Contacts of the helix formed by residues 553 - 563 (chain B) in PDB entry 2Y0P
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 PRO 553 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551B GLY 3.4 8.0 - - - +
552B LYS* 1.4 90.8 - - + +
554B TYR* 1.3 65.6 + - + +
555B SER* 3.1 18.4 - - - +
556B GLN* 3.1 29.8 + - + +
557B ILE* 3.2 12.0 + - - +
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Residues in contact with TYR 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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492B PHE* 3.5 29.4 - + - -
547B ALA* 3.7 21.9 + - + -
548B ASN* 2.7 15.2 + - - -
552B LYS 3.5 2.4 + - - -
553B PRO* 1.3 69.4 - - + +
555B SER* 1.4 56.2 + - - +
557B ILE* 3.2 6.1 + - - -
558B PHE* 2.8 54.1 + + + -
796B TYR* 2.7 42.4 + + - -
800B LEU* 3.6 19.3 - - + -
803B VAL* 3.9 17.3 - - + -
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Residues in contact with SER 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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553B PRO* 3.7 14.0 - - - +
554B TYR* 1.4 77.8 - - - +
556B GLN* 1.4 58.2 + - - +
559B SER* 2.9 30.6 + - - -
803B VAL* 3.5 15.5 - - - +
807B VAL* 3.5 28.1 - - - +
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Residues in contact with GLN 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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552B LYS* 3.4 28.1 - - - +
553B PRO* 3.1 33.0 + - + +
555B SER* 1.4 78.4 + - - +
557B ILE* 1.4 63.7 + - - +
559B SER* 2.6 21.8 + - - -
560B GLU* 3.3 24.3 + - - -
569B GLN* 3.6 27.6 + - - +
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Residues in contact with ILE 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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492B PHE* 3.9 23.6 - - + -
543B LEU* 4.2 20.4 - - + +
546B LEU* 4.3 1.6 - - + -
547B ALA* 3.8 25.4 - - + +
552B LYS* 3.8 51.8 - - + +
553B PRO 3.2 6.6 + - - +
554B TYR* 3.2 7.9 + - - +
556B GLN* 1.4 77.4 - - - +
558B PHE* 1.4 69.6 + - + +
560B GLU* 3.2 27.8 + - - +
561B PHE* 3.4 24.7 + - + -
577B LYS* 5.2 0.3 - - - +
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Residues in contact with PHE 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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492B PHE* 4.1 16.6 - + - -
495B PHE* 3.7 18.4 - + - -
496B LEU* 4.0 28.5 - - + -
500B TYR* 3.6 16.9 + + - +
554B TYR* 2.8 40.0 + + + +
555B SER* 4.0 2.9 - - - +
557B ILE* 1.4 72.2 - - + +
559B SER* 1.4 60.1 + - - +
561B PHE* 3.1 8.2 + - - +
562B GLU* 2.9 29.8 + - - +
800B LEU* 3.5 42.2 - - + -
803B VAL* 4.2 5.8 - - + -
804B PHE* 3.8 24.5 - + + -
807B VAL* 4.2 10.8 - - + -
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Residues in contact with SER 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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555B SER 2.9 15.0 + - - -
556B GLN* 2.6 23.9 + - - -
558B PHE* 1.4 74.8 - - - +
560B GLU* 1.4 56.7 + - - +
562B GLU* 3.4 3.0 + - - -
563B GLY* 3.0 23.6 + - - -
564B ASN* 3.2 29.6 + - - +
565B LEU* 4.1 2.5 - - - +
569B GLN* 3.3 21.8 + - - -
807B VAL* 3.8 16.5 - - - +
810B LEU* 5.9 3.8 - - - -
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Residues in contact with GLU 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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503B GLN* 4.4 1.2 - - - +
543B LEU* 5.0 1.4 - - - +
552B LYS* 3.2 32.3 + - - -
556B GLN* 3.6 14.5 + - - +
557B ILE* 3.2 21.1 + - - +
559B SER* 1.4 75.7 + - - +
561B PHE* 1.3 62.3 + - - +
563B GLY* 3.7 9.1 + - - -
565B LEU* 4.1 20.9 - - + -
569B GLN* 3.8 10.9 - - - +
577B LYS* 3.7 38.6 + - + +
580B LEU* 3.6 17.9 - - + +
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Residues in contact with PHE 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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496B LEU* 3.8 31.2 - - + -
500B TYR* 3.6 43.1 - + + -
503B GLN* 2.7 59.8 + - + +
504B LYS 4.7 0.9 - - - -
505B ARG* 3.8 14.1 - - + -
543B LEU* 3.6 27.1 - - + -
557B ILE* 3.4 26.1 + - + -
558B PHE 3.1 8.3 + - - +
560B GLU* 1.3 77.4 - - - +
562B GLU* 1.4 60.4 + - - +
563B GLY* 3.2 2.8 + - - -
577B LYS* 3.6 23.1 - - + +
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Residues in contact with GLU 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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500B TYR* 2.9 30.9 + - - +
558B PHE 2.9 18.8 + - - +
559B SER* 3.4 8.0 + - - +
561B PHE* 1.4 74.1 - - - +
563B GLY* 1.3 62.3 + - - +
564B ASN* 4.3 12.6 - - + +
804B PHE* 3.7 6.6 - - + -
807B VAL* 4.2 16.6 - - + +
808B ARG* 3.4 37.1 + - + +
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Residues in contact with GLY 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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1210A SER* 6.1 0.9 - - - -
1212A LYS* 5.3 9.2 - - - +
559B SER 3.0 6.4 + - - -
560B GLU* 3.7 8.7 + - - -
561B PHE 3.2 5.1 - - - -
562B GLU* 1.3 78.9 - - - +
564B ASN* 1.4 57.6 + - - +
565B LEU* 3.8 9.4 + - - -
815B ILE* 5.1 11.6 - - - +
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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