Contacts of the strand formed by residues 113 - 118 (chain E) in PDB entry 3HPN
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 THR 113 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 3.3 5.9 - - - -
96E TYR* 2.8 58.0 + - + +
111E LEU 4.1 2.8 + - - -
112E PHE* 1.3 71.6 + - - +
114E LYS* 1.3 76.1 + - - +
115E ILE 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ASN* 3.3 29.9 + - - +
94E LEU 3.7 8.1 - - - +
95E TYR* 3.3 35.6 - - + +
96E TYR* 5.1 0.3 - - - -
113E THR* 1.3 86.4 - - - +
115E ILE* 1.3 65.2 + - - +
116E ASP* 3.6 6.3 - - - +
117E THR* 2.9 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ILE* 4.1 6.1 - - + -
94E LEU* 2.7 47.7 + - + +
95E TYR 4.0 3.4 - - - +
96E TYR* 3.5 41.1 - - + -
113E THR 4.3 0.4 - - - +
114E LYS* 1.3 76.9 - - - +
116E ASP* 1.3 64.1 + - + +
141E ARG* 4.1 17.0 - - + -
142E SER 4.4 5.6 - - - +
143E VAL* 3.3 33.2 - - + -
153E LEU* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E LEU* 3.1 27.6 + - - +
114E LYS* 3.6 12.8 - - - +
115E ILE* 1.3 85.5 - - + +
117E THR* 1.3 87.9 + - - +
118E ILE* 3.6 1.9 + - + +
141E ARG* 2.5 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E THR* 3.8 34.1 - - + +
92E PHE 4.1 2.0 - - - +
93E ASN* 3.7 10.9 + - - +
114E LYS* 2.9 22.1 + - - +
116E ASP* 1.3 96.1 + - - +
118E ILE* 1.3 63.3 + - - +
119E ALA* 3.9 5.1 + - + +
141E ARG* 3.5 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LEU* 4.1 8.7 - - + -
73E PHE* 3.5 22.9 - - + -
91E THR* 3.4 7.1 - - - -
92E PHE* 2.7 75.5 + - + +
94E LEU* 3.9 31.2 - - + -
116E ASP 4.2 2.0 - - - +
117E THR* 1.3 76.8 - - - +
119E ALA* 1.3 60.3 + - - +
120E PRO* 4.5 0.7 - - - +
139E GLU* 4.0 11.0 - - + -
141E ARG* 3.9 40.2 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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