Contacts of the helix formed by residues 54 - 59 (chain B) in PDB entry 4A69
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 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A CYS* 3.8 35.2 - - - -
301A ARG* 4.4 4.9 + - - -
51B TYR* 4.6 2.4 + - - -
52B GLN 3.8 2.1 + - - -
53B ALA* 1.3 73.7 - - - +
55B GLN* 1.3 64.4 + - - +
56B HIS* 3.2 20.0 + - - +
57B ASP* 2.8 29.8 + - - +
58B MET* 3.2 19.8 + - - +
101B PHE* 4.7 2.5 - - - -
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A CYS* 5.4 1.6 - - - -
341A ASP* 5.5 3.5 - - - +
54B SER* 1.3 73.4 - - - +
56B HIS* 1.3 56.9 + - - +
58B MET* 3.3 3.5 + - - -
59B CYS* 2.9 41.8 + - + -
64B GLU* 3.4 33.9 + - - +
67B ILE* 3.8 15.5 - - + -
68B ASP* 3.0 25.3 + - - +
71B GLN* 2.9 39.8 + - - +
101B PHE* 4.3 5.3 - - - -
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 3.3 49.4 + - - +
333A ALA 3.3 26.2 - - - -
334A PRO* 4.1 13.1 - - + +
335A ASP* 5.9 0.2 - - - -
54B SER* 3.1 12.2 + - - +
55B GLN* 1.3 80.8 - - - +
57B ASP* 1.3 67.3 + - - +
59B CYS* 3.8 8.3 + - - +
60B ARG* 3.9 15.6 + - + +
501C I0P 4.6 6.6 + - - -
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Residues in contact with ASP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 5.4 2.1 + - - -
51B TYR* 2.6 28.9 + - - -
53B ALA* 3.4 10.8 - - + -
54B SER* 2.8 30.6 + - - +
56B HIS* 1.3 80.5 - - - +
58B MET* 1.3 66.1 + - - +
60B ARG* 3.3 35.1 + - - +
108B THR* 5.7 0.2 - - + -
112B LEU* 3.9 26.1 - - + +
152B ILE* 4.1 10.7 - - + +
505B GOL 5.2 1.7 + - - -
501C I0P 5.4 4.2 + - - -
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.9 14.8 - - + +
54B SER 3.2 10.0 + - - +
55B GLN 3.3 5.4 + - - +
57B ASP* 1.3 76.2 - - - +
59B CYS* 1.3 57.2 + - - +
60B ARG 3.2 0.2 - - - -
61B PHE* 3.0 7.4 + - - -
62B HIS* 3.0 26.5 + - + +
67B ILE* 4.0 21.5 - - + -
101B PHE* 3.6 35.9 - - + -
104B CYS* 4.0 7.0 - - + +
105B SER* 3.7 35.2 - - - +
108B THR* 4.5 6.3 - - + +
147B VAL* 3.9 28.3 - - + -
152B ILE* 3.6 16.0 - - + +
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Residues in contact with CYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN* 2.9 45.6 + - + +
56B HIS* 3.8 4.9 + - - +
57B ASP 3.3 0.2 - - - -
58B MET* 1.3 72.9 - - - +
60B ARG* 1.3 63.8 + - - +
61B PHE* 3.0 1.8 + - - -
62B HIS 3.2 20.1 - - - +
63B SER 3.9 5.6 - - - -
64B GLU* 3.9 13.5 - - + +
67B ILE* 3.7 20.9 - - - -
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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