Contacts of the helix formed by residues 494 - 505 (chain f) in PDB entry 5T0J
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 ALA 494 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467f GLU* 3.8 2.0 + - - -
490f HIS* 6.0 4.0 - - - +
491f GLN* 3.1 14.9 + - - +
492f GLY 4.1 0.4 - - - +
493f VAL* 1.3 77.7 - - - +
495f VAL* 1.3 63.1 + - - +
496f LEU* 3.1 5.3 + - - +
497f GLY* 3.5 11.0 + - - +
498f ILE* 3.7 10.9 + - - +
524f GLU* 3.3 26.0 - - - +
527f LEU* 3.6 28.6 - - + +
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Residues in contact with VAL 495 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431f PHE* 4.7 24.7 - - + -
435f LEU* 6.3 1.6 - - + -
467f GLU* 3.1 16.7 + - + +
468f GLU* 5.2 5.2 - - + -
471f ASP* 3.9 12.5 - - - +
493f VAL* 3.1 27.5 - - + +
494f ALA* 1.3 78.7 - - - +
496f LEU* 1.3 61.7 + - - +
497f GLY 3.4 0.2 - - - -
498f ILE* 3.3 21.0 - - + +
499f ALA* 3.6 12.1 + - + +
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Residues in contact with LEU 496 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467f GLU* 3.1 52.5 + - - +
470f LYS* 3.6 38.1 - - + +
471f ASP* 3.3 16.5 - - - +
489f ALA* 5.3 6.1 - - + -
490f HIS* 5.4 3.1 - - - +
491f GLN* 4.1 30.5 - - + +
494f ALA* 3.1 2.1 - - - +
495f VAL* 1.3 78.7 - - - +
497f GLY* 1.3 58.3 + - - +
499f ALA* 3.5 1.7 + - - -
500f LEU* 3.0 33.9 + - + +
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Residues in contact with GLY 497 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487f MET* 5.7 8.5 - - - -
490f HIS* 6.0 5.8 - - - -
494f ALA* 3.5 8.4 + - - +
495f VAL 3.4 0.4 - - - -
496f LEU* 1.3 79.0 - - - +
498f ILE* 1.3 61.0 + - - +
500f LEU* 3.8 8.6 - - - +
501f ILE* 3.4 25.1 + - - +
519f LEU* 4.4 12.7 - - - +
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Residues in contact with ILE 498 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494f ALA 3.7 13.4 + - - +
495f VAL* 3.3 24.2 - - + +
497f GLY* 1.3 74.9 - - - +
499f ALA* 1.3 64.6 + - + +
500f LEU 3.4 0.5 + - - -
501f ILE* 3.5 14.5 - - + +
502f ALA* 3.6 9.6 + - + +
516f PHE* 5.5 0.9 - - + -
519f LEU* 5.6 5.8 - - + -
527f LEU* 5.6 5.1 - - + +
530f ALA* 3.2 38.6 - - + +
531f VAL* 3.5 10.3 - - - +
533f LEU* 3.9 14.4 - - + -
534f ALA* 3.5 33.4 - - + +
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Residues in contact with ALA 499 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471f ASP* 4.1 23.3 - - + +
474f GLU* 2.9 26.2 - - - +
495f VAL* 3.8 15.0 - - + +
496f LEU 3.5 1.6 + - - +
497f GLY 3.4 0.2 - - - -
498f ILE* 1.3 84.8 - - + +
500f LEU* 1.3 59.2 + - - +
501f ILE 3.5 0.2 - - - -
502f ALA* 4.3 4.2 - - - +
503f MET* 3.6 12.5 + - - +
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Residues in contact with LEU 500 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470f LYS* 5.0 7.2 - - - +
471f ASP* 5.8 0.9 - - - +
474f GLU* 3.6 15.3 - - + -
483f ALA* 3.2 43.8 - - + +
484f PRO* 4.2 2.7 - - + -
486f ASP* 3.8 13.9 - - + +
487f MET* 3.7 43.5 - - + +
496f LEU* 3.0 21.5 + - + +
497f GLY* 3.8 5.6 - - - +
498f ILE 3.2 0.4 - - - -
499f ALA* 1.3 77.2 - - - +
501f ILE* 1.3 68.0 + - + +
504f GLY* 3.0 29.3 + - - -
505f GLU* 5.3 0.7 - - - +
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Residues in contact with ILE 501 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484f PRO* 6.5 0.4 - - + -
497f GLY 3.4 16.9 + - - +
498f ILE* 3.5 10.3 - - + +
500f LEU* 1.3 84.2 - - + +
502f ALA* 1.3 70.9 - - - +
505f GLU* 3.5 29.6 + - + +
512f ALA* 3.7 29.8 - - + -
515f THR* 4.0 28.5 - - + -
516f PHE* 4.8 12.3 - - + +
519f LEU* 4.2 17.5 - - + -
534f ALA* 4.3 14.4 - - + -
538f ILE* 4.7 6.8 - - + +
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Residues in contact with ALA 502 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498f ILE 3.6 13.8 + - - +
499f ALA* 4.5 4.0 - - - +
500f LEU 3.5 0.4 - - - -
501f ILE* 1.3 86.4 - - - +
503f MET* 1.3 59.6 + - + +
505f GLU 3.1 18.2 - - - +
533f LEU 5.3 0.7 - - - +
534f ALA* 4.0 27.1 - - + +
537f LEU* 3.6 30.5 - - + +
538f ILE* 4.4 6.0 - - - +
669f ARG* 4.2 2.4 + - - -
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Residues in contact with MET 503 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474f GLU* 3.3 14.1 - - - +
475f LYS* 3.6 50.9 - - + +
477f ASP 5.0 0.9 - - - +
478f LYS* 3.9 31.6 - - + -
479f ASP 4.2 8.7 + - - -
499f ALA 3.6 8.6 + - - +
502f ALA* 1.3 75.9 - - + +
504f GLY* 1.3 65.3 + - - +
505f GLU 3.1 7.0 + - - -
506f GLU* 4.4 4.5 + - - +
537f LEU* 4.1 4.0 - - + -
669f ARG* 2.6 49.3 + - - +
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Residues in contact with GLY 504 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474f GLU* 2.7 20.2 + - - -
477f ASP 5.2 1.6 - - - -
479f ASP* 3.2 22.9 - - - -
480f LYS 4.2 1.6 + - - -
481f LYS 4.5 1.2 + - - -
483f ALA* 3.8 16.8 - - - +
500f LEU 3.0 17.4 + - - -
503f MET* 1.3 74.8 - - - +
505f GLU* 1.3 72.7 + - - +
506f GLU 4.1 0.2 - - - -
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Residues in contact with GLU 505 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479f ASP* 4.5 1.9 - - - +
481f LYS* 2.7 39.2 + - - +
483f ALA* 5.9 0.2 - - + -
484f PRO* 3.3 35.1 - - + +
500f LEU 5.3 0.2 - - - +
501f ILE* 3.5 32.9 + - + +
502f ALA 3.1 16.1 - - - +
503f MET 3.1 1.1 - - - -
504f GLY* 1.3 84.9 - - - +
506f GLU* 1.3 60.7 + - - +
507f ILE* 4.1 15.5 + - + +
510f GLU 5.6 0.4 - - - +
512f ALA* 5.2 8.3 - - + -
538f ILE* 4.1 13.9 - - + +
669f ARG* 4.1 2.1 + - - -
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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