Contacts of the helix formed by residues 564 - 577 (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 GLU 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A LEU* 5.8 0.2 - - - +
560A ILE 4.3 4.1 + - - -
561A ALA 5.2 0.9 - - - -
563A THR* 1.3 90.4 + - - +
565A PHE* 1.3 67.6 + - + +
566A ASN* 3.4 25.1 - - + +
567A ALA* 3.4 25.8 - - - +
568A GLU* 2.4 42.0 + - - +
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Residues in contact with PHE 565 (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* 4.6 26.0 - - + +
560A ILE 5.3 1.5 + - - +
561A ALA* 6.2 2.9 - - - -
564A GLU* 1.3 75.6 - - + +
566A ASN* 1.3 76.3 + - + +
568A GLU* 4.3 5.4 - - - -
569A PHE* 3.0 35.5 + + + +
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Residues in contact with ASN 566 (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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564A GLU* 3.2 19.8 - - + +
565A PHE* 1.3 94.8 - - + +
567A ALA* 1.3 69.6 + - - +
569A PHE* 3.0 23.4 + - - +
570A GLU* 4.3 0.9 + - - +
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Residues in contact with ALA 567 (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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564A GLU* 3.4 23.6 - - - +
566A ASN* 1.3 81.3 - - - +
568A GLU* 1.3 73.9 + - - +
569A PHE 3.4 0.3 + - - -
570A GLU* 3.6 5.2 + - - +
571A PRO* 3.1 17.2 - - - +
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Residues in contact with GLU 568 (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* 5.4 3.8 - - + -
563A THR* 2.5 32.4 + - + +
564A GLU* 2.4 33.0 + - - +
565A PHE* 4.3 5.4 - - - +
566A ASN 3.1 1.0 - - - -
567A ALA* 1.3 85.9 - - - +
569A PHE* 1.3 65.1 + - - +
570A GLU 2.6 8.1 + - - -
571A PRO* 3.1 22.8 - - + +
572A LEU* 3.2 29.4 + - + +
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Residues in contact with PHE 569 (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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94A GLN* 5.2 9.9 - - - -
436A ARG* 3.8 27.4 - - - -
488A ASN* 6.2 3.4 - - - -
492A SER* 5.6 7.0 - - - -
565A PHE* 3.0 21.4 + + + +
566A ASN* 3.0 21.3 + - - +
568A GLU* 1.3 76.0 - - - +
570A GLU* 1.3 60.7 + - - +
572A LEU* 4.3 6.7 - - - +
573A LEU* 3.4 30.5 + - + +
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Residues in contact with GLU 570 (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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566A ASN 4.3 0.6 + - - -
567A ALA 3.6 5.6 + - - +
568A GLU 2.6 5.5 + - - -
569A PHE* 1.3 73.8 - - - +
571A PRO* 1.3 77.2 - - + +
572A LEU 3.0 0.9 - - - -
573A LEU* 2.8 17.3 + - - -
574A ASP* 2.8 34.9 + - - +
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Residues in contact with PRO 571 (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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567A ALA 3.1 20.0 - - - +
568A GLU* 3.1 17.9 - - + +
570A GLU* 1.3 95.7 - - + +
572A LEU* 1.3 58.7 + - + +
574A ASP* 3.3 8.2 + - + +
575A ASP* 3.0 30.1 + - - +
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Residues in contact with LEU 572 (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 ALA* 4.3 11.9 - - + +
487A ARG* 4.3 15.9 - - + -
488A ASN* 4.1 37.2 - - + +
491A LEU* 3.8 30.3 - - + -
565A PHE* 6.1 0.4 - - - +
568A GLU* 3.2 30.9 + - + +
569A PHE* 4.3 5.2 - - - +
570A GLU 2.8 4.2 + - - -
571A PRO* 1.3 78.9 - - + +
573A LEU* 1.3 50.9 + - - +
575A ASP* 5.1 2.0 - - - -
576A LEU* 2.5 44.5 + - - +
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Residues in contact with LEU 573 (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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82A LYS* 4.2 31.5 - - + +
86A ARG* 6.0 4.7 - - + +
433A LEU* 3.7 36.8 - - + -
488A ASN* 5.6 2.2 - - - +
569A PHE* 3.4 31.4 + - + +
570A GLU* 2.8 9.0 + - - +
572A LEU* 1.3 76.4 - - - +
574A ASP* 1.3 63.2 + - - +
576A LEU* 4.0 7.6 - - + -
577A LEU* 3.5 25.9 + - + +
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Residues in contact with ASP 574 (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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75A VAL* 5.1 2.1 - - - +
78A LYS* 3.4 36.3 - - + +
82A LYS* 5.0 10.6 - - - +
570A GLU* 2.8 38.5 + - - +
571A PRO* 3.5 10.3 - - + +
572A LEU 3.0 0.2 - - - -
573A LEU* 1.3 87.8 - - - +
575A ASP* 1.3 61.9 + - - +
577A LEU 3.8 2.6 + - - -
578A THR* 4.0 3.5 + - - -
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Residues in contact with ASP 575 (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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75A VAL* 6.3 0.4 - - - -
480A PRO 5.3 2.8 - - - +
481A TRP* 3.9 9.9 - - - -
483A LYS* 4.6 13.7 + - - -
484A ALA* 3.9 16.8 + - + +
571A PRO 3.0 15.4 + - - +
572A LEU* 4.3 1.6 - - - +
574A ASP* 1.3 76.5 - - - +
576A LEU* 1.3 64.3 + - - +
578A THR* 2.6 29.3 + - - +
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Residues in contact with LEU 576 (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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432A SER* 6.0 1.3 - - - +
433A LEU* 4.1 24.9 - - + -
456A ARG* 4.3 12.9 + - - +
481A TRP* 3.0 29.4 + - + +
484A ALA* 3.6 9.7 - - + +
485A TYR* 3.4 44.2 - - + +
488A ASN* 4.5 20.0 - - + +
572A LEU 2.5 28.7 + - - +
573A LEU* 4.1 8.1 - - + -
575A ASP* 1.3 69.3 - - - +
577A LEU* 1.3 60.5 + - + +
578A THR 2.6 18.6 + - - +
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Residues in contact with LEU 577 (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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78A LYS* 3.4 28.1 + - + -
81A TYR* 4.3 12.1 - - + +
82A LYS* 3.7 35.7 - - + -
85A LEU* 3.7 38.6 - - + -
429A ARG* 5.0 7.2 - - - +
433A LEU* 3.6 31.6 - - + -
456A ARG* 6.0 0.2 - - - +
573A LEU* 3.5 20.7 + - + +
574A ASP 3.8 2.7 + - - +
575A ASP 3.3 0.6 - - - -
576A LEU* 1.3 79.9 - - + +
578A THR* 1.3 61.1 + - - -
579A ILE* 4.3 1.0 + - - +
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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