Contacts of the strand formed by residues 146 - 153 (chain G) in PDB entry 4GUN
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 ALA 146 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E GLN* 4.0 7.4 - - - +
143E ASN* 5.2 0.4 - - - +
146E ALA* 4.5 5.8 - - + -
107G GLN* 4.1 4.0 - - - +
111G GLN* 3.5 18.8 - - - +
138G VAL* 3.9 0.7 - - - +
139G LYS* 3.8 0.4 - - - -
140G ASN* 2.9 32.2 + - - +
143G ASN* 3.3 37.4 + - - +
144G GLY 3.3 1.6 - - - -
145G GLY* 1.3 75.4 - - - +
147G LEU* 1.3 62.9 + - - +
148G ASP* 4.1 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ASN* 3.0 23.7 + - - -
104G LEU* 4.0 10.5 - - + -
107G GLN* 3.8 28.9 - - + -
108G ILE* 3.7 33.0 - - + +
111G GLN* 2.8 16.4 + - - +
112G TYR* 3.4 21.3 + - + +
118G LEU* 4.9 4.0 - - + -
137G ILE* 4.3 12.8 - - + -
138G VAL 3.2 22.4 - - - +
139G LYS* 4.3 0.2 - - - -
146G ALA* 1.3 73.2 - - - +
148G ASP* 1.3 61.3 + - - +
166G ILE* 4.3 2.2 - - + -
204G TYR* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ASN* 3.0 30.7 + - - -
142E GLN* 4.2 5.7 + - - -
143E ASN* 4.2 4.0 + - - +
148E ASP* 4.8 11.4 - - - +
162E HIS* 5.3 0.3 + - - -
163E LEU* 5.9 0.7 - - - +
112G TYR* 3.6 6.2 + - - -
137G ILE* 3.4 5.8 - - - +
138G VAL* 2.8 45.0 + - + +
140G ASN* 6.4 1.3 - - + -
146G ALA 5.1 1.3 - - - +
147G LEU* 1.3 75.9 - - - +
149G VAL* 1.3 82.3 + - - +
150G VAL* 5.5 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E GLN* 4.8 4.9 + - - +
162E HIS* 5.6 1.4 + - - -
112G TYR* 4.1 4.0 - - - +
118G LEU* 3.8 21.3 - - + -
121G ILE* 3.8 17.3 - - + -
122G THR* 3.7 38.6 - - + +
125G LYS* 3.4 42.2 + - + -
135G ALA* 5.0 0.9 - - + -
136G PHE 3.3 12.1 - - - +
137G ILE* 4.5 3.4 - - + -
148G ASP* 1.3 92.0 + - - +
150G VAL* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G LYS* 4.1 5.2 - - - +
135G ALA* 3.3 4.7 - - - +
136G PHE* 2.9 34.9 + - + +
138G VAL* 3.9 22.2 - - + -
148G ASP* 5.5 3.1 - - - +
149G VAL* 1.3 74.5 - - - +
151G THR* 1.3 83.7 + - - +
152G THR* 5.3 1.1 - - + -
158G ILE* 3.6 31.2 - - + -
163G LEU* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G LYS* 3.8 49.9 + - + +
129G ILE* 3.8 22.3 - - + +
134G TRP 3.1 9.6 - - - +
135G ALA* 4.2 3.1 - - + -
136G PHE* 5.2 0.2 - - - -
150G VAL* 1.3 89.1 - - - +
152G THR* 1.3 70.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G ILE* 4.9 2.9 - - - +
133G GLY* 3.3 3.3 - - - -
134G TRP* 2.9 37.0 + - - +
136G PHE* 3.5 30.1 - - + -
150G VAL* 5.2 1.8 - - + -
151G THR* 1.3 82.4 - - - +
153G ALA* 1.3 58.7 + - - +
156G ASP* 2.7 39.0 + - + +
157G THR 4.4 4.3 - - - +
158G ILE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ASN* 5.9 4.9 - - - +
129G ILE* 6.0 0.4 - - - -
130G GLN 6.0 1.8 - - - +
132G SER 3.6 7.6 - - - +
152G THR* 1.3 72.9 - - - +
154G ASN* 1.4 78.7 + - - +
155G GLN 3.2 0.2 + - - -
156G ASP* 3.0 36.1 + - - +
----------------------------------------------------------
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