Contacts of the helix formed by residues 504 - 514 (chain A) in PDB entry 5LUQ
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 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A SER* 1.3 82.3 + - - +
505A SER* 1.3 53.3 + - - +
507A ASP* 3.7 2.5 - - - +
508A HIS* 2.7 59.8 + - + +
765A LEU* 3.5 39.0 - - + +
766A ALA* 5.4 1.3 - - + +
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Residues in contact with SER 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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503A SER 3.4 1.9 + - - +
504A GLU* 1.3 79.3 - - - +
506A GLU* 1.3 62.1 + - - +
508A HIS* 3.1 13.9 + - - +
509A ARG* 2.9 26.7 + - - +
725A LEU* 5.7 1.1 - - - -
728A SER* 4.4 16.4 + - - -
729A CYS* 4.6 4.0 - - - -
732A PHE* 4.1 16.4 - - - -
763A THR* 5.3 9.6 - - - -
766A ALA* 5.0 5.4 - - - +
768A VAL* 4.0 21.8 - - - +
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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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496A VAL* 5.6 5.2 - - - +
503A SER* 3.4 14.6 + - - +
504A GLU 3.3 0.6 - - - -
505A SER* 1.3 82.5 + - - +
507A ASP* 1.3 67.4 - - - +
508A HIS 3.0 1.5 + - - -
509A ARG* 3.2 38.6 + - - +
510A ALA* 3.0 24.7 + - - +
618A LYS* 5.1 10.7 + - - -
732A PHE* 6.0 0.9 - - + -
768A VAL* 4.9 19.9 - - + +
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Residues in contact with ASP 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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496A VAL* 2.6 32.3 - - - +
497A LEU* 4.0 16.7 - - - -
503A SER* 2.9 26.8 + - - +
504A GLU* 3.7 4.8 - - - +
506A GLU* 1.3 76.5 - - - +
508A HIS* 1.3 63.2 + - + +
510A ALA* 3.6 6.3 + - - +
511A SER* 2.8 28.6 + - - -
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Residues in contact with HIS 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* 2.7 47.2 + - + +
505A SER* 3.2 12.1 - - - +
506A GLU 3.0 0.2 - - - -
507A ASP* 1.3 78.2 - - + +
509A ARG* 1.3 60.5 + - - +
511A SER* 2.4 25.3 + - - -
512A GLY 2.7 13.3 + - - -
725A LEU* 3.3 58.7 - - + +
726A LEU* 3.3 8.5 - - - +
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Residues in contact with ARG 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 SER 2.9 9.5 + - - +
506A GLU* 3.2 46.2 + - - +
508A HIS* 1.3 73.5 - - - +
510A ALA* 1.3 70.6 + - + +
512A GLY 2.8 12.1 + - - -
513A GLU* 2.9 3.6 + - - +
618A LYS* 3.9 21.0 - - - +
654A ILE* 2.8 22.0 - - + +
655A LEU* 3.3 26.9 - - + +
658A THR* 3.3 33.6 + - - +
659A ARG* 4.7 2.0 - - - +
726A LEU* 4.0 0.2 - - - -
729A CYS* 3.0 35.5 - - + +
732A PHE* 3.8 28.1 - - - -
768A VAL* 5.7 3.2 - - - +
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Residues in contact with ALA 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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496A VAL* 4.5 22.0 - - + +
506A GLU 3.0 16.5 + - - +
507A ASP* 4.0 6.1 - - - +
509A ARG* 1.3 78.3 - - + +
511A SER* 1.3 59.4 + - - +
513A GLU* 3.3 6.3 - - - +
514A VAL* 3.2 24.6 + - - +
515A ARG* 3.7 0.9 + - - -
614A PRO* 6.3 1.8 - - + -
618A LYS* 6.4 1.3 - - + -
655A LEU* 4.4 18.2 - - + -
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Residues in contact with SER 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 ASP 2.8 16.7 + - - -
508A HIS* 2.4 33.1 + - - -
510A ALA* 1.3 74.1 - - - +
512A GLY* 1.3 58.6 + - - +
513A GLU 3.1 2.7 - - - +
514A VAL 2.9 17.7 + - - -
515A ARG* 3.2 44.2 + - - +
602A MSE 4.6 5.1 - - - +
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Residues in contact with GLY 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 HIS 2.7 15.0 + - - -
509A ARG 2.8 4.8 + - - -
511A SER* 1.3 71.2 + - - +
513A GLU* 1.3 63.7 + - - +
602A MSE 3.4 41.7 - - - +
653A LEU* 4.2 6.2 - - - +
654A ILE* 3.8 6.1 - - - -
726A LEU* 3.4 15.0 - - - +
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Residues in contact with GLU 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 ARG 2.9 13.4 + - - +
510A ALA* 3.3 10.3 - - - +
511A SER 3.3 0.7 - - - -
512A GLY* 1.3 81.4 - - - +
514A VAL* 1.3 74.3 + - + +
568A PHE* 4.4 5.6 - - + -
602A MSE 6.0 0.7 - - - +
603A ILE 5.3 1.6 - - - -
604A PRO* 4.1 11.3 - - - +
613A HIS* 3.6 17.9 + - - -
614A PRO* 3.1 25.6 - - - +
617A PRO* 4.9 1.7 - - - +
653A LEU* 3.0 36.0 - - + +
654A ILE* 3.6 2.8 - - + +
655A LEU* 3.0 47.1 - - + +
656A GLN 4.0 1.0 + - - -
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Residues in contact with VAL 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 ALA 3.2 10.7 + - - +
511A SER 2.9 8.9 + - - -
513A GLU* 1.3 89.3 - - + +
515A ARG* 1.3 80.0 + - - +
516A THR 4.8 0.9 - - - -
568A PHE* 3.8 12.3 - - + -
604A PRO* 3.1 31.7 - - + +
607A ASP* 4.2 5.0 - - - +
610A ALA* 3.0 48.9 - - + +
611A ASN* 5.1 2.9 - - - +
613A HIS* 4.1 2.5 - - + -
614A PRO* 3.8 11.2 - - + -
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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