Contacts of the helix formed by residues 552 - 563 (chain A) in PDB entry 5XA0
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 ILE 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A ILE* 6.0 2.0 - - + -
465A ILE* 6.6 0.2 - - + -
473A VAL* 4.5 10.3 - - + -
474A THR* 2.9 40.8 - - + +
477A LEU* 3.0 41.8 - - + +
551A HIS* 1.3 96.3 - - + +
553A CYS* 1.3 66.9 + - - +
555A LEU* 3.1 14.6 + - + +
556A CYS* 3.2 16.6 + - - +
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Residues in contact with CYS 553 (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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551A HIS* 3.4 5.1 - - + +
552A ILE* 1.3 78.8 - - - +
554A ARG* 1.3 63.2 + - - +
556A CYS* 3.1 10.4 + - - +
557A TYR* 3.0 24.1 + - - +
590A LEU* 5.9 7.4 - - + -
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Residues in contact with ARG 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLU* 4.8 5.4 - - - +
551A HIS 3.4 23.0 + - - +
552A ILE 3.3 0.4 - - - -
553A CYS* 1.3 77.7 - - - +
555A LEU* 1.3 62.4 + - + +
557A TYR* 3.3 6.0 + - - +
558A ARG* 3.0 30.7 + - - +
590A LEU* 6.0 4.7 - - - +
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Residues in contact with LEU 555 (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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474A THR* 3.4 5.2 - - - +
477A LEU* 2.7 61.2 - - + +
478A GLU* 2.3 63.3 - - + +
481A VAL* 2.8 16.8 - - + -
551A HIS 3.9 9.4 - - - +
552A ILE* 3.1 6.6 + - + +
554A ARG* 1.3 72.7 - - - +
556A CYS* 1.3 65.9 + - - +
557A TYR 3.3 0.2 + - - -
558A ARG* 3.3 0.7 + - + +
559A VAL* 2.8 31.3 + - - +
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Residues in contact with CYS 556 (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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477A LEU* 5.0 0.6 - - - +
519A ILE* 3.5 50.7 - - + -
523A LEU* 5.6 1.1 - - - -
552A ILE* 3.2 13.3 + - - +
553A CYS* 3.1 12.6 + - - +
555A LEU* 1.3 78.5 - - - +
557A TYR* 1.3 57.2 + - - +
559A VAL* 3.5 5.0 + - - +
560A LEU* 2.9 29.9 + - - +
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Residues in contact with TYR 557 (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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553A CYS 3.0 15.6 + - - +
554A ARG* 3.8 6.3 - - - +
556A CYS* 1.3 77.1 - - - +
558A ARG* 1.3 57.4 + - - +
560A LEU* 3.1 9.8 + - - +
561A ARG* 3.0 30.8 + - - +
590A LEU* 5.0 21.1 - - + +
593A ASP* 6.0 4.5 - - + -
594A THR* 6.3 3.4 - - - +
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Residues in contact with ARG 558 (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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481A VAL* 2.9 37.6 - - + +
554A ARG 3.0 17.6 + - - +
557A TYR* 1.3 72.9 - - - +
559A VAL* 1.3 66.0 + - - +
561A ARG* 4.4 2.6 - - - +
562A HIS* 3.1 28.4 + - - +
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Residues in contact with VAL 559 (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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480A LEU* 3.8 22.7 - - + +
481A VAL* 3.6 24.9 - - - +
484A VAL* 3.8 19.2 - - + +
510A MET* 3.4 34.5 - - + -
515A ILE* 4.4 8.1 - - + -
519A ILE* 6.2 0.9 - - + -
555A LEU 2.8 21.3 + - - +
556A CYS* 3.8 5.2 - - - +
558A ARG* 1.3 74.1 - - - +
560A LEU* 1.3 64.1 + - - +
563A SER* 2.9 30.0 + - - +
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Residues in contact with LEU 560 (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 MET* 5.4 5.4 - - - +
520A PHE* 6.5 0.4 - - + -
556A CYS 2.9 15.4 + - - +
557A TYR* 3.1 12.5 + - - +
559A VAL* 1.3 77.3 - - - +
561A ARG* 1.3 59.5 + - - +
563A SER* 3.3 1.5 - - - -
564A GLN* 2.7 71.9 + - + +
570A ASN* 4.5 10.5 - - + -
594A THR* 5.3 13.5 - - - -
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Residues in contact with ARG 561 (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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557A TYR 3.0 17.4 + - - +
558A ARG* 4.4 2.2 - - - +
560A LEU* 1.3 77.1 - - - +
562A HIS* 1.3 67.0 + - - +
564A GLN* 3.4 16.4 + - - +
565A GLN* 4.0 2.3 + - - +
593A ASP* 5.7 7.4 - - + +
594A THR* 5.9 4.9 - - - -
597A ALA* 5.3 14.1 - - + -
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Residues in contact with HIS 562 (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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481A VAL* 5.9 0.4 - - + -
484A VAL* 2.2 54.1 + - + +
485A THR* 2.9 36.0 - - + +
501A LYS 3.8 15.9 + - - +
502A PRO* 2.7 19.7 - - + +
507A GLN* 2.8 40.7 + - - +
558A ARG 3.1 18.2 + - - +
561A ARG* 1.3 81.1 - - - +
563A SER* 1.3 56.6 + - - +
564A GLN 3.3 1.2 + - - -
565A GLN* 4.0 3.5 + - - +
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Residues in contact with SER 563 (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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484A VAL* 2.7 23.5 - - - +
506A ARG 4.3 4.2 + - - -
507A GLN* 2.9 50.0 + - - +
510A MET* 4.0 23.3 - - - +
559A VAL* 2.9 19.8 + - - +
560A LEU* 3.3 1.6 - - - -
562A HIS* 1.3 73.0 - - - +
564A GLN* 1.3 58.5 + - - +
565A GLN 4.1 0.2 + - - -
567A TYR* 5.0 4.2 - - - +
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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