Contacts of the strand formed by residues 80 - 88 (chain A) in PDB entry 5U2H
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 MET 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.9 3.4 - - - -
77A GLU* 2.6 41.7 + - - +
78A ASN 3.2 4.9 - - - +
79A GLY* 1.3 86.6 - - - +
81A LYS* 1.3 72.8 + - + +
82A LYS* 3.4 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 6.5 0.7 - - + -
76A LEU* 3.7 15.6 - - + +
80A MET* 1.3 86.7 - - + +
82A LYS* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.2 6.6 - - - +
75A ILE 2.8 43.5 + - - +
76A LEU* 3.9 0.2 - - - +
77A GLU* 4.7 11.2 - - + -
80A MET 3.4 5.3 + - - +
81A LYS* 1.3 76.9 - - - +
83A MET* 1.3 62.1 + - - +
84A VAL* 5.0 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 4.7 5.6 - - - +
73A ALA* 3.8 6.5 - - - +
74A GLU* 3.2 31.0 - - + +
82A LYS* 1.3 75.0 - - - +
84A VAL* 1.3 83.6 + - - +
85A SER* 4.3 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.0 18.2 - - + -
72A LYS* 3.2 2.9 - - - -
73A ALA 2.9 42.8 + - - +
75A ILE* 5.5 4.7 - - + +
82A LYS* 5.0 9.0 - - + +
83A MET* 1.3 82.8 - - - +
85A SER* 1.3 69.6 + - - +
88A PHE* 5.7 2.9 - - + -
108A PHE* 4.8 18.6 - - + -
181A LEU* 5.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL 3.0 9.4 - - - -
72A LYS* 4.3 11.7 - - - -
83A MET* 4.3 10.3 + - - +
84A VAL* 1.3 81.7 - - - +
86A GLY* 1.3 57.9 + - - +
88A PHE* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.4 3.2 - - - +
71A VAL* 2.8 34.3 + - - +
72A LYS* 5.2 0.6 - - - +
85A SER* 1.3 76.7 - - - +
87A VAL* 1.3 61.7 + - - -
88A PHE* 5.0 8.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.8 28.5 - - + -
69A ALA 3.4 16.4 - - - +
70A GLU* 3.5 20.4 - - + -
86A GLY* 1.3 75.9 - - - -
88A PHE* 1.3 74.8 + - - +
89A ASP 4.0 1.2 + - - -
92A ASP* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.4 21.5 - - - +
69A ALA* 2.9 20.0 + - + +
71A VAL* 3.7 20.0 - - + -
84A VAL* 5.7 3.8 - - + -
85A SER 6.4 0.2 - - - -
86A GLY* 5.0 8.1 - - - -
87A VAL* 1.3 82.3 - - - +
89A ASP* 1.3 66.0 + - - +
92A ASP* 3.8 22.7 - - + -
93A TYR* 4.0 12.3 - - + -
105A MET* 5.4 3.6 - - - -
108A PHE* 3.6 38.8 - + - -
182A LEU* 3.6 29.6 - - + -
----------------------------------------------------------
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