Contacts of the helix formed by residues 552 - 565 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B ILE* 6.1 6.3 - - + -
473B VAL* 4.4 11.0 - - + -
474B THR* 4.4 15.5 - - + -
477B LEU* 3.9 26.2 - - + +
551B HIS* 1.3 119.8 - - + +
553B CYS* 1.3 64.5 + - + +
555B LEU* 3.0 16.3 + - - +
556B CYS* 3.2 16.2 + - - -
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Residues in contact with CYS 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B HIS* 4.0 8.0 - - + +
552B ILE* 1.3 80.0 - - + +
554B ARG* 1.3 66.7 + - - +
556B CYS* 2.7 30.4 + - - +
557B TYR* 3.0 11.4 + - - +
584B GLN* 3.2 36.8 - - + +
591B ALA* 5.7 4.3 - - - -
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Residues in contact with ARG 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B HIS 2.9 23.3 + - - +
553B CYS* 1.3 75.8 - - - +
555B LEU* 1.3 65.4 + - + +
557B TYR* 3.0 19.9 + - - +
558B ARG* 3.1 12.6 + - - +
590B LEU* 5.6 9.2 - - + -
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B THR* 3.8 4.5 - - - +
477B LEU* 2.8 74.3 - - + +
478B GLU* 3.0 22.2 - - + +
480B LEU* 3.0 10.1 - - + -
481B VAL* 4.3 10.3 - - + -
551B HIS 3.8 5.6 + - - +
552B ILE* 3.0 13.4 + - - +
554B ARG* 1.3 79.1 - - + +
556B CYS* 1.3 60.4 + - - +
558B ARG* 3.0 3.4 + - + +
559B VAL* 2.7 31.9 + - + +
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Residues in contact with CYS 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ILE* 5.2 23.1 - - + -
523B LEU* 5.5 10.1 - - - -
552B ILE* 3.2 17.4 + - - -
553B CYS* 2.7 28.6 + - - +
555B LEU* 1.3 70.9 - - - +
557B TYR* 1.3 62.0 + - - +
559B VAL* 4.4 5.4 - - - -
560B LEU* 2.9 31.9 + - + +
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Residues in contact with TYR 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B CYS* 3.0 9.2 + - - +
554B ARG* 3.0 15.2 + - - +
556B CYS* 1.3 73.6 - - - +
558B ARG* 1.3 51.7 + - - +
560B LEU* 4.6 1.2 - - - +
561B ARG* 2.7 40.6 + - - +
590B LEU* 4.5 28.9 - - + +
591B ALA* 4.9 6.3 - - - +
594B THR* 6.0 0.6 - - - -
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Residues in contact with ARG 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU 4.9 0.7 - - - -
481B VAL* 2.9 38.4 - - + -
554B ARG 3.1 7.1 + - - +
555B LEU* 3.0 9.9 + - + +
557B TYR* 1.3 78.2 - - - +
559B VAL* 1.3 67.7 + - - +
561B ARG* 3.3 2.5 + - - +
562B HIS* 2.9 30.8 + - + +
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Residues in contact with VAL 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B LEU* 5.3 0.7 - - + -
480B LEU* 2.9 49.8 - - + +
483B PHE* 6.3 0.2 - - + -
484B VAL* 5.5 0.2 - - - -
510B MET* 5.7 5.2 - - + -
515B ILE* 5.3 7.4 - - + -
516B LEU* 5.2 6.5 - - + -
519B ILE* 3.8 33.7 - - + -
555B LEU* 2.7 25.6 + - + +
556B CYS* 4.2 3.4 - - - +
558B ARG* 1.3 74.0 - - - +
560B LEU* 1.3 64.7 + - - +
562B HIS* 3.2 8.6 + - - +
563B SER* 3.2 15.3 + - - -
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B LEU* 4.6 20.9 - - + +
519B ILE* 5.6 8.0 - - + +
520B PHE* 6.4 2.0 - - + -
556B CYS* 2.9 20.0 + - + +
557B TYR* 4.6 0.9 - - - +
559B VAL* 1.3 76.5 - - - +
561B ARG* 1.3 64.7 + - - +
563B SER* 3.2 3.0 + - - -
564B GLN* 2.9 75.4 + - + +
574B ILE* 5.0 14.1 - - + -
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Residues in contact with ARG 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B TYR 2.7 24.6 + - - +
558B ARG* 3.8 4.0 - - - +
560B LEU* 1.3 80.6 - - - +
562B HIS* 1.3 68.1 + - + +
564B GLN* 3.6 7.2 + - - +
565B GLN* 3.6 15.1 + - - +
594B THR* 5.2 16.2 - - - -
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Residues in contact with HIS 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B VAL* 3.6 10.3 + - + +
484B VAL* 2.5 66.2 + - + +
485B THR* 3.8 15.7 - - + -
501B LYS 6.1 0.2 - - - -
502B PRO* 4.7 10.4 - - + +
503B ASN 3.6 7.4 + - - +
507B GLN* 2.0 26.0 + - - +
558B ARG* 2.9 16.5 + - + +
559B VAL 3.2 2.0 + - - +
561B ARG* 1.3 84.1 - - + +
563B SER* 1.3 53.2 - - - +
565B GLN* 4.2 8.3 + - - +
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Residues in contact with SER 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B ARG* 3.2 5.2 + - - -
507B GLN* 2.6 42.0 - - - +
510B MET* 2.2 43.2 - - - +
516B LEU* 3.2 24.1 - - - +
559B VAL* 3.2 15.2 + - - -
560B LEU 4.1 1.1 - - - -
562B HIS* 1.3 75.3 - - - +
564B GLN* 1.3 60.6 + - - +
567B TYR* 4.3 1.9 - - - +
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Residues in contact with GLN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B ARG* 3.1 4.5 - - - +
511B ARG* 6.1 0.3 - - - +
516B LEU* 4.7 7.8 - - - +
560B LEU* 2.9 62.4 + - + +
561B ARG* 4.7 2.9 - - - +
562B HIS 3.6 0.4 - - - -
563B SER* 1.3 77.9 - - - +
565B GLN* 1.3 59.4 + - - +
566B ASP 3.0 0.5 + - - -
567B TYR* 2.8 32.9 + - - +
570B ASN* 3.0 44.3 + - + +
573B TYR* 4.9 9.3 - - - +
574B ILE* 5.4 2.0 - - - +
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Residues in contact with GLN 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B PRO* 3.5 34.8 - - + +
504B ARG* 2.6 24.9 + - - -
507B GLN* 4.5 1.6 - - - +
561B ARG 3.6 14.2 + - - +
562B HIS 4.5 2.2 - - - +
563B SER 3.4 2.0 - - - -
564B GLN* 1.3 73.5 - - - +
566B ASP* 1.3 63.6 + - - +
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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