Contacts of the helix formed by residues 584 - 595 (chain A) in PDB entry 1SNX
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 SER 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A ALA* 5.3 6.9 - - - +
552A PHE* 5.3 0.5 - - - -
579A LYS* 4.5 2.2 - - - -
582A LEU 3.2 9.6 + - - -
583A ALA* 1.3 77.3 - - - +
585A THR* 1.3 57.2 + - - +
586A HIS* 3.1 6.7 - - - -
587A VAL* 2.9 23.9 + - - +
588A TYR* 2.8 34.0 + - - +
615A ILE* 5.6 1.8 - - - -
619A GLY* 4.9 18.0 + - - -
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Residues in contact with THR 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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579A LYS* 3.5 25.7 + - + +
583A ALA 4.1 0.2 + - - -
584A SER* 1.3 73.5 - - - +
586A HIS* 1.3 79.3 + - - +
587A VAL 3.2 0.6 + - - -
588A TYR* 3.9 3.6 + - - +
589A GLN* 3.1 21.7 + - - +
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Residues in contact with HIS 586 (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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584A SER* 3.1 3.4 - - - -
585A THR* 1.3 100.9 + - - +
587A VAL* 1.3 62.4 + - - +
589A GLN* 2.4 50.1 + - - +
590A ILE* 3.5 2.3 - - - +
615A ILE* 2.9 41.7 - - + +
619A GLY 4.6 15.7 - - - -
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Residues in contact with VAL 587 (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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460A LEU* 5.0 7.0 - - + -
548A MET* 4.1 8.5 - - + -
552A PHE* 3.7 36.3 - - + -
583A ALA* 4.2 2.0 - - + -
584A SER* 3.0 35.2 - - - +
586A HIS* 1.3 76.7 - - - +
588A TYR* 1.3 55.7 + - - +
589A GLN 2.7 15.1 + - - -
590A ILE* 2.7 25.8 + - + +
591A MET* 3.1 32.2 + - + -
615A ILE* 4.7 13.2 - - + -
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Residues in contact with TYR 588 (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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576A ARG* 4.0 11.1 + - - +
577A LEU 2.4 32.7 + - - -
578A TYR* 3.3 6.1 - - - -
579A LYS* 3.3 62.4 - - + +
584A SER 2.8 8.5 + - - +
585A THR 4.2 4.5 - - - +
587A VAL* 1.3 76.4 - - - +
589A GLN* 1.3 57.0 + - - +
590A ILE 3.3 0.2 - - - -
591A MET* 3.9 20.6 - - + -
592A ASN* 2.5 75.1 + - - -
595A TRP* 4.4 7.2 - + - -
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Residues in contact with GLN 589 (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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585A THR 3.1 20.2 - - - +
586A HIS* 2.4 55.9 + - - +
587A VAL 2.7 2.2 + - - -
588A TYR* 1.3 81.2 - - - +
590A ILE* 1.3 60.9 + - + +
592A ASN* 3.7 5.7 + - - +
593A HIS* 2.8 34.3 + - + +
615A ILE* 4.8 3.4 - - - +
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Residues in contact with ILE 590 (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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460A LEU* 5.8 0.2 - - + -
548A MET* 4.6 10.5 - - + -
586A HIS 3.5 8.7 - - - +
587A VAL* 2.7 20.5 + - + +
589A GLN* 1.3 70.2 - - + +
591A MET* 1.3 59.2 + - - +
592A ASN 2.8 2.5 - - - -
593A HIS* 2.3 38.6 + - + +
594A CYS* 2.7 16.8 + - - +
608A LEU* 3.7 30.7 - - + -
611A GLN* 4.0 18.2 - - + +
612A LEU* 3.3 36.8 - - + +
615A ILE* 3.6 22.2 - - + -
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Residues in contact with MET 591 (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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545A GLY* 5.3 1.3 - - - -
548A MET* 4.1 16.2 - - + -
549A TRP* 3.4 40.4 - - + -
552A PHE* 5.6 1.6 - - + -
580A PRO* 3.9 11.7 - - + -
583A ALA* 4.4 6.3 - - - -
587A VAL* 3.6 33.7 - - + +
588A TYR* 3.9 23.3 - - + +
590A ILE* 1.3 78.1 - - - +
592A ASN* 1.3 52.1 + - - +
594A CYS* 3.2 9.6 - - - +
595A TRP* 2.6 83.1 + - + -
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Residues in contact with ASN 592 (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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576A ARG* 3.6 12.3 - - + +
588A TYR* 2.5 55.6 + - - +
589A GLN* 3.9 5.8 + - - +
590A ILE 2.6 4.2 + - - -
591A MET* 1.3 70.5 - - - +
593A HIS* 1.3 51.8 + - - +
594A CYS 2.9 5.4 - - - -
595A TRP* 3.0 25.9 - - + +
596A LYS* 2.6 42.3 + - + +
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Residues in contact with HIS 593 (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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589A GLN* 2.8 36.0 + - + +
590A ILE* 2.3 32.9 + - + +
592A ASN* 1.3 72.0 - - - +
594A CYS* 1.3 56.0 + - - -
596A LYS* 3.6 29.7 - - - +
601A ASP 5.0 1.4 + - - -
602A ARG* 3.5 14.9 - - - +
603A PRO* 3.1 44.5 - - + +
611A GLN* 4.6 13.5 + - - -
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Residues in contact with CYS 594 (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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541A VAL* 3.2 36.8 - - - +
542A TRP* 3.3 25.5 - - - +
544A PHE* 4.2 14.6 - - - -
545A GLY* 3.8 22.0 - - - -
548A MET* 4.8 4.7 - - - -
590A ILE* 2.7 25.2 + - - -
591A MET* 3.2 14.6 - - - +
593A HIS* 1.3 81.6 - - - +
595A TRP* 1.3 58.3 + - + +
596A LYS 3.4 1.0 + - - -
602A ARG* 3.9 8.0 - - - -
608A LEU* 4.7 5.2 - - - -
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Residues in contact with TRP 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A TRP* 3.3 34.9 + + + +
545A GLY* 3.6 20.4 - - - -
546A VAL* 3.4 25.1 - - + +
549A TRP* 4.4 2.9 - - + -
559A TYR* 5.0 4.0 - - - -
576A ARG* 2.9 55.7 + - + +
577A LEU* 4.1 26.2 - - + -
588A TYR* 4.4 2.9 - + - -
591A MET* 2.6 62.6 + - + +
592A ASN* 2.8 32.5 + - - +
594A CYS* 1.3 83.2 - - + +
596A LYS* 1.3 66.8 + - - +
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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