Contacts of the helix formed by residues 500 - 509 (chain A) in PDB entry 6EJ9
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 ARG 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A LEU 5.0 0.6 + - - -
409A LEU* 3.9 33.3 + - + +
411A MET 5.5 2.4 + - - -
412A THR* 6.3 0.4 - - - +
414A TRP 4.0 4.4 + - - -
415A PRO* 4.5 3.3 - - - +
416A TRP* 3.3 79.7 + - + +
417A ASP* 3.0 18.9 + - - +
499A ASN* 1.3 73.6 - - - +
501A ARG* 1.3 57.8 + - - +
503A VAL* 3.3 1.6 + - - +
504A GLU* 2.9 55.8 + - - +
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Residues in contact with ARG 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ASP* 6.1 0.9 - - - -
499A ASN* 3.2 11.0 + - - +
500A ARG* 1.3 80.2 - - - +
502A PHE* 1.3 59.4 + - - +
504A GLU* 3.5 20.2 + - - +
505A TYR* 3.2 19.9 + - - +
541A HIS* 4.0 30.6 + - + +
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ASN* 3.7 28.5 - - - +
498A LEU* 4.0 30.3 - - + -
499A ASN* 3.0 16.8 + - - +
501A ARG* 1.3 75.8 - - - +
503A VAL* 1.3 67.7 + - - +
505A TYR* 3.2 16.0 + + - -
506A VAL* 2.9 46.4 + - + +
532A PHE* 4.2 13.2 - + - -
535A VAL* 4.2 6.1 - - + -
536A LEU* 3.7 48.2 - - + -
539A SER* 4.3 2.5 - - - -
541A HIS* 4.1 19.5 - - + -
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Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A MET* 3.6 44.4 - - + -
409A LEU* 4.0 9.4 - - + -
416A TRP* 4.0 27.4 - - + -
419A PHE* 4.2 11.4 - - + -
498A LEU* 4.0 21.1 - - + -
499A ASN 3.2 14.8 + - - +
500A ARG 3.7 5.8 - - - +
502A PHE* 1.3 74.6 - - - +
504A GLU* 1.3 62.6 + - - +
506A VAL* 3.4 6.5 + - - +
507A THR* 2.9 30.3 + - - -
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A LEU* 3.6 27.4 - - + +
500A ARG* 2.9 44.3 + - - +
501A ARG* 3.5 24.8 + - - +
502A PHE 3.2 0.2 - - - -
503A VAL* 1.3 76.3 - - - +
505A TYR* 1.3 62.0 + - - +
507A THR* 3.2 1.0 + - - -
508A PHE* 3.0 37.4 + - + +
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Residues in contact with TYR 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A PHE* 4.6 0.3 - - - -
501A ARG 3.2 5.2 + - - +
502A PHE* 3.2 23.9 + + - +
504A GLU* 1.3 78.9 - - - +
506A VAL* 1.3 66.6 + - + +
509A SER* 3.0 44.8 + - - +
511A ASP* 2.7 31.5 + - - -
513A LEU* 4.0 7.4 - - - +
514A VAL* 3.6 20.4 - - + +
535A VAL* 4.0 7.4 - - + -
539A SER* 3.6 30.8 - - - -
540A PRO* 3.7 16.6 - - + +
541A HIS* 3.7 28.7 - + + +
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LEU* 3.7 29.4 - - + -
405A MET* 4.9 3.4 - - - -
498A LEU* 6.2 0.2 - - + -
502A PHE* 2.9 52.1 + - + +
503A VAL* 3.8 7.2 - - - +
505A TYR* 1.3 81.5 - - + +
507A THR* 1.3 62.1 + - - +
514A VAL* 3.6 11.3 - - + +
518A LYS* 2.9 24.5 + - - -
531A PHE* 4.0 17.9 - - + -
532A PHE* 4.5 12.3 - - + -
535A VAL* 4.4 9.2 - - + -
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Residues in contact with THR 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LEU* 4.9 4.8 + - - +
405A MET* 3.9 15.9 - - - +
406A ARG* 3.1 68.4 + - + +
409A LEU* 3.7 17.8 - - + +
503A VAL* 2.9 17.7 + - - +
504A GLU 3.8 2.7 - - - -
505A TYR 3.1 0.2 - - - -
506A VAL* 1.3 81.4 - - - +
508A PHE* 1.3 67.6 + - + +
509A SER 3.7 0.6 - - - +
518A LYS* 3.6 9.9 + - - +
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Residues in contact with PHE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ARG* 3.7 23.8 - - + -
409A LEU* 3.9 31.6 - - + -
410A GLU* 5.0 16.6 - - + -
504A GLU* 3.0 23.0 + - + +
507A THR* 1.3 88.1 - - + +
509A SER* 1.3 67.0 + - - +
510A THR* 3.5 10.7 + - - +
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Residues in contact with SER 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A GLU 4.3 0.2 + - - -
505A TYR* 3.0 40.9 + - - +
506A VAL 4.6 0.2 + - - -
507A THR 3.7 2.0 - - - +
508A PHE* 1.3 80.0 + - - +
510A THR* 1.3 62.8 + - - +
511A ASP* 3.2 30.4 + - - +
514A VAL* 3.9 23.4 - - - +
515A THR* 4.9 1.0 + - - -
518A LYS* 5.0 2.3 + - - -
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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