Contacts of the strand formed by residues 91 - 95 (chain U) in PDB entry 3J45
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 LYS 91 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821 U 3.4 27.7 + - - -
831 A 3.6 37.7 + - - +
5U ARG* 5.0 9.7 + - - -
84U PHE* 4.0 28.6 - - + +
87U GLU* 3.5 28.3 + - - +
90U LYS* 1.3 91.5 - - + +
92U VAL* 1.4 60.6 + - - +
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Residues in contact with VAL 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83U GLY 3.3 12.0 - - - +
84U PHE* 3.5 15.1 - - - -
86U PHE* 3.3 29.8 + - + +
88U ASP* 3.4 35.9 - - + +
90U LYS* 3.9 6.7 - - + +
91U LYS* 1.4 73.6 - - - +
93U ARG* 1.4 60.1 + - - +
94U PHE* 4.1 2.6 - - - -
103U LYS* 4.0 24.9 - - + +
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Residues in contact with ARG 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2U ALA* 3.3 30.1 + - - +
3U LYS* 3.6 18.5 + - - +
4U ILE 3.1 25.0 + - - -
5U ARG* 3.6 43.0 - - - +
71U ILE* 6.1 0.4 - - - -
82U VAL* 4.2 16.8 - - + -
83U GLY 3.4 5.4 - - - -
84U PHE* 3.9 15.0 - - + -
92U VAL* 1.4 73.7 - - - +
94U PHE* 1.3 75.1 + - - +
95U PHE* 5.3 10.3 - - + -
103U LYS* 3.4 35.2 + - - +
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Residues in contact with PHE 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82U VAL* 3.5 8.1 - - - +
83U GLY* 3.0 49.5 + - - -
85U ARG* 3.8 12.6 - - + -
86U PHE* 3.6 47.3 - + + -
92U VAL 4.1 3.8 - - - -
93U ARG* 1.3 79.1 - - - +
95U PHE* 1.4 75.5 + - - +
96U LYS* 3.4 40.6 - - + -
101U THR* 3.8 38.8 - - + -
102U ILE 3.9 8.7 - - - +
103U LYS* 4.6 6.1 - - + -
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Residues in contact with PHE 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71U ILE* 4.2 19.3 - - + -
72U PHE 4.9 2.5 - - - -
73U ASN* 3.2 60.1 - - + +
74U ALA* 5.3 0.2 - - + -
82U VAL* 4.3 7.6 - - + -
93U ARG* 5.3 10.8 - - + -
94U PHE* 1.4 85.8 - - - +
96U LYS* 1.3 60.9 + - - +
97U SER* 3.5 8.1 - - - +
99U SER* 3.3 15.7 - - - +
100U GLU* 3.6 32.3 - - + +
101U THR* 3.5 7.8 + - - +
102U ILE* 2.9 40.8 - - + -
103U LYS* 4.8 6.5 - - - -
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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