Contacts of the strand formed by residues 73 - 79 (chain J) in PDB entry 5DSV
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 VAL 73 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J ASN* 3.6 10.0 - - - +
69J VAL* 3.2 32.7 + - + -
70J ASP* 3.5 16.4 + - + +
71J ARG 3.4 0.4 - - - -
72J HIS* 1.3 111.9 - - + +
74J GLY* 1.3 72.6 + - - +
95J ALA* 5.9 0.2 - - + -
106J ILE* 4.9 2.0 - - + -
108J LEU* 3.7 31.9 - - + -
111J LEU* 4.1 17.3 - - + -
137J LEU* 4.3 6.5 - - + -
138J GLY 3.4 2.7 - - - +
139J SER* 4.2 0.2 - - - -
224J HIS* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J PHE* 3.9 6.0 - - - -
67J PHE 3.4 7.2 - - - -
69J VAL 5.0 0.2 - - - -
73J VAL* 1.3 78.2 - - - +
75J MET* 1.3 60.3 + - - -
136J MET 3.5 0.9 - - - +
137J LEU* 3.2 6.4 - - - -
138J GLY 2.8 34.5 + - - -
224J HIS* 3.4 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J PHE* 5.2 0.8 - - - -
65J ARG 3.8 0.3 - - - +
66J LEU* 3.3 7.3 - - - +
67J PHE* 2.9 41.3 + - + +
69J VAL* 3.7 30.0 - - + +
74J GLY* 1.3 75.4 - - - +
76J ALA* 1.3 65.5 + - - +
77J VAL* 3.7 25.8 - - + -
84J ALA* 3.9 10.1 - - - +
87J LEU* 4.3 5.2 - - + -
88J ALA* 3.8 34.5 - - + +
91J ALA* 4.9 3.1 - - - -
135J PHE* 3.7 26.5 - - + -
136J MET 3.2 4.3 - - - +
137J LEU* 3.8 16.6 - - + -
224J HIS* 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ALA* 5.6 4.3 - - + -
37J ILE 5.5 1.6 - - - +
47J PHE* 3.6 28.9 - - + -
49J VAL* 5.2 3.6 - - + -
65J ARG 3.5 4.9 - - - -
66J LEU* 3.4 21.5 - - + -
75J MET* 1.3 75.5 - - - +
77J VAL* 1.3 61.0 + - - +
135J PHE* 3.1 2.3 - - - -
136J MET* 2.7 40.2 + - + -
165J ILE* 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ALA* 4.2 6.4 - - - +
65J ARG* 3.1 46.0 + - + +
67J PHE* 3.8 27.1 - - + -
75J MET* 3.7 34.1 - - + -
76J ALA* 1.3 79.7 - - - +
78J ALA* 1.3 64.1 + - - +
81J LEU* 4.1 16.4 - - + -
84J ALA* 3.9 16.2 - - + -
134J SER 3.7 5.6 - - - +
135J PHE* 3.7 4.5 - - + -
165J ILE* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J VAL* 3.8 13.9 - - + +
33J SER* 4.4 0.2 - - - +
34J SER 4.3 3.1 - - - +
36J ALA* 4.9 0.9 - - + -
65J ARG* 3.6 16.4 - - - +
77J VAL* 1.3 77.9 - - - +
79J GLY* 1.3 61.6 + - - +
84J ALA* 6.2 0.2 - - - -
133J CYS* 3.4 6.6 - - - +
134J SER 3.0 32.5 + - - +
165J ILE* 3.5 36.3 - - + +
166J GLY* 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ALA 3.6 14.1 - - - -
30J VAL* 3.7 7.4 - - - +
33J SER* 3.1 36.0 + - - -
65J ARG* 5.8 0.9 - - - -
78J ALA* 1.3 73.5 - - - +
80J LEU* 1.3 64.0 + - - -
81J LEU* 3.2 9.6 + - - +
84J ALA* 6.2 0.2 - - - -
132J GLY 3.8 1.8 - - - -
133J CYS* 4.6 0.4 - - - -
----------------------------------------------------------
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