Contacts of the strand formed by residues 144 - 149 (chain I) in PDB entry 5T0G
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 GLY 144 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I GLY 3.7 0.2 - - - +
139I TRP* 3.2 21.0 - - - -
140I ASP* 2.4 56.9 + - - +
141I LYS 4.4 1.0 + - - -
142I HIS 3.5 1.4 - - - -
143I TYR* 1.3 71.6 - - - +
145I PHE* 1.3 63.6 + - - -
146I GLN* 3.6 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ALA 3.9 17.3 - - - +
40I ASN* 4.9 0.9 - - - -
41I ASP* 3.4 15.9 - - - -
42I GLY* 3.2 33.4 - - - +
43I VAL* 5.5 9.9 - - + -
138I GLY 3.3 7.2 - - - +
139I TRP* 3.1 35.9 - + + -
143I TYR 3.5 6.4 + - - +
144I GLY* 1.3 71.6 - - - -
146I GLN* 1.3 65.5 + - - +
147I LEU* 5.8 1.6 - - + -
216I LEU* 5.5 5.2 - - + -
218I ARG* 3.4 31.6 - - + -
57J ARG* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I VAL* 5.4 0.3 - - - +
107I CYS* 3.0 35.0 - - - +
108I GLU* 2.7 27.5 + - - +
136I TYR 4.5 0.3 - - - -
137I ILE* 3.6 18.4 - - - +
138I GLY 3.1 8.4 + - - -
140I ASP* 2.9 17.9 + - - +
143I TYR* 3.1 19.9 - - + +
144I GLY 3.9 5.4 - - - +
145I PHE* 1.3 80.7 - - - +
147I LEU* 1.3 75.6 + - - +
148I TYR* 3.3 20.1 - - + -
57J ARG* 3.2 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I GLY* 4.9 3.6 - - - -
37I ILE 3.4 28.3 - - - +
38I LEU* 4.6 3.4 - - + +
43I VAL* 3.9 14.4 - - + -
45I LEU* 5.6 1.8 - - + -
136I TYR 3.7 2.9 - - - +
137I ILE* 3.7 25.6 - - + -
145I PHE* 5.8 1.1 - - + -
146I GLN* 1.3 85.6 - - - +
148I TYR* 1.3 74.0 + - - +
158I GLY 3.8 0.5 - - - -
159I TRP 2.7 34.2 + - - +
160I LYS* 3.0 31.0 - - + +
161I ALA* 4.5 2.0 - - - +
58J THR* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I CYS* 3.8 17.9 - - + -
108I GLU* 3.8 17.2 - - - +
111I VAL* 4.1 17.5 - - + -
135I LEU* 3.5 9.1 - - - +
136I TYR* 2.9 47.6 + - + +
146I GLN* 3.3 35.8 + - + -
147I LEU* 1.3 81.0 - - - +
149I GLN* 1.3 64.1 + - - +
156I TYR* 4.1 15.3 - + + -
158I GLY* 3.4 17.7 - - - -
159I TRP 4.5 0.7 - - - +
57J ARG* 3.0 33.0 + - - -
58J THR* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I SER* 3.7 3.1 + - - -
134I LEU 2.9 23.7 + - - +
135I LEU* 3.4 17.6 - - + +
136I TYR* 3.8 4.7 - - - -
148I TYR* 1.3 78.5 - - - +
150I SER* 1.3 81.9 + - - +
151I ASP* 3.9 13.7 - - - +
156I TYR* 3.2 7.4 - - - +
157I GLY* 2.4 50.6 + - - +
158I GLY* 3.6 3.3 + - - -
159I TRP* 5.3 1.6 - - + +
162I THR* 3.5 7.1 + - - +
163I CYS 4.7 0.8 + - - -
164I ILE* 3.2 40.1 - - - +
----------------------------------------------------------
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