Contacts of the helix formed by residues 553 - 567 (chain B) in PDB entry 2XOY
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 ASN 553 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B GLY* 4.0 1.7 + - - -
550B LEU 2.9 14.8 + - - +
551B ASN 4.1 0.4 - - - +
552B ASN* 1.3 75.3 - - - +
554B SER* 1.3 54.7 + - - +
555B TYR 3.0 6.4 + - - -
556B GLU* 2.9 39.9 + - + +
557B SER* 2.7 36.8 + - - -
644B GLN* 3.2 44.4 + - - +
650B ALA* 3.4 21.9 - - - +
655B HIS* 3.9 7.7 + - - +
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Residues in contact with SER 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A LYS* 4.0 20.7 + - - -
548B GLY* 4.7 6.5 - - - +
552B ASN 3.8 4.8 + - - -
553B ASN* 1.3 71.3 + - - +
555B TYR* 1.3 63.8 + - - +
557B SER* 4.2 5.8 - - - -
558B ASP* 2.8 38.2 + - - -
644B GLN 5.1 0.6 + - - -
645B VAL* 6.0 0.4 - - - +
647B ALA* 4.9 13.5 - - - +
650B ALA* 5.6 0.4 - - - +
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Residues in contact with TYR 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ASN* 3.0 8.3 + - - +
554B SER* 1.3 84.2 + - - +
556B GLU* 1.3 65.3 + - - +
558B ASP* 3.9 4.7 - - - +
559B ILE* 3.4 43.7 + - + +
628B ALA* 5.6 1.9 - - - +
629B VAL* 4.8 7.4 + - - +
632B ARG* 3.2 39.3 + - - -
647B ALA* 5.0 4.5 - - + +
650B ALA* 3.4 28.6 - - + +
651B MET* 3.8 33.5 + - + +
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Residues in contact with GLU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LEU* 3.6 24.3 - - + +
553B ASN* 2.9 36.3 + - + +
555B TYR* 1.3 74.9 - - + +
557B SER* 1.3 64.9 + - - +
559B ILE* 3.4 16.8 + - - +
560B LEU 3.2 16.6 + - - -
617B ARG* 4.0 13.5 + - - -
632B ARG* 3.1 28.7 + - - -
650B ALA 4.5 0.4 - - - +
653B PHE 4.0 1.0 - - - +
654B ASN* 3.7 3.2 - - - +
655B HIS* 3.3 21.9 + - + +
656B ILE* 3.9 27.0 - - + +
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Residues in contact with SER 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B LEU 3.8 10.2 - - - +
548B GLY 3.3 19.2 - - - -
549B VAL* 3.2 7.2 + - - +
550B LEU* 3.1 32.9 + - - +
553B ASN 2.7 22.6 + - - -
554B SER* 4.0 3.8 - - - -
556B GLU* 1.3 74.4 - - - +
558B ASP* 1.3 60.8 + - - +
560B LEU* 3.3 3.9 + - - +
561B LYS* 2.9 34.8 + - - +
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Residues in contact with ASP 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A THR* 3.5 31.4 + - + +
646A LYS* 2.9 32.5 + - - +
554B SER* 2.8 26.7 + - - +
555B TYR* 3.9 6.7 - - - +
557B SER* 1.3 75.4 - - - +
559B ILE* 1.3 65.7 + - + +
561B LYS* 3.1 32.0 + - - +
562B ASN* 3.0 29.5 + - - -
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Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A TRP* 4.1 15.8 - - + +
555B TYR* 3.4 44.2 + - + +
556B GLU* 3.4 15.9 + - - +
558B ASP* 1.3 76.8 - - + +
560B LEU* 1.3 58.8 + - - +
562B ASN* 3.1 10.2 + - - +
563B TYR* 2.8 26.2 + - - +
617B ARG* 4.9 10.3 - - - +
625B LEU* 4.2 24.5 - - + -
629B VAL* 3.8 35.2 - - + -
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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
----------------------------------------------------------
546B LEU* 4.5 7.6 - - + -
549B VAL* 4.3 13.0 - - + -
550B LEU* 4.2 14.1 - - + -
556B GLU 3.2 10.5 + - - +
557B SER 3.8 5.8 - - - +
558B ASP 3.3 0.4 - - - -
559B ILE* 1.3 80.7 - - - +
561B LYS* 1.3 63.1 + - - +
563B TYR* 4.2 5.2 - - + -
564B LEU* 3.1 31.5 + - + +
574B MET* 3.9 8.7 - - - -
