Contacts of the helix formed by residues 503 - 513 (chain M) 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 THR 503 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501M GLN* 3.1 5.8 - - - +
502M SER* 1.3 76.5 - - - +
504M LYS* 1.3 58.4 + - - +
505M ALA 3.3 2.2 - - - -
506M VAL* 3.4 13.8 + - - +
507M TYR* 2.9 25.5 + - - +
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Residues in contact with LYS 504 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491M ALA* 4.2 22.0 - - + -
492M ASP* 4.9 7.3 - - + +
500M PHE* 4.3 5.4 - - + -
501M GLN* 2.9 33.3 + - + +
503M THR* 1.3 76.0 - - - +
505M ALA* 1.3 58.6 + - - +
507M TYR* 3.0 11.2 + - + +
508M ASP* 2.9 27.0 + - - +
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Residues in contact with ALA 505 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492M ASP* 5.4 6.6 - - + +
501M GLN 4.2 3.0 + - - +
502M SER 4.3 7.4 + - - +
503M THR 3.3 0.6 - - - -
504M LYS* 1.3 78.4 - - - +
506M VAL* 1.3 56.7 + - - +
508M ASP* 3.2 8.0 + - - +
509M ARG* 2.9 28.9 + - - +
523M ASN 5.5 1.8 - - - +
526M MET* 5.4 4.3 - - + -
527M PHE* 4.4 28.7 - - + +
530M GLU* 5.9 4.5 - - + -
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Residues in contact with VAL 506 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502M SER 4.9 1.3 + - - +
503M THR* 3.4 17.0 + - - +
504M LYS 3.3 0.2 - - - -
505M ALA* 1.3 78.0 - - - +
507M TYR* 1.3 57.6 + - - +
508M ASP 3.3 0.2 - - - -
509M ARG* 3.9 7.3 - - - +
510M ILE* 2.9 29.5 + - - +
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Residues in contact with TYR 507 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487M TRP* 4.8 4.3 - - + +
503M THR 2.9 14.6 + - - +
504M LYS* 3.0 17.0 + - + +
506M VAL* 1.3 76.6 - - - +
508M ASP* 1.3 58.3 + - - +
510M ILE* 3.8 4.4 - - - +
511M LEU* 2.9 25.3 + - - +
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Residues in contact with ASP 508 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484M LEU* 5.4 7.6 - - + +
487M TRP* 4.6 14.6 - - + +
488M SER* 5.8 1.6 - - - +
492M ASP* 6.1 4.3 - - + -
504M LYS 2.9 11.6 + - - +
505M ALA* 3.6 8.7 - - - +
507M TYR* 1.3 75.8 - - - +
509M ARG* 1.3 59.5 + - - +
511M LEU* 2.9 22.4 + - - +
512M ASP* 2.9 14.9 + - - +
523M ASN* 6.3 3.6 - - + -
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Residues in contact with ARG 509 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505M ALA 2.9 15.8 + - - +
506M VAL* 4.2 7.6 - - - +
508M ASP* 1.3 76.0 - - - +
510M ILE* 1.3 57.6 + - - +
512M ASP* 3.6 6.8 + - - +
513M LEU* 3.1 20.8 + - - -
464O ASP* 4.7 12.0 - - + +
466O ARG* 5.6 10.8 - - + -
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Residues in contact with ILE 510 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506M VAL 2.9 20.9 + - - +
507M TYR* 3.8 6.5 - - - +
509M ARG* 1.3 73.5 - - - +
511M LEU* 1.3 64.6 + - - +
513M LEU* 3.3 21.0 + - - +
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Residues in contact with LEU 511 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479M ARG* 4.2 5.9 - - - +
483M SER* 4.0 30.0 - - - +
484M LEU* 4.8 2.7 - - - -
487M TRP* 4.0 18.8 - - + -
507M TYR 2.9 20.0 + - - +
508M ASP* 2.9 14.2 + - - +
510M ILE* 1.3 76.4 - - - +
512M ASP* 1.3 62.8 + - - +
513M LEU* 4.2 2.6 - - - +
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Residues in contact with ASP 512 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479M ARG* 5.4 2.9 - - - +
480M VAL* 4.6 16.7 + - + +
484M LEU* 5.4 5.2 - - + +
508M ASP 2.9 11.0 + - - +
509M ARG* 3.9 8.5 - - - +
511M LEU* 1.3 75.1 - - - +
513M LEU* 1.3 60.1 + - - +
514M ARG* 2.8 18.7 + - - +
515M ILE* 4.2 6.8 + - - +
516M ALA* 3.7 36.6 - - + +
464O ASP* 5.7 0.4 - - + +
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Residues in contact with LEU 513 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509M ARG 3.1 14.3 + - - -
510M ILE* 3.3 19.7 + - - +
511M LEU 4.2 3.1 - - - +
512M ASP* 1.3 75.5 - - - +
514M ARG* 1.3 57.6 + - - +
427O LYS* 5.4 8.0 - - - +
428O GLU* 5.7 5.0 + - - +
464O ASP* 4.5 7.0 - - - +
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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