Contacts of the strand formed by residues 140 - 145 (chain G) in PDB entry 3STJ
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 PHE 140 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G GLY 4.4 0.2 - - - -
139G ASP* 1.3 76.7 - - - +
141G ALA* 1.3 60.1 + - - +
156G SER* 5.6 4.9 - - - +
157G GLY 3.6 7.9 - - - +
158G ILE* 3.7 24.0 - - + -
193G ASN* 3.9 18.9 - - - +
194G LEU* 3.8 35.2 + - + +
199G ILE* 4.8 2.9 - - - +
13I PRO* 3.2 34.1 + - + -
14I SER* 3.7 18.6 - - - -
15I LEU* 3.8 25.1 - - + -
156I SER* 5.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G ASP 3.8 0.2 + - - -
140G PHE* 1.3 76.2 - - - +
142G VAL* 1.4 65.7 + - - +
143G ALA 4.4 0.2 + - - -
156G SER* 3.6 3.3 + - - -
157G GLY 2.9 34.7 + - - +
158G ILE 4.5 1.1 - - - -
159G VAL* 4.5 9.0 - - + -
178G THR* 4.2 12.8 - - - +
180G ALA* 4.5 1.9 - - - +
191G LEU* 3.9 23.1 - - + -
192G LEU 3.2 9.2 - - - +
199G ILE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 3.7 26.5 - - + -
18G MET* 4.1 20.2 - - + -
19G LEU* 4.1 24.9 - - + -
141G ALA* 1.4 78.5 - - - +
143G ALA* 1.3 64.5 + - - +
144G VAL* 4.2 5.4 - - + -
154G ALA* 4.3 8.3 - - + -
155G THR 3.3 16.4 - - - +
156G SER* 4.5 3.6 - - - +
190G ALA 3.6 1.9 - - - +
191G LEU* 3.5 3.9 - - - -
192G LEU* 2.8 45.7 + - + +
193G ASN 4.9 0.7 - - - +
194G LEU* 4.9 8.5 - - + -
158H ILE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G ALA 4.3 0.6 - - - -
142G VAL* 1.3 71.7 - - - +
144G VAL* 1.3 60.2 + - - +
145G GLY 4.2 0.4 - - - -
153G THR 3.6 1.0 - - - +
154G ALA* 3.2 5.0 - - - -
155G THR* 2.7 53.9 + - - +
180G ALA* 4.0 9.1 - - + +
181G SER 4.4 0.4 - - - +
182G ILE* 4.0 19.5 - - + -
186G ASN* 4.6 5.3 - - - +
190G ALA 3.3 5.2 - - - -
191G LEU* 4.2 6.4 - - + +
202G ASN* 3.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 4.3 0.2 - - + -
23G LEU* 3.6 33.9 - - + -
26G VAL* 3.5 28.2 - - + +
142G VAL* 4.2 11.7 - - + -
143G ALA* 1.3 77.2 - - - +
145G GLY* 1.3 60.4 + - - +
152G GLN* 3.7 19.3 - - + -
153G THR 3.4 5.6 - - - +
154G ALA* 4.3 3.4 - - + -
186G ASN* 4.4 2.2 - - - +
189G GLY* 3.4 3.1 - - - -
190G ALA 2.8 36.4 + - - +
192G LEU* 3.8 25.4 - - + -
202G ASN* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G VAL* 4.6 4.0 - - - -
27G VAL 5.7 0.2 - - - -
66G SER* 3.3 16.2 - - - -
144G VAL* 1.3 76.8 - - - +
146G ASN* 1.3 57.1 + - - -
147G PRO* 3.5 7.3 - - - +
152G GLN* 3.5 5.9 - - - +
153G THR 2.8 34.5 + - - +
186G ASN* 3.8 14.7 + - - -
189G GLY* 4.7 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