Contacts of the helix formed by residues 504 - 513 (chain M) in PDB entry 2DFS
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 GLY 504 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497M ASN 4.6 2.0 - - - -
498M LEU* 3.2 17.9 - - - -
499M ILE 4.2 1.3 - - - -
501M ALA* 3.0 18.7 + - - +
502M LYS 3.2 1.4 + - - -
503M MET* 1.3 80.2 - - - +
505M VAL* 1.3 60.1 + - - -
506M LEU 3.5 2.0 - - - -
507M ASP* 3.3 3.3 + - - +
508M LEU* 3.0 29.1 + - - +
531M HIS* 4.1 6.3 - - - -
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Residues in contact with VAL 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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452M PHE* 3.6 31.9 - - + -
498M LEU* 2.9 30.6 + - + +
499M ILE* 3.7 2.2 + - + +
504M GLY* 1.3 70.2 - - - +
506M LEU* 1.4 60.5 + - - +
509M LEU* 3.2 23.0 + - - +
523M TRP* 3.6 25.8 + - + -
527M LEU* 4.0 13.7 - - + -
531M HIS* 4.1 16.4 - - + +
538M PHE* 4.8 2.7 - - + -
548M PHE* 4.1 11.7 - - + -
550M ILE* 4.6 12.1 - - + -
564M PHE* 5.7 0.4 - - + -
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Residues in contact with LEU 506 (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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449M PHE* 4.7 5.6 - - + -
452M PHE* 3.8 22.4 - - + -
453M CYS* 5.5 3.4 - - - -
456M TYR* 3.5 37.0 - - + +
499M ILE* 3.3 29.3 + - + +
500M GLU* 4.7 4.9 - - + -
505M VAL* 1.4 73.0 - - + +
507M ASP* 1.3 59.1 + - - +
509M LEU* 3.4 20.2 + - + +
510M ASP* 2.9 34.2 + - - +
637M GLY* 4.6 28.9 - - - +
641M ARG* 5.2 5.2 - - + -
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Residues in contact with ASP 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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499M ILE 4.7 0.6 + - - -
500M GLU 5.7 0.9 - - - +
501M ALA 3.7 17.7 + - - +
502M LYS* 2.6 44.2 + - - +
503M MET* 2.7 30.3 + - - +
504M GLY 3.3 7.9 + - - +
506M LEU* 1.3 77.3 - - - +
508M LEU* 1.3 57.0 + - - +
510M ASP* 3.2 7.6 + - - +
511M GLU* 2.9 33.1 + - - +
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Residues in contact with LEU 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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503M MET* 3.6 38.8 - - + +
504M GLY 3.0 14.3 + - - +
505M VAL 4.2 0.4 - - - +
507M ASP* 1.3 75.1 - - - +
509M LEU* 1.3 56.9 + - - +
511M GLU* 3.5 10.4 - - + +
512M GLU* 3.0 29.3 + - - +
523M TRP* 3.6 16.6 - - + +
526M LYS* 4.2 30.0 - - + +
527M LEU* 4.1 6.3 - - + -
530M THR* 3.8 16.6 - - - +
531M HIS* 3.4 37.5 - - + +
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Residues in contact with LEU 509 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449M PHE* 3.9 19.5 - - + -
505M VAL 3.2 19.3 + - - +
506M LEU* 3.4 15.9 - - + +
508M LEU* 1.3 75.9 - - - +
510M ASP* 1.3 54.9 + - - +
512M GLU* 3.2 3.5 + - - +
513M CYS* 3.0 33.7 + - - -
523M TRP* 3.2 29.7 - - + +
564M PHE* 4.0 26.5 - - + +
565M LEU* 3.7 29.4 - - + -
568M ASN* 3.7 28.7 - - + +
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Residues in contact with ASP 510 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506M LEU* 2.9 18.8 + - - +
507M ASP* 3.7 8.5 - - - +
509M LEU* 1.3 74.7 - - - +
511M GLU* 1.4 61.7 + - - +
513M CYS* 3.5 11.3 + - - +
514M LYS* 3.5 19.4 + - - +
568M ASN* 2.7 31.8 + - - +
633M LYS* 5.1 5.0 - - - +
635M THR* 2.6 33.3 + - - +
637M GLY* 4.9 1.4 - - - -
638M HIS* 4.0 13.9 + - - +
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Residues in contact with GLU 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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502M LYS* 2.8 30.7 + - - +
503M MET* 5.3 2.9 - - + -
507M ASP* 2.9 24.9 + - - +
508M LEU* 3.5 17.9 - - + +
510M ASP* 1.4 71.6 - - - +
512M GLU* 1.4 62.3 + - - +
514M LYS* 2.6 53.3 + - - +
515M MET* 3.6 28.5 - - + +
526M LYS* 5.5 6.1 - - + +
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Residues in contact with GLU 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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508M LEU 3.0 17.6 + - - +
509M LEU 3.2 4.0 + - - +
511M GLU* 1.4 73.8 - - - +
513M CYS* 1.3 56.1 + - - +
515M MET* 3.1 45.4 + - - +
518M GLY* 3.9 11.7 - - - -
519M SER 3.9 13.0 - - - +
522M THR* 2.7 36.8 + - - +
523M TRP* 3.4 20.2 + - + -
526M LYS* 2.7 34.9 + - + +
565M LEU* 4.1 12.9 - - + +
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Residues in contact with CYS 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 LEU* 3.0 26.8 + - - +
510M ASP* 3.7 9.0 - - - +
511M GLU 3.2 0.4 - - - -
512M GLU* 1.3 76.5 - - - +
514M LYS* 1.3 55.9 + - - +
515M MET 3.5 3.0 - - - +
565M LEU* 3.8 41.3 - - - -
568M ASN* 3.6 22.2 - - - +
569M LYS* 4.7 13.8 - - + +
633M LYS* 3.3 31.5 + - - +
635M THR* 5.0 0.9 - - + -
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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