Contacts of the helix formed by residues 550 - 557 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B GLY* 1.3 72.3 - - - +
551B ALA* 1.3 61.8 + - - +
553B PHE* 3.7 3.5 - - - +
554B ASN* 2.8 29.4 + - - +
574B ILE* 4.1 9.1 - - + +
575B LEU 3.8 4.5 + - - +
576B ASN* 3.3 28.4 - - - +
577B ASN* 2.9 10.0 + - - +
578B GLU* 3.6 6.6 - - - +
600B GLN* 2.9 25.6 + - - -
602B ASN* 3.2 20.6 + - - +
605B PHE* 4.2 8.0 - - + -
1699B MG 2.3 29.7 - - - -
1700B TPP 3.5 0.6 + - - -
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Residues in contact with ALA 551 (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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113A TYR* 3.7 12.9 + - - +
137A LYS 4.8 0.5 - - - +
525B MET* 3.6 17.5 - - + +
550B ASP* 1.3 78.5 - - - +
552B SER* 1.3 64.3 + - - +
554B ASN* 3.2 17.0 + - - +
555B MET* 3.6 5.7 + - - +
582B MET* 4.3 10.3 - - + -
600B GLN* 3.8 24.5 - - - +
1700B TPP 2.9 27.2 + - - +
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Residues in contact with SER 552 (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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496B GLY* 4.1 0.2 - - - -
497B VAL 3.0 28.4 + - - -
525B MET* 3.4 17.6 - - - +
526B GLY* 3.3 32.8 - - - +
548B ASP* 3.4 18.6 - - - -
549B GLY 3.9 2.7 - - - -
551B ALA* 1.3 72.6 - - - +
553B PHE* 1.3 64.2 + - - +
555B MET* 3.1 11.7 + - - +
1700B TPP 2.8 25.0 + - - -
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Residues in contact with PHE 553 (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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526B GLY* 5.4 0.7 - - - -
529B LEU* 4.0 21.3 - - + -
546B ASP* 4.7 0.4 - - - -
548B ASP* 3.6 23.1 + - - +
549B GLY 2.9 20.2 + - - +
550B ASP 3.7 4.0 - - - +
552B SER* 1.3 78.6 - - - +
554B ASN* 1.3 62.0 + - - +
555B MET 3.3 0.5 + - - -
556B THR* 3.4 4.2 + - - -
557B LEU* 3.1 39.0 + - + +
560B LEU* 3.7 25.1 - - + -
572B ILE* 3.6 23.3 - - + -
574B ILE* 3.3 28.0 - - + -
605B PHE* 3.7 23.3 - + - -
608B LEU* 4.1 5.8 - - + -
640B LEU* 3.7 12.8 - - + -
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Residues in contact with ASN 554 (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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137A LYS* 3.6 38.3 - - + +
558A THR* 2.8 30.4 + - - +
561A SER* 4.3 1.8 + - - -
612A MET* 5.6 0.4 - - - +
550B ASP 2.8 21.5 + - - +
551B ALA 3.6 8.5 - - - +
552B SER 3.2 1.0 - - - -
553B PHE* 1.3 77.2 - - - +
555B MET* 1.3 64.0 + - - +
556B THR 3.2 0.9 + - - -
557B LEU* 3.5 20.7 + - - +
600B GLN* 3.3 2.9 - - - +
602B ASN* 3.0 18.0 - - - +
603B PRO* 3.5 26.4 - - - +
605B PHE* 4.0 5.4 - - - -
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Residues in contact with MET 555 (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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113A TYR* 4.9 5.6 - - - -
137A LYS 3.3 27.8 + - - +
138A HIS* 3.3 42.8 - - + +
139A GLU* 3.6 9.0 - - - +
169A ASN* 3.4 25.4 - - - +
558A THR* 4.4 6.6 - - - +
140B GLN* 5.2 1.6 - - - +
525B MET* 3.6 32.1 - - + +
526B GLY* 3.8 8.5 - - - -
551B ALA 3.9 7.2 - - - +
552B SER 3.1 14.1 + - - +
554B ASN* 1.3 79.1 - - - +
556B THR* 1.3 60.2 + - + +
1700B TPP 3.5 20.4 - - + -
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Residues in contact with THR 556 (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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138A HIS* 4.8 0.2 - - + -
140B GLN* 4.3 27.8 - - + +
141B GLY* 5.9 2.5 - - - +
144B HIS* 5.2 0.4 - - + -
526B GLY* 2.6 38.2 + - - +
529B LEU* 3.8 6.7 - - - +
530B PRO* 3.6 16.0 - - + +
553B PHE* 3.4 4.9 + - - -
555B MET* 1.3 84.7 - - + +
557B LEU* 1.3 58.2 + - - +
558B THR* 2.9 17.5 + - - -
559B GLU* 3.0 26.0 + - + +
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Residues in contact with LEU 557 (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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557A LEU* 4.2 5.6 - - + -
558A THR* 3.3 38.1 - - - +
612A MET* 4.5 11.0 - - + -
529B LEU* 4.1 9.4 - - - -
553B PHE* 3.1 31.9 + - + +
554B ASN* 3.5 36.3 - - - +
556B THR* 1.3 75.9 - - - +
558B THR* 1.3 70.0 + - - +
559B GLU 3.0 0.7 - - - -
560B LEU* 3.1 25.1 + - - +
603B PRO* 4.7 2.5 - - + -
608B LEU* 3.7 25.6 - - + -
612B MET* 4.1 4.8 - - + +
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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