Contacts of the helix formed by residues 584 - 595 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ALA* 5.5 5.7 - - - +
552B PHE* 5.3 0.2 - - - -
579B LYS* 4.0 3.1 - - - -
582B LEU 3.4 6.7 + - - -
583B ALA* 1.3 76.2 - - - +
585B THR* 1.3 59.3 - - - +
586B HIS* 3.2 6.5 - - - -
587B VAL* 3.3 33.4 - - - +
588B TYR* 2.4 38.8 + - - +
615B ILE* 5.4 2.4 - - - +
619B GLY 5.9 4.3 - - - -
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Residues in contact with THR 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B LYS* 3.1 26.3 + - - +
584B SER* 1.3 73.3 - - - +
586B HIS* 1.3 79.5 + - - +
588B TYR* 3.9 2.8 - - - +
589B GLN* 2.6 36.9 + - - +
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Residues in contact with HIS 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B SER* 3.2 3.3 - - - -
585B THR* 1.3 97.4 + - - +
587B VAL* 1.3 61.6 + - - +
589B GLN* 2.6 49.9 + - - +
590B ILE* 3.6 3.5 - - - +
615B ILE* 3.2 33.8 - - + +
619B GLY 3.3 28.1 + - - -
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Residues in contact with VAL 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 5.2 7.4 - - + -
548B MET* 4.1 13.0 - - + -
552B PHE* 3.5 43.7 - - + -
583B ALA* 4.4 2.5 - - - -
584B SER* 3.3 32.3 - - - +
586B HIS* 1.3 75.0 - - - +
588B TYR* 1.3 55.8 + - - +
589B GLN 2.6 15.4 + - - -
590B ILE* 2.9 18.2 + - + +
591B MET* 3.4 12.8 + - - +
615B ILE* 3.7 28.5 - - + -
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Residues in contact with TYR 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ARG* 4.2 9.5 + - - +
577B LEU 2.3 33.9 + - - -
578B TYR* 3.3 4.3 - - - -
579B LYS* 3.2 55.4 - - + -
580B PRO* 3.9 2.2 - - + -
583B ALA* 4.6 0.7 - - + -
584B SER 2.4 32.3 + - - +
585B THR 3.9 3.4 - - - +
587B VAL* 1.3 67.4 - - - +
589B GLN* 1.3 52.5 + - - +
591B MET* 3.6 21.9 - - - +
592B ASN* 2.6 57.0 + - - -
595B TRP* 3.9 16.7 - + - -
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Residues in contact with GLN 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B THR* 2.6 22.9 + - - +
586B HIS* 2.6 48.7 + - - +
587B VAL 2.6 4.8 + - - -
588B TYR* 1.3 72.9 - - - +
590B ILE* 1.3 69.1 + - + +
592B ASN* 3.1 15.6 + - - +
593B HIS* 3.4 18.5 + - + +
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Residues in contact with ILE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B PHE* 5.9 1.8 - - + -
548B MET* 5.1 9.2 - - + -
586B HIS 3.6 11.9 - - - +
587B VAL* 2.9 7.8 + - + +
589B GLN* 1.3 74.2 - - + +
591B MET* 1.3 56.9 + - + +
593B HIS* 2.2 47.5 + - + +
594B CYS* 3.0 11.4 + - - -
608B LEU* 3.8 28.5 - - + -
611B GLN* 4.3 17.0 - - + +
612B LEU* 3.5 33.2 - - + +
615B ILE* 3.2 27.6 - - + -
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Residues in contact with MET 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B GLY* 5.0 2.5 - - - +
548B MET* 3.3 29.1 - - + +
549B TRP* 3.4 41.3 - - + +
552B PHE* 5.5 1.8 - - + -
580B PRO* 4.1 14.4 - - + -
583B ALA* 4.5 0.9 - - - -
587B VAL* 3.7 10.1 - - - +
588B TYR* 3.6 33.2 - - + +
590B ILE* 1.3 78.2 - - - +
592B ASN* 1.3 56.7 + - - +
594B CYS* 3.3 10.5 + - - +
595B TRP* 2.8 75.4 + - + -
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Residues in contact with ASN 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ARG* 3.9 15.9 - - - +
588B TYR* 2.6 50.6 + - - -
589B GLN* 3.1 8.8 + - - +
590B ILE 2.6 4.9 + - - -
591B MET* 1.3 71.6 - - - +
593B HIS* 1.3 54.9 + - - +
594B CYS 3.1 1.3 - - - -
595B TRP* 2.8 23.3 + - + -
596B LYS* 2.7 41.0 + - - +
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Residues in contact with HIS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B GLN* 3.4 23.5 + - + +
590B ILE* 2.2 40.4 + - + +
592B ASN* 1.3 70.1 - - - +
594B CYS* 1.3 58.9 + - - +
596B LYS* 3.1 45.5 + - - +
601B ASP 4.6 2.4 + - - -
602B ARG* 3.6 5.2 - - - +
603B PRO* 3.6 41.3 - - + +
611B GLN* 5.0 8.7 - - - -
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Residues in contact with CYS 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B VAL* 3.3 40.4 - - - +
542B TRP* 3.2 29.5 + - - +
544B PHE* 4.1 14.8 - - - -
545B GLY* 3.7 21.5 - - - -
548B MET* 5.2 1.3 - - - -
590B ILE* 3.0 28.7 + - - -
591B MET* 3.4 9.2 - - - +
593B HIS* 1.3 77.9 - - - +
595B TRP* 1.3 59.3 + - - +
596B LYS 3.4 1.2 + - - -
602B ARG* 4.2 5.5 - - - -
603B PRO* 5.9 0.2 - - - -
608B LEU* 4.6 6.3 - - - -
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Residues in contact with TRP 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B TRP* 3.3 35.5 - + + +
545B GLY 3.7 11.9 - - - -
546B VAL* 3.4 23.6 - - + +
549B TRP* 4.3 0.9 - - + -
559B TYR* 4.9 3.4 - - - -
576B ARG* 2.5 64.6 + - + +
577B LEU* 3.9 33.7 - - + -
588B TYR* 3.9 22.7 - + - -
591B MET* 2.8 59.8 + - + +
592B ASN* 2.8 26.5 + - - +
594B CYS* 1.3 84.6 - - + +
596B LYS* 1.3 55.0 + - - +
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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