Contacts of the helix formed by residues 508 - 520 (chain F) in PDB entry 2A07
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 508 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F PRO* 4.1 24.2 - - + +
507F PHE* 1.3 79.5 - - - +
509F TYR* 1.3 64.7 + - - +
510F ALA* 3.2 10.9 + - - +
511F THR* 3.1 30.7 + - + +
512F LEU* 3.1 22.8 + - - +
540G TYR* 3.6 11.2 - - - -
584G ARG* 4.1 8.1 + - - +
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Residues in contact with TYR 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508F THR* 1.3 72.9 - - - +
510F ALA* 1.3 57.5 + - - +
512F LEU* 3.7 6.3 - - + +
513F ILE* 2.9 42.2 + - + +
534F PHE* 4.1 17.9 - + - -
538F PHE* 4.8 5.6 - + - -
540G TYR* 3.4 21.7 + + - -
544G ASN* 3.2 33.2 + - + +
547G THR* 3.4 11.1 + - - -
548G TRP* 3.7 20.7 - - + -
551G ALA* 3.2 35.0 - - + +
552G VAL* 4.4 5.2 - - + -
555G ASN* 3.6 27.1 - - + +
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Residues in contact with ALA 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508F THR* 3.0 9.3 + - - +
509F TYR* 1.3 80.7 - - - +
511F THR* 1.3 62.8 + - - +
513F ILE 3.4 0.2 + - - -
514F ARG* 3.0 21.3 + - - +
555G ASN* 3.9 13.3 + - - +
559G HIS* 4.8 9.2 - - + +
561G CYS* 5.9 0.9 - - - -
562G PHE* 3.4 28.7 - - + -
580G TYR* 4.2 6.9 - - + -
584G ARG* 4.1 11.4 - - - +
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Residues in contact with THR 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505F PRO 6.2 0.2 - - - +
506F PRO 4.6 3.0 + - - +
507F PHE* 3.8 15.3 - - - +
508F THR* 3.1 30.1 + - + +
510F ALA* 1.3 75.6 - - - +
512F LEU* 1.3 60.5 + - - +
514F ARG* 3.4 6.6 + - - +
515F GLN* 2.9 29.1 + - - +
580G TYR* 3.3 13.2 - - - +
584G ARG* 2.9 34.1 - - - +
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Residues in contact with LEU 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507F PHE* 3.6 28.5 - - + -
508F THR 3.1 18.0 + - - +
509F TYR* 3.7 1.3 - - + +
511F THR* 1.3 79.7 + - - +
513F ILE* 1.3 65.7 + - - +
515F GLN* 3.2 6.6 + - - +
516F ALA* 3.0 20.1 + - - +
533F TRP* 3.6 31.1 - - + -
534F PHE* 3.6 29.4 - - + -
537F THR* 4.7 1.1 - - + -
538F PHE* 5.0 1.3 - - + -
507G PHE* 4.1 11.7 - - + -
540G TYR* 4.1 17.5 - - + +
541G PHE* 3.9 28.0 - - + -
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Residues in contact with ILE 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F TYR* 2.9 23.2 + - + +
512F LEU* 1.3 75.4 - - - +
514F ARG* 1.3 62.6 + - - +
516F ALA* 3.3 4.4 + - - +
517F ILE* 3.1 34.2 + - + +
530F ILE* 4.6 7.4 - - + -
534F PHE* 3.9 21.5 - - + -
552G VAL* 4.1 25.1 - - + -
555G ASN* 3.9 27.4 - - + -
556G LEU* 3.9 23.8 - - + -
562G PHE* 3.5 28.3 - - + -
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Residues in contact with ARG 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510F ALA 3.0 16.6 + - - +
511F THR* 3.7 6.8 + - - +
513F ILE* 1.3 78.2 - - - +
515F GLN* 1.3 59.6 + - - +
517F ILE* 3.4 0.9 + - - +
518F MET* 2.8 76.8 + - + +
562G PHE* 4.1 2.9 - - + -
575G VAL* 4.0 22.2 - - + -
577G GLU* 3.2 25.9 + - - -
580G TYR* 3.2 48.7 + - + -
581G GLN* 5.4 2.8 - - - +
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Residues in contact with GLN 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507F PHE* 4.5 5.0 - - - -
511F THR 2.9 18.3 + - - +
512F LEU* 3.2 11.3 + - - +
514F ARG* 1.3 80.1 - - - +
516F ALA* 1.3 56.7 + - - +
518F MET* 4.6 4.5 - - - -
519F GLU* 2.8 69.0 + - + +
533F TRP* 3.9 9.1 - - + -
506G PRO 3.8 14.6 + - - -
507G PHE* 3.3 40.3 - - - -
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Residues in contact with ALA 516 (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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512F LEU 3.0 9.9 + - - +
513F ILE* 3.3 10.1 + - - +
515F GLN* 1.3 76.1 - - - +
517F ILE* 1.3 63.8 - - + +
519F GLU* 4.1 1.8 - - - +
520F SER* 3.4 15.9 + - - -
525F LEU* 3.4 23.2 - - + +
530F ILE* 5.3 4.5 - - + -
533F TRP* 3.4 49.5 - - + +
534F PHE* 5.2 2.2 - - + -
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Residues in contact with ILE 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513F ILE* 3.1 30.6 + - + +
516F ALA* 1.3 77.3 - - - +
518F MET* 1.3 62.3 + - + +
520F SER* 2.5 25.3 + - - -
523F ARG* 3.3 32.8 - - + +
524F GLN* 3.8 3.8 - - - +
525F LEU* 4.1 14.1 - - + -
530F ILE* 4.5 5.8 - - + -
562G PHE* 4.8 2.0 - - + -
573G TRP* 3.6 33.9 - - + +
574G THR 4.0 3.1 - - - +
575G VAL* 3.6 37.2 - - + +
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Residues in contact with MET 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514F ARG* 2.8 74.6 + - + +
515F GLN* 3.9 4.9 - - - +
517F ILE* 1.3 78.3 - - + +
519F GLU* 1.3 62.4 + - + +
520F SER 3.2 5.1 + - - +
523F ARG* 3.1 56.0 + - - +
575G VAL* 5.2 6.5 - - + -
577G GLU* 4.3 10.8 - - + +
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Residues in contact with GLU 519 (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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515F GLN* 2.8 53.7 + - + +
516F ALA* 4.1 4.0 - - - +
518F MET* 1.3 77.2 - - + +
520F SER* 1.3 62.3 + - - +
521F SER 4.0 0.5 + - - -
533F TRP* 4.1 10.9 + - - +
506G PRO* 3.9 26.8 - - - +
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Residues in contact with SER 520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516F ALA 3.4 8.8 + - - -
517F ILE* 2.5 22.2 + - - -
518F MET 3.2 6.6 - - - +
519F GLU* 1.3 82.0 - - - +
521F SER* 1.3 66.6 + - - +
522F ASP 4.6 0.4 - - - -
523F ARG* 3.1 8.8 + - - +
524F GLN 3.1 21.6 + - - -
525F LEU* 3.5 29.2 - - - -
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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