Contacts of the helix formed by residues 550 - 557 (chain A) in PDB entry 1JSC
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 ASP 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A GLY* 1.3 72.4 - - - +
551A ALA* 1.3 66.7 + - - +
553A PHE* 3.7 2.8 - - - +
554A ASN* 2.8 29.2 + - - +
574A ILE* 4.1 9.6 - - + +
575A LEU 3.8 4.7 + - - +
576A ASN* 3.7 27.6 - - - +
577A ASN* 3.3 9.1 + - - +
578A GLU* 3.5 13.2 - - - +
600A GLN* 6.2 0.7 - - - +
602A ASN* 3.3 26.2 + - - +
605A PHE* 4.2 10.3 - - + -
699A MG 2.1 31.6 - - - -
700A TPP 3.3 0.6 + - - -
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Residues in contact with ALA 551 (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 MET* 3.6 16.6 - - + +
550A ASP* 1.3 78.9 - - - +
552A SER* 1.3 66.1 + - - +
554A ASN* 3.2 20.5 + - - +
555A MET* 3.6 5.4 + - - +
600A GLN* 5.9 9.4 - - + -
602A ASN* 5.3 1.1 - - - -
700A TPP 2.9 32.8 + - + +
113B TYR* 3.8 14.3 + - - +
137B LYS 5.0 0.2 - - - +
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Residues in contact with SER 552 (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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496A GLY* 4.1 0.4 - - - -
497A VAL 3.0 29.2 + - - -
525A MET* 3.4 17.4 - - - +
526A GLY* 3.3 32.6 - - - +
548A ASP* 3.4 17.7 - - - -
549A GLY 3.9 2.7 - - - -
550A ASP 3.3 0.2 - - - -
551A ALA* 1.3 72.6 - - - +
553A PHE* 1.3 63.8 + - - +
555A MET* 3.1 11.8 + - - +
700A TPP 2.7 24.9 + - - -
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Residues in contact with PHE 553 (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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526A GLY* 5.4 0.9 - - - -
529A LEU* 4.0 22.7 - - + -
546A ASP* 4.7 0.4 - - - -
548A ASP* 3.6 22.8 + - - +
549A GLY 2.9 19.1 + - - +
550A ASP* 3.7 4.3 - - - +
552A SER* 1.3 78.0 - - - +
554A ASN* 1.3 60.9 + - - +
555A MET 3.3 0.2 + - - -
556A THR* 3.4 3.8 + - - -
557A LEU* 3.1 37.8 + - + +
560A LEU* 3.7 25.6 - - + -
572A ILE* 3.6 22.9 - - + -
574A ILE* 3.3 28.7 - - + -
605A PHE* 3.7 22.9 - + - -
608A LEU* 4.1 7.9 - - + -
640A LEU* 3.7 12.1 - - + -
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Residues in contact with ASN 554 (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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550A ASP 2.8 24.8 + - - +
551A ALA* 3.6 10.0 - - - +
552A SER 3.2 1.4 - - - -
553A PHE* 1.3 77.8 - - - +
555A MET* 1.3 64.2 + - - +
556A THR 3.2 0.7 + - - -
557A LEU* 3.5 19.6 + - - +
600A GLN* 5.7 0.7 - - - +
602A ASN* 3.0 18.4 - - - +
603A PRO* 3.4 27.0 - - - +
605A PHE* 4.0 6.0 - - - -
137B LYS* 3.6 37.6 - - + +
558B THR* 2.8 28.3 + - - +
561B SER* 4.4 1.6 + - - -
612B MET* 5.7 0.6 - - - +
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Residues in contact with MET 555 (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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140A GLN* 5.3 2.2 - - - +
525A MET* 3.6 31.4 - - + +
526A GLY* 3.8 8.5 - - - -
551A ALA 3.6 7.6 + - - +
552A SER 3.1 15.2 + - - +
554A ASN* 1.3 79.5 - - - +
556A THR* 1.3 61.4 + - + +
700A TPP 3.4 31.6 - - + -
113B TYR* 4.8 5.6 - - - +
137B LYS 3.3 25.1 + - - +
138B HIS* 3.4 37.8 - - + +
139B GLU* 3.6 13.5 - - - +
169B ASN* 3.5 14.6 - - - +
558B THR* 4.4 6.2 - - - +
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Residues in contact with THR 556 (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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140A GLN* 4.4 26.9 - - + +
141A GLY* 6.1 2.5 - - - +
144A HIS* 5.2 1.3 - - + -
526A GLY* 2.6 37.9 + - - +
529A LEU* 3.8 7.4 - - - +
530A PRO* 3.7 15.1 - - + +
552A SER 4.1 0.2 + - - -
553A PHE* 3.4 4.9 + - - -
555A MET* 1.3 86.4 - - + +
557A LEU* 1.3 58.0 + - - +
558A THR* 2.9 17.1 + - - -
559A GLU* 3.0 25.4 + - + +
138B HIS* 4.8 0.7 - - + -
558B THR* 6.0 0.2 - - - -
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Residues in contact with LEU 557 (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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529A LEU* 4.1 9.4 - - - -
553A PHE* 3.1 31.8 + - + +
554A ASN* 3.5 40.1 + - - +
556A THR* 1.3 75.0 - - - +
558A THR* 1.3 70.0 + - - +
559A GLU 3.0 0.4 - - - -
560A LEU* 3.1 25.4 + - - +
603A PRO* 4.5 2.2 - - + -
608A LEU* 3.7 25.8 - - + -
612A MET* 4.0 4.2 - - + +
557B LEU* 4.2 5.6 - - + -
558B THR* 3.4 33.0 - - - +
612B MET* 4.4 11.0 - - + -
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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