Contacts of the strand formed by residues 115 - 120 (chain G) in PDB entry 3TGX
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 TYR 115 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G VAL* 4.5 9.6 - - + -
110G THR 3.7 1.3 - - - -
111G PHE* 3.6 31.6 - + + -
114G GLN* 1.3 70.1 - - - +
116G GLN* 1.3 60.5 + - - +
117G ILE* 3.4 13.0 - - + +
165G SER* 3.4 3.6 - - - -
166G LEU* 2.8 46.0 + - + +
168G PRO* 3.6 33.4 + - + +
171G PHE* 3.5 35.3 - + + +
172G ARG 5.2 0.5 + - - -
204G PHE* 4.1 16.6 - + - -
205G GLN 5.2 1.1 - - - -
206G THR* 3.7 22.5 - - + +
207G GLN* 3.1 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G THR 3.4 5.5 - - - +
109G VAL* 4.4 0.4 - - - +
110G THR* 2.8 46.3 + - - +
112G SER* 4.2 17.0 + - - +
114G GLN* 3.8 27.9 + - - +
115G TYR* 1.3 70.2 - - - +
117G ILE* 1.3 62.1 + - - +
118G SER* 4.0 2.9 + - - -
163G SER* 6.0 1.0 - - - -
164G VAL 3.6 5.4 + - - +
165G SER* 2.5 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G VAL* 4.3 8.1 - - + -
108G THR 3.4 3.6 - - - +
109G VAL* 3.7 12.8 - - + -
115G TYR* 3.4 26.5 - - + +
116G GLN* 1.3 72.3 - - - +
118G SER* 1.3 64.7 + - - +
119G TRP* 3.7 22.6 - - + -
139G LEU* 4.2 6.3 - - + -
163G SER* 3.2 3.1 - - - -
164G VAL* 2.8 45.6 + - + +
166G LEU* 3.7 32.8 - - + -
171G PHE* 4.9 1.8 - - + -
179G LEU* 3.7 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G ASP 3.7 0.2 - - - +
107G VAL* 3.2 2.9 - - - +
108G THR* 2.7 58.6 + - - -
116G GLN 4.5 3.2 + - - -
117G ILE* 1.3 77.3 - - - +
119G TRP* 1.3 66.7 + - - +
162G ARG 3.2 12.6 - - - -
163G SER* 4.0 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PRO* 3.8 21.3 - - + -
105G PHE 4.0 1.6 - - - +
106G ASP 3.8 7.2 - - - -
107G VAL* 3.9 20.2 - - + -
117G ILE* 3.7 29.2 - - + -
118G SER* 1.3 84.1 - - - +
120G ARG* 1.3 70.8 + - - +
124G GLU* 4.8 0.3 - - - +
137G TYR* 3.2 38.3 - + + -
139G LEU* 4.0 16.4 - - + -
157G ILE* 4.5 10.8 - - + -
161G SER 3.2 23.6 - - - -
162G ARG* 3.0 48.9 + - + +
163G SER 4.3 2.5 - - - -
164G VAL* 4.4 13.2 - - + -
181G VAL* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PRO* 3.3 9.5 - - - +
105G PHE* 2.8 65.1 + - + +
106G ASP* 3.7 24.9 + - + +
119G TRP* 1.3 78.8 - - - +
121G SER* 1.3 61.7 + - - +
124G GLU* 2.7 44.8 + - - +
162G ARG* 4.1 3.8 - - - +
----------------------------------------------------------
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