Contacts of the helix formed by residues 578 - 585 (chain A) in PDB entry 5ZR1
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 ILE 578 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A PRO* 3.3 30.1 - - + +
522A THR* 5.0 0.7 - - + -
524A CYS* 3.5 25.8 - - - -
525A TYR* 3.4 17.3 - - + +
565A LEU* 5.5 0.3 - - - +
568A LEU* 6.0 2.0 - - + -
571A MET* 3.3 44.4 - - + +
572A VAL* 3.7 16.6 - - + -
576A GLN* 4.8 0.7 - - - +
577A ASP* 1.3 81.8 - - + +
579A MET* 1.3 65.5 + - - +
580A TYR 3.3 1.6 - - - -
581A ASN* 3.7 1.8 + - - +
582A PHE* 3.2 35.8 + - + -
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Residues in contact with MET 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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476A TYR* 4.6 0.4 - - + -
568A LEU* 3.7 29.2 - - + -
572A VAL* 3.6 26.2 - - + -
576A GLN* 4.2 6.2 + - - +
578A ILE* 1.3 82.4 - - - +
580A TYR* 1.3 61.4 + - - +
582A PHE* 4.0 2.1 + - - -
583A PHE* 3.4 55.7 + - + -
604A LEU* 3.9 22.9 - - + +
605A PRO* 3.7 35.9 - - + -
608A GLN* 4.5 12.3 - - + -
609A LEU* 4.5 9.2 - - + -
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Residues in contact with TYR 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLN* 4.2 4.4 + - - +
577A ASP 4.6 0.4 - - - +
578A ILE 3.3 1.4 - - - +
579A MET* 1.3 79.0 - - - +
581A ASN* 1.3 68.3 + - - +
583A PHE* 3.4 1.7 + - - +
584A ASN* 2.8 60.9 + - + +
609A LEU* 3.7 22.6 - - + +
613A ILE* 3.7 35.2 - - + -
616A ARG* 3.4 16.8 + - - -
617A ILE* 5.6 1.8 - - + -
558B LEU* 3.6 41.5 - - + -
561B HIS* 3.7 27.2 + + + +
562B LEU* 3.9 22.8 - - + +
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Residues in contact with ASN 581 (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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525A TYR* 2.5 34.4 + - + +
543A MET* 3.7 23.7 - - - +
547A GLU* 5.7 0.3 - - - +
577A ASP* 2.7 16.3 + - - +
578A ILE 3.7 3.2 + - - +
579A MET 3.4 0.4 - - - -
580A TYR* 1.3 91.3 - - - +
582A PHE* 1.3 57.5 + - - +
584A ASN* 4.5 2.2 - - - +
585A TRP* 3.0 58.0 + - + +
555B GLU* 4.9 4.4 + - - -
558B LEU* 5.0 5.1 - - - +
561B HIS* 5.1 9.9 + - - -
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Residues in contact with PHE 582 (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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513A ILE* 5.5 0.9 - - + -
524A CYS* 3.5 38.8 - - + -
525A TYR* 4.3 14.8 - + - -
528A LEU* 3.6 32.3 - - + -
563A VAL* 4.5 6.7 - - + -
565A LEU* 3.6 48.0 - - + -
578A ILE* 3.2 26.3 + - + +
579A MET 4.5 1.1 - - - +
580A TYR 3.4 0.2 - - - -
581A ASN* 1.3 79.3 - - - +
583A PHE* 1.3 65.7 + - + +
585A TRP* 3.9 21.1 + + - +
586A THR* 3.4 23.0 + - - +
593A LEU* 4.2 1.1 - - + +
595A VAL* 3.5 19.1 - - + +
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Residues in contact with PHE 583 (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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474A THR* 3.6 29.6 - - + -
476A TYR* 4.7 5.2 - + + -
565A LEU* 4.7 5.2 - - + -
568A LEU* 4.1 12.3 - - + -
579A MET* 3.4 44.1 + - + +
580A TYR* 3.4 3.6 + - - +
581A ASN 3.2 0.4 - - - -
582A PHE* 1.3 81.1 - - + +
584A ASN* 1.3 62.8 + - - +
585A TRP 3.3 0.2 - - - -
586A THR* 2.5 24.2 + - - -
587A THR* 3.7 9.4 - - - +
595A VAL* 3.9 9.4 - - + -
597A ALA* 3.8 27.1 - - + -
605A PRO* 4.8 7.2 - - + -
609A LEU* 4.0 15.3 - - + -
617A ILE* 3.6 28.9 - - + +
619A PHE* 4.7 10.5 - + - -
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Residues in contact with ASN 584 (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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580A TYR* 2.8 53.1 + - + +
581A ASN* 4.0 4.0 - - - +
583A PHE* 1.3 74.3 - - - +
585A TRP* 1.3 66.4 + - + +
587A THR* 2.6 33.0 + - - -
588A TYR* 3.6 18.7 + - - +
616A ARG* 2.8 29.2 + - - +
617A ILE* 5.1 0.8 - - - +
561B HIS* 3.9 22.0 + - - +
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Residues in contact with TRP 585 (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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525A TYR* 3.7 20.9 - + - -
528A LEU* 4.5 0.7 - - + -
543A MET* 4.0 15.5 - - + -
546A LEU* 3.6 40.8 - - + -
547A GLU* 3.8 25.7 + - + +
550A PHE* 3.8 26.7 - + + -
581A ASN* 3.0 40.4 + - + +
582A PHE* 3.9 36.3 - + - +
583A PHE 3.3 0.2 - - - -
584A ASN* 1.3 79.6 - - + +
586A THR* 1.3 59.5 + - - +
587A THR 3.3 0.4 + - - -
588A TYR* 3.6 31.4 + + - -
591A ALA* 3.2 26.2 - - - +
593A LEU* 3.8 16.8 - - + +
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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