Contacts of the helix formed by residues 499 - 514 (chain A) in PDB entry 1Q6S
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 GLU 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A LYS* 2.7 18.4 + - + +
498A LEU* 1.3 72.2 - - - +
500A PHE* 1.3 62.6 + - + +
501A MET 2.9 9.9 + - - -
502A GLU* 3.1 30.0 + - + +
503A MET* 3.8 6.3 + - - +
739A LYS 4.5 2.4 - - - +
740A ASP* 2.5 32.8 - - - +
741A PRO* 2.9 20.2 - - - +
742A SER* 2.8 34.4 + - - +
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Residues in contact with PHE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LYS* 3.9 16.6 - - + +
498A LEU 3.1 1.4 - - - -
499A GLU* 1.3 81.9 - - + +
501A MET* 1.3 58.3 + - - +
502A GLU 3.3 0.7 - - - -
503A MET* 4.0 28.6 - - + +
504A GLU* 2.9 41.5 + - + +
741A PRO* 4.4 22.7 - - + -
775A ILE* 4.4 1.1 - - + +
778A ALA* 3.5 34.5 - - + -
779A LYS* 3.5 26.2 - - + -
782A MET* 3.6 35.2 - - + -
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Residues in contact with MET 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 3.0 23.6 + - + +
499A GLU 2.9 1.0 - - - -
500A PHE* 1.3 77.6 - - - +
502A GLU* 1.3 65.5 + - - +
504A GLU* 4.0 8.4 - - - +
505A LYS* 3.1 26.7 + - - +
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Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU 4.0 9.3 - - - +
499A GLU* 3.1 20.6 + - + +
501A MET* 1.3 80.6 - - - +
503A MET* 1.3 56.3 + - + +
505A LYS* 2.6 31.8 + - - +
506A GLU* 2.6 37.4 + - - +
742A SER* 5.1 8.7 - - - -
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Residues in contact with MET 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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499A GLU 3.8 2.4 + - - +
500A PHE* 4.0 42.4 - - + +
502A GLU* 1.3 78.1 - - - +
504A GLU* 1.3 57.1 + - - +
506A GLU* 3.3 7.7 + - - +
507A PHE* 2.8 29.8 + - - +
735A MET* 3.3 39.7 - - + -
741A PRO* 4.6 4.7 - - - -
742A SER* 3.9 32.5 - - - +
775A ILE* 3.7 36.0 - - + +
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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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500A PHE* 2.9 25.4 + - - +
501A MET* 4.1 7.4 - - - +
502A GLU 3.1 0.8 - - - -
503A MET* 1.3 73.4 - - - +
505A LYS* 1.3 56.8 + - - +
507A PHE* 3.8 7.3 - - - +
508A GLU* 2.8 48.2 + - + +
775A ILE* 3.9 18.6 - - + -
779A LYS* 3.6 32.1 + - - +
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Residues in contact with LYS 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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501A MET 3.1 19.9 + - - +
502A GLU* 2.6 36.1 + - - +
504A GLU* 1.3 70.1 - - - +
506A GLU* 1.3 65.3 + - - +
508A GLU* 3.4 10.9 + - - +
509A GLN* 2.9 27.5 + - + +
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Residues in contact with GLU 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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502A GLU* 2.6 16.1 + - - +
503A MET* 3.5 12.6 - - - +
505A LYS* 1.3 79.0 + - + +
507A PHE* 1.3 60.0 + - - +
509A GLN* 2.9 27.4 + - - +
510A ILE* 2.9 45.3 + - + +
771A TYR* 6.1 2.9 - - + -
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Residues in contact with PHE 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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503A MET 2.8 17.7 + - - +
504A GLU* 3.8 7.0 - - - +
506A GLU* 1.3 76.5 - - - +
508A GLU* 1.3 67.8 + - + +
510A ILE* 3.5 10.5 + - - +
511A ASP* 2.9 47.5 + - - +
516A TRP* 3.4 24.3 - + - -
768A ARG* 3.8 31.4 - - + -
771A TYR* 3.7 29.8 - + + -
772A LEU* 3.5 34.3 - - + -
775A ILE* 3.8 18.4 - - + -
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Residues in contact with GLU 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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504A GLU* 2.8 35.5 + - + +
505A LYS* 3.8 9.3 - - - +
506A GLU 3.2 0.2 - - - -
507A PHE* 1.3 81.9 - - + +
509A GLN* 1.3 55.8 + - - +
511A ASP* 3.5 7.9 - - - +
512A LYS* 2.7 34.5 + - - +
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Residues in contact with GLN 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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505A LYS* 2.9 16.0 + - + +
506A GLU* 2.9 32.0 + - - +
508A GLU* 1.3 72.9 - - - +
510A ILE* 1.3 66.9 + - - +
512A LYS* 2.7 31.5 + - + +
513A SER* 2.7 35.3 + - - -
515A SER* 4.3 1.4 + - - -
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Residues in contact with ILE 510 (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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506A GLU* 2.9 35.0 + - + +
507A PHE* 3.8 5.4 - - - +
509A GLN* 1.3 91.8 + - - +
511A ASP* 1.3 57.6 + - - +
513A SER* 3.3 2.4 + - - -
514A GLY* 2.8 25.3 + - - -
515A SER* 3.2 16.3 + - - +
516A TRP* 3.3 50.3 + - + +
519A ILE* 3.6 29.6 - - + -
771A TYR* 4.4 14.6 - - + +
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Residues in contact with ASP 511 (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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507A PHE* 2.9 27.9 + - - +
508A GLU* 3.5 10.3 - - - +
510A ILE* 1.3 78.3 - - - +
512A LYS* 1.3 60.2 + - - +
514A GLY* 3.3 10.9 + - - -
516A TRP* 2.7 31.2 + - - +
768A ARG* 2.9 34.9 + - - -
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Residues in contact with LYS 512 (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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508A GLU 2.7 15.9 + - - +
509A GLN* 2.7 19.4 + - + +
511A ASP* 1.3 69.8 - - - +
513A SER* 1.3 61.2 + - - +
514A GLY* 3.0 4.4 + - - -
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Residues in contact with SER 513 (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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509A GLN* 2.7 28.2 + - - -
510A ILE 3.3 2.4 + - - -
512A LYS* 1.3 73.4 - - - +
514A GLY* 1.3 64.4 + - - +
515A SER* 2.7 32.2 + - - -
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Residues in contact with GLY 514 (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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510A ILE 2.8 11.6 + - - -
511A ASP* 3.3 8.7 + - - -
512A LYS 3.0 5.1 + - - -
513A SER* 1.3 78.6 - - - +
515A SER* 1.3 58.9 + - - -
516A TRP* 3.4 8.1 + - - -
517A ALA* 4.9 3.8 + - - +
1180B PRO* 5.4 6.8 - - - +
1181B ASP* 5.3 7.3 - - - +
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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