613B THR* 3.6 32.1 - - + +
616B TYR* 4.1 20.4 - - + -
617B ARG* 4.6 10.1 - - + +
620B ILE* 3.8 27.6 - - + -
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Residues in contact with LYS 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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642A ARG* 4.6 16.7 - - + +
646A LYS* 4.9 5.7 - - - +
546B LEU* 3.8 43.5 - - + +
547B ASP* 2.6 35.4 + - - +
548B GLY 5.2 0.4 - - - +
557B SER* 2.9 18.8 + - - +
558B ASP* 3.2 35.4 + - - +
560B LEU* 1.3 76.6 - - - +
562B ASN* 1.3 58.2 + - - +
564B LEU* 3.6 2.5 + - - +
565B ALA* 3.1 27.8 + - - +
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Residues in contact with ASN 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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637A TRP* 3.4 47.1 - - + +
640A ASN 4.6 0.3 - - - +
641A CYS* 3.4 11.3 - - - -
642A ARG* 2.9 30.8 + - - +
643A THR* 3.1 26.9 + - - +
558B ASP 3.0 17.2 + - - -
559B ILE* 3.1 3.7 + - - +
561B LYS* 1.3 75.9 - - - +
563B TYR* 1.3 65.9 + - - +
564B LEU 3.2 0.2 - - - -
565B ALA* 3.9 4.2 - - - +
566B THR* 2.7 32.3 + - - -
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Residues in contact with TYR 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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637A TRP* 3.9 15.6 - + + -
559B ILE 2.8 15.4 + - - +
560B LEU* 3.3 9.2 + - + +
562B ASN* 1.3 79.5 - - - +
564B LEU* 1.3 72.7 - - + +
566B THR* 3.5 3.7 + - - -
567B ARG* 3.0 58.6 + - + +
616B TYR* 3.8 20.4 - + - -
620B ILE* 3.5 48.9 - - + +
621B PRO* 4.6 3.5 - - - +
624B GLU* 3.1 44.7 + - + -
625B LEU* 4.2 6.5 - - + -
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Residues in contact with LEU 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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546B LEU* 4.2 27.1 - - + -
560B LEU* 3.1 25.2 + - + +
561B LYS 4.0 2.9 - - - +
563B TYR* 1.3 78.0 - - + +
565B ALA* 1.3 64.3 + - - +
567B ARG* 3.0 9.3 + - - -
569B LEU* 3.0 52.8 + - + +
570B THR 4.7 0.9 - - - +
571B TRP* 4.6 7.9 - - - +
574B MET* 3.8 32.8 - - + -
616B TYR* 3.7 34.5 - - + +
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Residues in contact with ALA 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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640A ASN 5.9 0.2 - - - +
642A ARG* 3.6 47.0 + - + +
561B LYS 3.1 18.8 + - - +
562B ASN* 3.3 5.1 + - - +
564B LEU* 1.3 76.3 - - - +
566B THR* 1.3 62.0 + - - +
568B GLY* 3.1 13.3 + - - +
569B LEU 4.3 5.6 + - - +
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Residues in contact with THR 566 (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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637A TRP* 3.3 23.7 - - + +
659A GLN* 3.3 34.5 + - + +
661A ARG* 5.4 5.8 + - - +
562B ASN* 2.7 24.6 + - - +
563B TYR* 3.7 5.4 - - - -
565B ALA* 1.3 74.7 - - - +
567B ARG* 1.3 63.1 + - + +
568B GLY 3.4 0.6 + - - -
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Residues in contact with ARG 567 (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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563B TYR* 3.0 55.9 + - + +
564B LEU 3.0 5.7 + - - +
566B THR* 1.3 82.2 - - + +
568B GLY* 1.3 62.4 + - - +
569B LEU* 3.3 36.3 + - + +
616B TYR* 3.9 13.1 + - - -
624B GLU* 4.6 4.0 + - - -
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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