Contacts of the helix formed by residues 604 - 615 (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 ALA 604 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B GLU* 3.5 17.7 - - - +
538B LYS* 3.7 15.5 - - - +
541B VAL* 5.0 0.7 - - - -
603B PRO* 1.3 74.8 - - - +
605B PHE* 1.3 70.1 + - - +
606B SER* 2.7 13.6 + - - +
607B ARG* 2.7 21.7 + - + +
608B LEU* 3.3 7.8 + - - -
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Residues in contact with PHE 605 (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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467B CYS* 3.8 18.4 - - - +
470B MET* 3.2 42.8 - - + -
471B ALA* 3.6 17.3 - - + -
474B GLU* 2.7 43.3 + - + +
537B SER* 3.5 11.4 - - - -
540B ASP* 4.3 8.1 - - + -
541B VAL* 3.1 43.3 - - + -
544B PHE* 3.8 27.1 - + + -
604B ALA* 1.3 68.5 - - - +
606B SER* 1.3 63.8 + - - +
608B LEU* 3.0 14.3 + - + +
609B LEU* 2.9 22.3 + - - +
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Residues in contact with SER 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ALA* 4.5 9.4 - - - +
474B GLU* 2.9 13.4 + - - -
604B ALA* 2.7 15.0 + - - +
605B PHE* 1.3 75.8 - - - +
607B ARG* 1.3 79.0 + - - -
609B LEU* 3.2 11.9 + - - +
610B ARG* 3.0 38.4 + - - +
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Residues in contact with ARG 607 (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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603B PRO* 5.0 3.4 - - + -
604B ALA* 2.7 19.7 + - - +
606B SER* 1.3 88.3 + - - +
608B LEU* 1.3 48.5 + - - +
610B ARG* 2.8 27.8 - - + +
611B GLN* 2.6 55.0 + - + +
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Residues in contact with LEU 608 (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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467B CYS* 3.7 9.0 - - - -
541B VAL* 4.2 20.6 - - + -
544B PHE* 4.3 23.8 - - + -
590B ILE* 3.8 28.3 - - + -
593B HIS* 5.4 0.2 - - + -
594B CYS* 4.6 5.6 - - - -
603B PRO* 3.8 24.7 - - + -
604B ALA 3.3 7.1 + - - +
605B PHE* 3.0 31.3 + - + +
607B ARG* 1.3 77.2 - - - +
609B LEU* 1.3 53.2 + - - +
611B GLN* 3.1 12.7 + - - +
612B LEU* 2.6 41.8 + - + +
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Residues in contact with LEU 609 (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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464B LEU* 3.2 29.0 - - + +
467B CYS* 3.9 6.0 - - + -
468B GLU* 3.2 54.5 - - + +
471B ALA* 4.3 13.5 - - + -
605B PHE 2.9 9.7 + - - +
606B SER* 3.2 11.4 + - - +
608B LEU* 1.3 73.7 - - - +
610B ARG* 1.3 78.6 + - - +
613B ALA* 2.9 21.8 + - - +
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Residues in contact with ARG 610 (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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606B SER* 3.0 50.7 + - - +
607B ARG* 2.8 28.5 + - + +
609B LEU* 1.3 84.8 - - - +
611B GLN* 1.3 55.8 - - + +
613B ALA* 2.6 30.6 + - - +
614B GLU* 3.1 8.4 + - - +
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Residues in contact with GLN 611 (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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590B ILE* 4.3 21.0 - - + +
593B HIS* 5.0 10.7 - - - -
603B PRO* 3.8 17.7 - - - +
607B ARG* 2.6 54.1 + - + +
608B LEU* 3.1 23.9 + - + +
610B ARG* 1.3 68.6 - - + +
612B LEU* 1.3 58.6 + - - +
613B ALA 2.9 1.3 - - - -
614B GLU* 2.5 49.6 + - - +
615B ILE* 3.2 7.5 + - + +
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Residues in contact with LEU 612 (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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460B LEU* 3.4 25.4 - - + +
463B CYS* 3.8 27.6 - - + +
464B LEU* 3.0 36.1 - - + +
467B CYS* 3.9 15.9 - - + -
544B PHE* 4.4 7.6 - - + -
548B MET* 5.0 11.7 - - + -
587B VAL* 6.4 0.4 - - + -
590B ILE* 3.5 28.5 - - + -
608B LEU* 2.6 19.1 + - + +
611B GLN* 1.3 69.4 - - - +
613B ALA* 1.3 65.9 + - - +
614B GLU 3.1 0.3 + - - -
615B ILE* 4.6 4.5 - - + +
616B ALA* 3.1 25.6 + - - +
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Residues in contact with ALA 613 (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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464B LEU* 4.2 10.5 - - + +
609B LEU 2.9 17.0 + - - +
610B ARG* 2.6 19.7 - - - +
612B LEU* 1.3 79.4 - - - +
614B GLU* 1.3 62.0 + - - +
616B ALA* 3.7 5.0 + - - +
617B GLU* 3.0 25.8 + - - +
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Residues in contact with GLU 614 (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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610B ARG* 3.1 9.1 + - - +
611B GLN* 2.5 32.8 + - - +
613B ALA* 1.3 70.4 - - - +
615B ILE* 1.3 56.1 + - + +
617B GLU* 2.7 45.7 + - - +
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Residues in contact with ILE 615 (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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460B LEU* 4.0 12.6 - - + +
584B SER* 5.4 1.3 - - - -
586B HIS* 3.2 44.0 - - + +
587B VAL* 3.7 25.1 - - + -
590B ILE* 3.2 28.0 - - + -
611B GLN* 3.2 9.8 + - + +
612B LEU* 4.1 4.0 - - + +
614B GLU* 1.3 85.8 - - + +
616B ALA* 1.3 62.8 + - - +
617B GLU 3.0 7.5 + - - -
618B SER 4.3 1.0 - - - -
619B GLY* 4.1 23.2 + - - +
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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