Contacts of the strand formed by residues 55 - 58 (chain H) in PDB entry 3IU3
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 55 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H TRP* 3.3 19.7 - - + -
49H ILE* 3.5 0.9 - - - -
50H TYR* 3.0 29.9 + - + +
53H ASN* 2.2 37.4 + - - +
54H SER* 1.3 64.8 - - - +
56H THR* 1.3 62.9 + - - +
27I ASN* 5.3 1.3 - - - +
28I CYS 4.4 6.2 - - - +
29I GLU* 4.4 10.0 - - - +
36I ARG* 2.7 37.7 + - - +
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Residues in contact with THR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ALA 3.3 8.3 - - - +
49H ILE* 3.8 20.0 - - + -
54H SER* 3.6 10.8 + - - +
55H ASP* 1.3 82.2 + - - +
57H SER* 1.3 60.7 + - - +
58H TYR* 3.3 31.0 + - - +
68H LEU* 3.7 24.7 - - + +
36I ARG* 4.0 12.4 + - - +
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Residues in contact with SER 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H TRP* 4.9 1.5 - - - -
45H TRP* 3.9 17.5 - - - -
47H GLY* 3.1 4.3 - - - -
48H ALA* 2.9 36.4 + - - +
55H ASP 4.4 0.2 + - - -
56H THR* 1.3 75.2 - - - +
58H TYR* 1.3 69.8 + - - +
36I ARG* 3.9 25.8 + - - +
39I SER* 5.2 9.7 + - - -
40I GLY 5.3 3.8 + - - -
41I SER 6.0 0.3 - - - -
42I LEU* 5.1 11.1 - - - +
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Residues in contact with TYR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H TRP* 3.8 9.6 - - - -
46H ILE* 3.7 9.0 - - + -
56H THR* 3.3 31.0 + - - +
57H SER* 1.3 85.2 + - - +
59H ASN* 1.3 65.2 + - - +
60H GLN 3.7 1.6 + - - -
62H PHE 4.6 8.3 - - - -
63H GLU* 3.7 33.3 - - + +
66H ALA* 3.2 27.1 - - + -
67H LYS* 3.6 9.5 - - + +
68H LEU* 2.9 51.1 + - + +
38I LYS* 5.8 1.0 - - - +
39I SER* 4.9 14.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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