Contacts of the helix formed by residues 568 - 579 (chain A) in PDB entry 1YI1
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 LEU 568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A MET* 4.4 13.5 - - + -
539A GLY* 4.2 9.6 - - - -
567A HIS* 1.3 71.7 - - - +
569A GLY* 1.3 64.4 + - - +
570A MET 3.5 1.8 - - - -
571A VAL* 3.1 12.9 + - + +
572A MET* 3.0 20.1 + - - +
585A HIS 4.1 19.5 - - - +
586A THR* 3.0 23.4 + - + +
588A LEU* 3.9 31.9 - - + -
700A P22 3.4 31.2 - - + +
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Residues in contact with GLY 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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487A GLN* 3.2 26.0 + - - -
565A ASN* 3.9 5.8 - - - -
567A HIS 3.2 2.0 - - - -
568A LEU* 1.3 72.5 - - - +
570A MET* 1.3 56.9 + - - +
572A MET* 2.9 10.8 + - - +
573A GLN 2.8 26.7 + - - -
700A P22 2.6 24.1 + - - -
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Residues in contact with MET 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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352A HIS* 4.1 15.5 - - + +
486A GLY* 3.7 23.1 - - - -
487A GLN* 3.4 33.7 - - + +
490A MET* 3.9 17.9 - - + -
568A LEU 3.3 0.8 + - - -
569A GLY* 1.3 71.8 - - - +
571A VAL* 1.3 62.1 + - + +
573A GLN* 3.4 10.4 + - - +
574A TRP* 3.3 39.4 + - - -
647A VAL* 4.0 8.5 - - + -
695A 1TB 3.8 27.8 - - + +
700A P22 3.0 16.2 + - + +
701A FAD 4.7 9.0 - - + -
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Residues in contact with VAL 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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568A LEU* 3.1 16.2 + - + +
570A MET* 1.3 75.5 - - + +
572A MET* 1.3 63.1 + - - +
574A TRP* 3.1 6.4 + - + +
575A GLU* 3.1 26.2 + - + +
584A ALA 5.7 0.2 - - - +
586A THR* 3.5 22.2 - - + -
695A 1TB 3.7 19.5 - - + -
700A P22 4.2 15.7 - - + -
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Residues in contact with MET 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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487A GLN* 4.6 1.3 - - - +
565A ASN* 3.9 9.0 - - - +
567A HIS* 3.4 30.5 - - + -
568A LEU 3.0 10.7 + - - +
569A GLY* 2.9 13.6 + - - +
571A VAL* 1.3 75.5 - - - +
573A GLN* 1.3 65.6 + - - +
575A GLU* 3.0 24.5 + - - +
576A ASP* 3.0 21.2 + - - +
583A ARG* 3.5 38.6 - - - +
586A THR* 4.3 6.2 - - - +
643A HIS* 3.2 44.9 - - + +
644A GLN* 4.9 2.2 - - - -
645A GLU 5.1 3.4 - - - +
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Residues in contact with GLN 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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352A HIS* 4.3 4.0 - - - -
487A GLN* 3.0 15.3 + - - +
569A GLY 2.8 15.1 + - - +
570A MET* 3.7 16.7 - - - +
571A VAL 3.3 0.2 - - - -
572A MET* 1.3 74.3 - - - +
574A TRP* 1.3 66.1 + - + +
576A ASP* 3.4 3.1 + - - +
577A ARG* 3.1 29.2 + - - +
646A HIS* 3.3 34.8 - - + +
647A VAL* 2.7 54.9 + - - +
650A MET* 3.8 22.6 - - - -
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Residues in contact with TRP 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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351A MET* 4.5 9.1 - - + -
352A HIS* 5.5 1.4 + - - -
377A ARG* 4.4 2.7 - - - -
570A MET* 3.3 25.9 - - - +
571A VAL* 3.1 11.2 + - + +
573A GLN* 1.3 83.4 - - + +
575A GLU* 1.3 63.5 + - - +
578A PHE* 2.9 60.0 + + - +
579A TYR* 3.6 11.9 - + + -
650A MET* 4.4 22.9 - - + +
652A PRO* 6.1 0.2 - - + -
653A SER* 4.1 16.4 - - - -
695A 1TB 3.3 85.8 + + + -
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Residues in contact with GLU 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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571A VAL* 3.1 15.9 + - + +
572A MET* 3.0 12.8 + - - +
574A TRP* 1.3 75.2 - - + +
576A ASP* 1.3 59.0 + - - +
579A TYR* 2.8 40.2 + - + -
581A ALA 3.0 12.1 + - - -
582A ASN 3.5 15.6 - - - +
583A ARG* 3.2 21.6 - - - +
584A ALA* 2.7 36.3 + - - +
586A THR* 2.7 35.5 + - - +
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Residues in contact with ASP 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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572A MET* 3.0 21.9 + - - +
573A GLN 3.5 7.2 - - - +
574A TRP 3.2 0.2 - - - -
575A GLU* 1.3 78.8 - - - +
577A ARG* 1.3 60.2 + - - +
580A LYS* 4.1 6.1 + - - -
581A ALA* 3.3 23.8 + - + +
583A ARG* 2.8 36.4 + - - -
646A HIS* 2.9 32.2 + - + -
666A GLY* 3.5 19.1 - - - +
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Residues in contact with ARG 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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573A GLN* 3.1 25.0 + - - +
576A ASP* 1.3 77.5 - - - +
578A PHE* 1.3 86.5 + - + +
580A LYS 5.2 0.4 - - - -
646A HIS* 3.5 20.6 + - + -
648A LEU* 3.8 12.1 - - - +
650A MET* 4.2 15.9 - - - -
661A ILE* 3.8 37.4 - - - +
663A GLU 3.3 17.6 + - - -
664A GLY* 2.9 34.1 + - - -
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Residues in contact with PHE 578 (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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574A TRP* 2.9 61.2 + + + +
577A ARG* 1.3 100.7 - - + +
579A TYR* 1.3 82.8 + - + +
580A LYS* 3.8 2.2 - - - -
650A MET* 3.6 28.7 - - + -
652A PRO* 4.4 14.6 - - + -
661A ILE* 5.1 5.8 - - + -
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Residues in contact with TYR 579 (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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574A TRP* 3.6 20.6 - + + -
575A GLU* 2.8 29.1 + - + +
578A PHE* 1.3 92.6 - + + +
580A LYS* 1.3 72.5 + - - +
581A ALA 3.1 2.0 - - - -
582A ASN* 3.0 26.4 + - + +
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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