Contacts of the strand formed by residues 87 - 96 (chain C) in PDB entry 3RT0
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 87 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU* 4.5 13.7 - - - +
77C VAL 3.1 13.2 - - - +
78C ASP* 4.3 11.4 - - - +
79C LEU* 4.1 6.2 - - - +
85C ALA* 3.8 0.4 - - - +
86C THR* 1.3 89.4 + - - +
88C SER* 1.3 62.9 + - - +
109C GLY* 3.3 8.0 - - - -
110C ASP* 3.2 50.8 + - - +
111C HIS* 3.5 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ARG 3.8 1.4 - - - +
76C GLU* 3.1 8.2 - - - +
77C VAL* 2.9 40.5 + - - +
79C LEU* 5.3 7.6 - - - -
87C LYS* 1.3 77.8 - - - +
89C THR* 1.3 60.4 + - - +
90C GLU* 2.9 27.1 + - - -
106C ILE* 3.6 8.5 - - - +
108C GLY 3.6 6.1 - - - -
109C GLY* 3.9 1.1 - - - -
111C HIS* 3.2 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 3.9 22.9 - - + -
75C ARG 3.6 1.6 - - - +
76C GLU* 2.2 30.9 + - + +
88C SER* 1.3 71.5 + - - +
90C GLU* 1.3 64.7 + - - +
106C ILE* 3.4 5.5 - - - +
107C VAL* 2.8 44.8 + - + -
108C GLY* 2.9 28.6 + - - -
109C GLY* 4.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 3.6 3.7 - - + -
56C LYS* 5.5 1.3 + - - -
59C ILE* 5.8 0.7 - - - +
74C VAL* 3.4 4.5 - - - +
75C ARG* 2.7 81.9 + - + +
77C VAL* 4.0 11.0 - - - +
88C SER* 2.9 25.3 + - - +
89C THR* 1.3 79.8 - - - +
91C VAL* 1.3 59.5 + - - +
104C ILE* 4.2 11.4 - - + -
105C ARG 3.3 6.7 - - - +
106C ILE* 3.7 26.9 - - + +
107C VAL* 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 3.9 3.4 - - - -
72C GLY* 3.6 21.5 - - - +
73C SER 3.3 12.3 - - - +
74C VAL* 4.0 10.8 - - + -
90C GLU* 1.3 74.1 - - - +
92C LEU* 1.3 69.9 + - - +
93C GLU* 3.4 9.5 + - + +
104C ILE* 3.4 3.5 - - - +
105C ARG* 2.9 56.1 + - + +
107C VAL* 4.0 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 3.4 42.5 - - + -
69C LEU* 4.3 2.2 - - + -
70C GLU* 3.7 36.8 - - - +
71C VAL* 3.7 5.0 - - - +
72C GLY* 2.9 27.2 + - - -
73C SER 2.9 13.4 + - - +
91C VAL* 1.3 73.4 - - - +
93C GLU* 1.3 59.7 + - - +
94C ILE 3.3 27.1 - - - +
95C LEU* 4.0 20.0 - - + -
102C LEU* 3.5 18.8 - - + -
103C GLY 3.4 10.5 - - - +
104C ILE* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 3.5 24.5 - - - +
91C VAL* 3.4 10.5 + - + +
92C LEU* 1.3 77.1 - - - +
94C ILE* 1.3 69.7 + - + +
103C GLY* 2.8 17.1 + - - +
104C ILE 4.2 4.7 - - - +
105C ARG* 3.3 50.5 + - + +
117C SER* 4.3 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 4.5 1.3 - - - -
92C LEU* 3.3 10.3 - - - +
93C GLU* 1.3 91.7 - - + +
95C LEU* 1.3 63.5 + - - +
96C ASP* 4.1 17.5 - - + +
101C ILE* 4.1 23.3 - - + +
102C LEU* 3.3 5.5 - - - -
103C GLY* 2.8 38.5 + - - +
119C THR* 5.3 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 4.2 19.7 - - + -
47C ARG* 4.0 32.5 - - + +
69C LEU* 4.4 23.1 - - + +
70C GLU* 4.6 4.5 - - - -
71C VAL* 4.3 13.7 - - + +
92C LEU* 4.0 24.5 - - + -
94C ILE* 1.3 75.6 - - - +
96C ASP* 1.3 59.4 + - - +
97C ASP* 3.5 14.0 + - - +
101C ILE 3.8 1.3 - - - -
102C LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.4 4.5 - - - -
94C ILE* 4.0 8.7 - - + -
95C LEU* 1.3 72.2 - - - +
97C ASP* 1.3 57.6 + - - +
98C ASN* 2.7 42.5 + - - +
99C GLU* 3.0 29.5 + - - +
100C HIS* 2.8 31.2 + - - -
101C ILE* 2.9 31.8 + - + +
----------------------------------------------------------
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