Contacts of the strand formed by residues 53 - 57 (chain A) in PDB entry 4O8H
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 PHE 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.4 8.5 - - + -
10A VAL* 4.3 8.3 - - + -
20A VAL* 6.2 0.9 - - + -
52A THR* 1.3 71.3 + - - +
54A HIS* 1.3 61.5 + - - +
55A ARG 3.6 0.7 - - - -
56A VAL* 4.0 10.1 - - + -
62A CYS* 3.8 34.8 - - + -
63A GLN 3.3 18.8 - - - +
64A ALA* 3.6 13.9 - - + -
112A PHE* 4.4 14.8 - + - -
114A ILE* 4.6 11.9 - - + -
142A ILE* 4.1 22.7 - - + -
152A THR* 3.6 17.9 + - - +
156A ILE* 3.0 43.3 + - + +
158A ILE* 3.9 26.7 - - + -
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Residues in contact with HIS 54 (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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52A THR* 3.6 11.5 + - - +
53A PHE* 1.3 73.6 - - - +
55A ARG* 1.3 72.6 + - + +
63A GLN* 3.1 27.4 + - + -
64A ALA* 4.2 7.8 - - - -
66A ASP* 4.3 10.3 - - + +
70A HIS 3.7 19.7 - - - +
71A ASN* 3.4 24.9 - - - -
72A GLY* 3.2 18.8 + - - -
111A GLN* 3.3 24.5 + - - -
150A GLY 3.5 10.3 - - - +
151A ARG* 4.7 1.7 - - - -
152A THR* 4.4 10.1 + - - +
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Residues in contact with ARG 55 (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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53A PHE 3.6 0.4 - - - -
54A HIS* 1.3 98.7 - - + +
56A VAL* 1.3 61.5 + - - +
57A ILE* 3.9 18.1 - - + +
60A PHE* 4.1 7.1 - - - -
61A MET* 3.8 14.0 - - + +
63A GLN* 2.8 64.9 + - + +
149A SER 5.3 2.1 + - - +
150A GLY* 3.3 17.3 - - - -
201A PEG 3.0 50.6 + - - -
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Residues in contact with VAL 56 (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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53A PHE* 4.0 14.6 - - + -
55A ARG* 1.3 80.5 - - - +
57A ILE* 1.3 63.6 + - - +
61A MET 3.7 3.1 - - - +
62A CYS* 3.9 13.9 - - - -
142A ILE* 3.4 40.4 - - + +
143A GLU* 3.6 18.4 - - + +
146A GLY* 3.2 14.6 - - - -
147A SER 3.0 25.1 + - - +
150A GLY* 2.9 12.0 + - - +
152A THR* 3.6 20.4 - - + -
156A ILE* 5.4 0.4 - - + -
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Residues in contact with ILE 57 (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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55A ARG* 3.9 29.6 - - - +
56A VAL* 1.3 79.7 - - - +
58A PRO* 1.4 79.0 - - + +
59A SER 3.4 0.2 + - - -
60A PHE* 3.0 45.2 + - + -
61A MET* 3.0 22.2 + - + +
143A GLU* 4.5 2.0 - - - +
147A SER 3.5 13.2 - - - +
148A LYS* 4.0 19.3 - - + +
149A SER 4.8 1.3 - - - +
150A GLY* 3.7 11.9 - - - +
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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