Contacts of the helix formed by residues 449 - 459 (chain T) 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 GLU 449 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1965A HIS* 4.3 28.1 + - + +
447T LYS 3.7 4.8 + - - +
448T THR* 1.3 72.2 - - - +
450T ILE* 1.3 58.3 + - - +
451T ASN* 4.1 3.1 - - - +
452T LEU* 3.8 24.9 - - + +
453T VAL* 3.9 16.6 + - - +
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Residues in contact with ILE 450 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448T THR* 3.1 13.3 + - - +
449T GLU* 1.3 71.9 - - - +
451T ASN* 1.3 61.1 + - - +
452T LEU 3.3 1.1 - - - -
453T VAL* 4.6 3.6 - - - +
454T SER* 2.9 32.4 - - - +
159t TYR* 3.7 16.6 - - + +
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Residues in contact with ASN 451 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448T THR 4.9 0.2 + - - -
449T GLU* 3.4 2.7 - - + +
450T ILE* 1.3 80.1 - - - +
452T LEU* 1.3 63.4 + - - +
454T SER* 4.3 1.3 - - - -
455T PHE* 3.4 18.9 + - - +
149t ASP* 5.0 18.6 - - + -
159t TYR* 3.3 28.3 - - + +
160t GLN* 5.7 1.9 - - - -
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Residues in contact with LEU 452 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449T GLU* 3.8 21.7 - - + +
450T ILE* 3.3 0.6 - - - +
451T ASN* 1.3 76.3 - - - +
453T VAL* 1.3 59.1 + - - +
455T PHE* 2.7 28.4 + - - +
456T ARG* 2.9 13.1 + - - +
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Residues in contact with VAL 453 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965A HIS* 6.3 1.6 - - + -
449T GLU 3.9 16.4 + - - +
450T ILE* 5.0 1.8 - - - -
452T LEU* 1.3 79.4 - - - +
454T SER* 1.3 57.3 + - - +
456T ARG* 3.2 9.9 + - + +
457T ARG* 2.9 29.3 + - - +
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Residues in contact with SER 454 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450T ILE* 2.9 26.7 + - - +
451T ASN* 4.4 1.8 - - - -
452T LEU 3.1 1.0 + - - -
453T VAL* 1.3 78.6 - - - +
455T PHE* 1.3 61.3 + - - +
457T ARG* 3.8 11.6 + - - +
458T THR* 3.9 11.1 + - - -
159t TYR* 4.9 9.0 - - - -
160t GLN* 5.8 7.6 - - - -
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Residues in contact with PHE 455 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451T ASN 3.4 13.1 + - - +
452T LEU* 2.7 17.5 + - - +
454T SER* 1.3 69.5 - - - +
456T ARG* 1.3 62.5 + - - +
457T ARG 2.9 6.0 + - - -
458T THR* 3.0 14.0 + - - -
459T ILE* 3.5 10.7 + - - +
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Residues in contact with ARG 456 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452T LEU 2.9 12.1 + - - +
453T VAL* 3.2 12.3 + - + +
455T PHE* 1.3 75.3 - - - +
457T ARG* 1.3 61.3 + - - +
459T ILE* 4.3 4.2 - - - +
460T TYR* 3.6 18.4 + - - +
492T MET* 5.2 17.8 - - + +
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Residues in contact with ARG 457 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476A GLN 6.1 0.4 - - - +
453T VAL 2.9 15.6 + - - +
454T SER* 3.9 9.9 - - - +
455T PHE 2.9 0.6 + - - -
456T ARG* 1.3 79.2 - - - +
458T THR* 1.3 59.7 + - - +
460T TYR* 3.1 20.4 + - - +
461T LEU* 3.3 12.5 + - - +
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Residues in contact with THR 458 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454T SER 3.9 6.7 + - - -
455T PHE* 3.0 7.8 + - - -
457T ARG* 1.3 79.1 - - - +
459T ILE* 1.3 57.3 + - - +
460T TYR 3.2 1.3 - - - -
461T LEU* 3.6 9.9 - - - -
462T ALA* 2.9 26.5 + - - +
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Residues in contact with ILE 459 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455T PHE 3.5 10.4 + - - +
456T ARG* 4.3 4.0 - - - +
457T ARG 3.3 0.4 - - - -
458T THR* 1.3 75.9 - - - +
460T TYR* 1.3 57.8 + - - +
461T LEU 3.0 4.3 - - - -
462T ALA* 4.4 8.1 - - + +
463T ILE* 4.1 15.2 - - - +
476T LEU* 6.3 3.6 - - + -
489T LEU* 6.1 5.6 - - + -
492T MET* 5.3 16.7 - - + +
493T ILE* 6.1 0.5 - - - -
496T CYS* 5.5 4.0 - - - +
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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