Contacts of the helix formed by residues 552 - 561 (chain A) in PDB entry 1Y8B
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 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A GLU 5.8 0.8 + - - -
548A TYR* 4.7 2.2 - - - -
549A HIS* 3.4 22.8 + - - +
550A GLN 3.7 3.6 + - - -
551A THR* 1.3 72.3 + - - +
553A VAL* 1.3 62.9 + - - +
554A GLN* 3.4 13.4 + - + +
555A SER* 3.7 20.9 + - - +
556A VAL* 4.4 5.5 + - - +
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Residues in contact with VAL 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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526A LEU* 3.7 31.6 - - + +
527A ARG* 6.0 0.4 - - - +
529A GLY* 6.3 0.7 - - - -
530A ALA 4.6 4.7 - - - +
531A ASN* 5.1 4.5 - - + +
548A TYR* 3.1 50.0 + - + +
551A THR* 3.5 13.2 - - - +
552A ASN* 1.3 71.9 - - - +
554A GLN* 1.3 68.0 + - + +
555A SER 3.2 0.2 - - - -
556A VAL* 3.2 9.8 + - + +
557A GLN* 2.8 35.4 + - + +
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Residues in contact with GLN 554 (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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211A ARG* 4.8 14.9 + - - +
234A ASN* 3.6 28.1 - - - +
552A ASN* 3.2 10.2 - - + -
553A VAL* 1.3 88.9 - - + +
555A SER* 1.3 53.2 + - - +
557A GLN* 4.4 6.7 - - - +
558A ALA* 2.4 48.7 + - + +
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Residues in contact with SER 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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552A ASN* 3.7 17.8 + - - +
553A VAL 3.2 0.4 - - - -
554A GLN* 1.3 79.0 - - - +
556A VAL* 1.3 59.1 + - - +
558A ALA* 4.5 1.3 - - - -
559A ASN* 2.6 52.1 + - - +
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Residues in contact with VAL 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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487A ARG* 4.6 14.1 - - - +
526A LEU 5.6 2.0 - - - +
527A ARG* 3.9 34.3 - - + +
529A GLY* 5.6 3.8 - - - +
551A THR* 6.0 1.1 - - - +
552A ASN 4.5 8.3 - - - +
553A VAL* 3.2 11.1 + - + +
554A GLN 3.1 0.4 - - - -
555A SER* 1.3 79.1 - - - +
557A GLN* 1.3 66.6 + - - +
559A ASN* 3.0 3.6 + - - +
560A ILE* 2.9 39.3 + - + +
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Residues in contact with GLN 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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490A VAL* 4.1 20.2 - - + -
494A LEU* 3.3 15.4 - - + +
495A PHE* 3.1 34.8 - - - -
529A GLY* 6.4 2.0 - - - -
553A VAL* 2.8 27.6 + - + +
554A GLN* 4.1 5.0 - - - +
556A VAL* 1.3 75.1 - - - +
558A ALA* 1.3 62.4 + - - +
560A ILE* 3.1 22.6 - - - +
561A ALA* 3.9 1.0 + - - +
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Residues in contact with ALA 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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495A PHE* 5.7 0.4 - - - -
554A GLN* 2.4 42.2 + - + +
555A SER* 4.2 1.8 - - - +
557A GLN* 1.3 78.4 - - - +
559A ASN* 1.3 65.2 + - - +
561A ALA* 3.8 5.8 + - - +
562A GLN* 3.1 24.8 + - - +
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Residues in contact with ASN 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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555A SER* 2.6 38.9 + - - +
556A VAL* 3.0 4.9 + - - +
558A ALA* 1.3 82.6 + - - +
560A ILE* 1.3 56.8 - - + +
561A ALA 2.9 4.9 - - - -
562A GLN* 2.4 39.8 + - - +
563A THR* 3.5 5.6 + - - +
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Residues in contact with ILE 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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487A ARG* 3.9 29.6 - - + +
490A VAL* 4.2 8.5 - - + -
491A LEU* 4.0 39.0 - - + +
495A PHE* 4.2 6.7 - - + -
556A VAL* 2.9 22.8 + - + +
557A GLN* 3.1 32.3 - - - +
559A ASN* 1.3 74.6 - - + +
561A ALA* 1.3 78.9 + - + +
563A THR* 2.9 25.7 - - - +
564A GLU 4.3 4.5 + - - -
565A PHE 5.3 0.5 + - - -
568A GLU* 5.9 0.3 - - - +
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Residues in contact with ALA 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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491A LEU* 5.8 1.1 - - - -
495A PHE* 2.9 48.7 - - + -
557A GLN 4.1 4.3 - - - +
558A ALA 3.8 5.3 + - - +
559A ASN 2.7 2.4 + - - -
560A ILE* 1.3 82.8 - - + +
562A GLN* 1.3 64.4 + - - +
563A THR 3.4 2.4 - - - -
564A GLU* 5.2 0.9 - - - -
565A PHE* 6.2 3.6 - - - +
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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