Contacts of the helix formed by residues 555 - 560 (chain B) in PDB entry 1JB0
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 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B ARG 4.0 0.7 - - - -
553B MET* 3.9 6.4 - - - +
554B PRO* 1.3 73.2 - - - +
556B LYS* 1.3 65.1 + - - +
557B LYS* 3.1 9.6 - - - +
558B ASP* 2.8 36.3 + - - +
559B PHE* 3.5 8.2 - - - -
61C PHE* 3.2 18.6 - - + -
65C ARG* 3.0 47.0 + - - +
67C TYR* 4.5 0.2 + - - -
119D ILE* 3.3 19.2 - - + +
120D GLY* 6.2 1.3 - - - -
13E GLU* 6.4 0.2 - - + -
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Residues in contact with LYS 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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699A GLU* 2.7 38.0 + - - -
543B GLY 5.6 0.6 + - - -
546B ASP* 3.1 20.3 + - - +
547B ALA* 3.0 24.7 - - - +
548B ARG 3.5 7.7 + - - +
549B GLY* 3.6 2.0 - - - -
550B SER* 4.3 4.7 - - - -
553B MET* 3.3 29.4 + - + +
555B ASP* 1.3 76.2 + - - +
557B LYS* 1.3 64.0 + - - +
559B PHE* 2.8 18.5 + - - +
560B GLY 3.7 6.1 + - - +
563B PHE* 3.8 23.3 - - + -
576B ILE* 2.8 30.7 + - - +
577B SER* 4.6 3.5 - - - +
578B ALA 4.8 3.4 - - - +
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Residues in contact with LYS 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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398B VAL* 4.1 20.5 - - + +
547B ALA 4.3 1.8 - - - -
548B ARG* 2.8 57.6 + - + +
554B PRO 5.4 2.7 - - - -
555B ASP* 3.0 9.6 + - - +
556B LYS* 1.3 72.5 - - - +
558B ASP* 1.3 76.5 + - - +
559B PHE 3.2 0.9 + - - -
560B GLY* 3.4 8.7 + - - -
120D GLY 5.7 3.4 + - - -
122D ASN* 4.6 12.5 + - - -
124D ASN* 2.4 42.0 + - - +
125D PRO* 3.7 21.2 - - + +
140F PRO* 6.0 4.5 - - - +
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Residues in contact with ASP 558 (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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555B ASP* 2.8 29.9 + - - +
557B LYS* 1.3 92.9 - - - +
559B PHE* 1.3 67.5 + - + +
560B GLY 3.5 0.2 - - - -
67C TYR* 4.1 23.3 + - + -
119D ILE 4.9 0.5 - - - +
122D ASN* 3.2 26.4 + - - +
123D PRO 4.1 3.5 - - - +
125D PRO* 4.1 4.6 - - - +
135D PRO* 3.3 40.1 - - + +
136D TYR* 5.5 1.4 - - - -
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Residues in contact with PHE 559 (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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553B MET* 3.3 19.7 - - + -
555B ASP* 3.5 24.0 - - - -
556B LYS 2.8 8.2 + - - +
558B ASP* 1.3 81.8 - - + +
560B GLY* 1.3 61.6 + - - +
562B ALA 4.1 6.2 - - - +
563B PHE* 3.5 34.5 - + + +
566B ASP* 4.1 10.5 - - - -
5002B LMG 5.3 1.9 + - - -
51C LYS* 4.4 1.3 - - - -
65C ARG* 3.1 40.6 - - + -
66C VAL 3.7 20.0 - - - -
67C TYR* 3.7 33.0 - + - -
68C LEU 5.6 1.3 - - - -
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Residues in contact with GLY 560 (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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398B VAL* 3.7 19.8 - - - +
399B ARG* 5.7 4.0 - - - -
547B ALA 5.3 0.3 - - - +
556B LYS* 3.7 6.2 + - - +
557B LYS 3.4 9.0 + - - -
558B ASP 3.5 0.8 - - - -
559B PHE* 1.3 79.3 - - - +
561B TYR* 1.3 64.6 + - - +
562B ALA 3.5 1.8 - - - -
563B PHE* 3.2 19.8 - - - -
578B ALA 5.6 0.2 + - - -
5002B LMG 5.7 3.6 - - - -
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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