Contacts of the strand formed by residues 113 - 120 (chain C) in PDB entry 3LON
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 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 4.5 2.2 - - - +
2A PRO* 3.7 15.0 - - + -
34B LYS* 3.5 24.7 - - + +
35B PRO* 3.6 29.2 - - + -
105C TYR* 3.7 34.3 - - + -
106C LEU 3.3 5.4 - - - +
107C VAL* 4.6 7.4 - - + -
111C ALA 4.2 2.2 - - - +
112C ASP* 1.3 78.3 - - - +
114C ILE* 1.3 63.6 + - - +
115C PRO* 3.8 7.8 - - + +
130C ARG* 5.7 2.4 + - - -
134C TYR* 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C TYR* 3.3 3.4 - - - -
106C LEU* 2.7 48.0 + - + +
108C THR* 3.7 22.4 - - + -
112C ASP 4.8 0.2 - - - -
113C VAL* 1.3 79.8 - - - +
115C PRO* 1.3 75.5 - - + +
116C VAL* 3.4 4.3 + - + +
126C LEU* 4.0 29.6 - - + -
128C SER 5.1 4.0 - - - +
130C ARG* 4.5 7.4 - - + +
134C TYR* 3.4 40.6 - - + +
135C LEU* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA 5.1 3.8 - - - +
104C LEU 3.5 7.6 - - - +
105C TYR* 3.9 23.6 - - + -
113C VAL* 3.8 8.3 - - + +
114C ILE* 1.3 86.7 - - + +
116C VAL* 1.3 61.5 + - - +
126C LEU* 3.7 1.6 - - - -
127C LEU* 3.0 49.8 + - + +
128C SER* 4.7 2.4 + - - +
130C ARG* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C SER 3.5 0.2 - - - +
103C ASP* 3.8 1.7 - - - -
104C LEU* 2.8 51.2 + - + +
106C LEU* 4.1 16.2 - - + +
114C ILE* 3.6 11.4 - - + +
115C PRO* 1.3 79.3 - - - +
117C ARG* 1.3 61.4 - - - +
124C GLY* 3.5 34.3 - - - +
125C SER 3.4 6.1 - - - +
126C LEU* 3.7 22.7 - - + -
127C LEU* 4.3 2.7 - - - +
143C LEU* 4.3 11.4 - - + -
167C VAL* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C SER* 3.4 31.5 + - - -
103C ASP* 2.9 34.2 + - - +
116C VAL* 1.3 72.0 - - - +
118C ARG* 1.3 80.7 + - - +
119C ARG* 3.3 27.3 + - - +
124C GLY* 4.0 0.4 - - - -
125C SER* 2.7 47.1 + - - +
127C LEU* 3.5 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLY* 5.6 5.7 + - - -
101C SER 4.6 12.6 + - - -
102C SER* 2.8 33.1 + - - +
104C LEU* 3.7 21.1 - - + +
116C VAL 3.7 1.6 + - - -
117C ARG* 1.3 87.2 + - - +
119C ARG* 1.3 63.2 + - - +
120C GLY 3.3 16.2 + - - +
121C ASP* 2.9 36.6 + - - +
123C ARG 3.6 10.5 - - - +
124C GLY* 4.0 2.7 - - - -
151C VAL* 4.1 16.0 + - - +
169C PHE* 3.5 16.0 - - + -
171C PRO* 4.3 7.3 - - - +
173C GLU* 4.7 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG* 3.5 36.2 + - - +
118C ARG* 1.3 75.6 + - - +
120C GLY* 1.3 58.9 + - - +
123C ARG* 2.7 24.0 + - + +
124C GLY* 4.2 0.9 - - - -
125C SER* 2.7 40.6 + - - +
127C LEU* 5.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ARG* 3.3 16.9 + - - +
119C ARG* 1.3 78.9 - - - +
121C ASP* 1.3 58.2 + - - -
122C SER 2.7 16.4 + - - -
123C ARG* 2.9 22.2 + - - +
169C PHE* 3.9 0.2 - - - -
----------------------------------------------------------
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