412q ALA* 3.8 5.2 - - - +
414q ALA* 1.3 79.5 - - - +
416q HIS* 1.3 61.8 + - + +
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Residues in contact with HIS 416 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412q ALA 3.0 14.0 + - - +
413q ILE* 3.2 17.3 - - - +
414q ALA 5.2 0.2 - - - -
415q ASN* 1.3 81.4 - - + +
417q GLN* 1.3 64.7 + - - +
418q VAL* 3.7 21.3 - - - +
419q LEU* 5.3 3.2 - - + +
548q LYS* 4.9 5.0 - - - +
569q PRO* 5.4 10.5 - - + -
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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