Contacts of the helix formed by residues 670 - 677 (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 MET 670 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226f PHE* 5.6 13.7 - - + -
405f LEU* 6.1 2.9 - - + -
572f MET* 5.8 4.5 - - + -
663f VAL* 3.9 38.9 + - + +
668f PRO* 4.3 1.3 - - - -
669f ARG* 1.3 70.9 - - - +
671f LEU* 1.3 61.5 + - - +
672f VAL* 3.4 24.2 - - + +
673f THR* 3.0 36.1 + - + +
674f PHE* 3.2 19.6 - - + -
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Residues in contact with LEU 671 (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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401f LEU* 4.5 4.4 - - + +
404f GLY 4.9 4.0 - - - +
405f LEU* 3.7 45.9 - - + +
408f LEU* 6.2 4.9 - - + -
440f ALA* 5.4 14.1 - - + -
475f LYS* 5.8 9.2 - - + +
669f ARG* 3.3 17.0 + - + +
670f MET* 1.3 73.2 - - - +
672f VAL* 1.3 61.0 + - - +
673f THR 3.4 0.7 - - - -
674f PHE* 4.3 11.4 - - + +
675f ASP* 3.2 27.2 + - - +
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Residues in contact with VAL 672 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365f MET* 3.8 30.5 - - + -
398f TRP* 5.9 0.7 - - + -
401f LEU* 3.8 23.8 - - + -
405f LEU* 4.0 22.4 - - + -
670f MET* 3.8 25.6 - - + -
671f LEU* 1.3 77.4 - - - +
673f THR* 1.3 71.6 + - + +
675f ASP 4.2 0.2 - - - -
676f GLU* 3.5 28.6 + - + +
694f VAL* 4.0 20.2 - - + +
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Residues in contact with THR 673 (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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572f MET* 4.1 27.8 - - - +
670f MET* 3.0 30.7 + - + +
672f VAL* 1.3 81.7 - - + +
674f PHE* 1.3 84.1 + - - +
676f GLU* 4.6 0.4 - - - +
677f GLU* 3.2 36.9 + - - +
694f VAL* 4.1 26.7 - - + -
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Residues in contact with PHE 674 (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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536f ALA* 4.3 21.1 - - + -
537f LEU* 3.5 33.4 - - + -
572f MET* 4.6 14.1 - - + -
669f ARG* 3.6 30.1 - - + -
670f MET* 3.2 25.2 + - + +
671f LEU* 4.1 9.6 + - + +
673f THR* 1.3 90.1 + - - +
675f ASP* 1.3 67.5 + - - +
677f GLU* 4.0 5.6 + - + +
678f LEU* 3.6 24.8 + - + +
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Residues in contact with ASP 675 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397f ARG 4.4 1.2 - - - +
401f LEU* 3.2 26.7 - - + +
435f LEU* 5.5 0.9 - - - +
436f VAL* 3.1 40.6 - - + +
671f LEU 3.2 20.7 + - - +
672f VAL* 4.1 4.0 - - - +
673f THR 3.3 0.2 - - - -
674f PHE* 1.3 80.8 - - - +
676f GLU* 1.3 81.2 + - - +
677f GLU 3.4 0.2 + - - -
678f LEU* 3.6 11.4 + - - +
679f ARG* 2.4 40.6 + - - -
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Residues in contact with GLU 676 (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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397f ARG* 5.6 0.9 - - - +
398f TRP* 3.2 38.7 + - + -
672f VAL* 3.5 20.2 + - - +
673f THR 4.6 0.2 - - - +
675f ASP* 1.3 100.7 - - - +
677f GLU* 1.3 64.0 + - + +
678f LEU 3.0 1.9 + - - -
679f ARG* 3.1 26.8 + - - +
680f PRO* 3.1 15.9 - - - +
690f ALA* 3.2 34.2 - - - +
691f VAL* 3.3 26.1 - - + +
694f VAL* 5.2 4.7 - - + -
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Residues in contact with GLU 677 (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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564f TYR* 6.0 0.2 - - - -
568f PHE* 3.1 45.6 - - + -
601f PHE* 5.0 8.5 - - - -
605f LEU* 5.4 7.5 - - - +
673f THR* 3.2 30.6 + - - +
674f PHE* 4.6 4.0 - - + +
675f ASP 3.3 0.8 - - - -
676f GLU* 1.3 75.3 - - + +
678f LEU* 1.3 60.6 + - + +
679f ARG 3.3 0.2 - - - -
680f PRO* 3.3 21.0 - - - +
681f LEU* 4.0 12.5 - - - +
691f VAL* 3.3 24.9 - - + +
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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