Contacts of the helix formed by residues 567 - 576 (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 567 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A LEU 3.6 0.4 + - - -
566A ASP* 1.3 81.8 - - + +
568A PHE* 1.3 54.0 + - - +
569A VAL 3.3 2.2 - - - -
570A LYS* 3.0 19.0 + - + +
571A SER* 2.6 32.9 + - - -
605A THR* 5.9 0.3 - - - +
606A SER* 3.0 41.4 + - - +
608A PRO* 4.6 11.5 - - + +
609A ALA* 3.9 8.2 - - + +
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Residues in contact with PHE 568 (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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513A GLU* 4.4 6.1 - - - -
514A VAL* 3.8 16.4 - - + -
564A LEU* 3.3 25.7 + - + +
567A GLU* 1.3 76.6 - - - +
569A VAL* 1.3 59.3 + - - +
571A SER* 2.4 49.1 + - - -
572A VAL* 3.1 18.0 + - + +
604A PRO* 4.9 2.2 - - + -
606A SER* 4.1 1.7 - - - -
609A ALA* 3.4 18.7 - - + +
610A ALA* 3.7 9.4 - - + +
613A HIS* 3.0 42.2 - + + -
653A LEU* 3.4 37.5 - - + -
656A GLN* 4.1 14.4 - - - -
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Residues in contact with VAL 569 (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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564A LEU* 3.2 10.4 + - + +
565A TYR* 3.3 25.4 - - + +
566A ASP 3.2 24.0 - - - +
568A PHE* 1.3 80.3 - - - +
570A LYS* 1.3 74.9 + - + +
572A VAL* 3.3 19.6 - - - +
573A LEU* 4.4 7.3 + - - +
651A TYR* 3.4 45.0 - - + +
656A GLN* 6.3 0.2 - - - +
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Residues in contact with LYS 570 (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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565A TYR 3.7 7.9 + - - -
566A ASP* 2.4 33.8 + - - +
567A GLU* 3.0 17.4 + - + +
569A VAL* 1.3 81.3 - - + +
571A SER* 1.3 65.3 + - - +
572A VAL 3.0 1.0 + - - -
573A LEU* 3.3 6.1 + - - +
574A LYS* 2.8 42.5 + - + +
606A SER* 5.2 0.2 - - - +
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Residues in contact with SER 571 (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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567A GLU 2.6 7.7 + - - -
568A PHE* 2.4 47.8 + - - -
570A LYS* 1.3 71.8 - - - +
572A VAL* 1.3 65.0 + - - +
574A LYS* 4.0 0.2 - - - -
575A ILE* 3.0 3.5 + - - +
604A PRO* 4.1 3.9 - - - +
605A THR* 2.4 40.9 + - - -
606A SER* 3.1 41.3 - - - -
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Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A PHE* 4.2 13.9 - - + +
569A VAL* 3.3 18.8 - - - +
571A SER* 1.3 88.3 + - - +
573A LEU* 1.3 83.7 + - + +
574A LYS 2.9 4.6 + - - -
575A ILE* 4.2 0.2 - - - +
576A VAL* 3.0 36.9 + - + +
600A VAL* 5.0 11.0 - - + -
602A MSE 6.4 0.9 - - + -
603A ILE 4.6 8.3 - - - +
604A PRO* 4.9 2.2 - - + -
651A TYR* 4.6 14.8 - - + +
652A GLU 5.0 10.1 - - - +
653A LEU* 6.3 2.7 - - + -
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Residues in contact with LEU 573 (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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569A VAL* 4.6 6.1 - - + +
570A LYS* 3.3 5.7 + - - +
572A VAL* 1.3 96.9 - - + +
574A LYS* 1.3 52.9 + - - +
576A VAL* 4.4 8.8 - - + +
577A GLU* 2.8 37.5 + - - +
600A VAL* 5.9 6.5 - - + -
651A TYR* 5.2 18.4 - - + +
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Residues in contact with LYS 574 (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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570A LYS* 2.8 37.2 + - + +
571A SER* 4.7 0.2 - - - -
572A VAL 2.9 1.4 + - - -
573A LEU* 1.3 74.9 - - - +
575A ILE* 1.3 59.9 + - - +
576A VAL 3.1 0.9 - - - -
577A GLU* 2.7 34.4 + - + +
578A LYS* 2.8 42.1 + - - +
605A THR* 3.0 18.4 - - + +
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Residues in contact with ILE 575 (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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571A SER 3.0 3.8 + - - +
574A LYS* 1.3 72.4 - - - +
576A VAL* 1.3 61.4 + - - +
578A LYS* 2.7 24.8 + - + -
579A LEU* 3.0 65.3 + - + +
580A ASP 3.6 4.5 + - - -
603A ILE* 3.0 43.2 - - + +
604A PRO* 3.1 24.0 - - + +
605A THR* 2.5 27.7 + - + +
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Residues in contact with VAL 576 (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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572A VAL* 3.0 26.1 + - + +
573A LEU* 4.5 7.2 - - + +
575A ILE* 1.3 80.9 - - - +
577A GLU* 1.3 52.1 + - + +
580A ASP* 2.6 25.0 - - - +
596A GLU* 5.8 0.7 - - + -
600A VAL* 3.5 39.0 - - + -
601A TRP* 3.1 45.7 - - + +
602A MSE 4.3 2.7 - - - +
603A ILE 3.7 16.2 - - - +
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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