Contacts of the strand formed by residues 145 - 151 (chain G) in PDB entry 3SDI
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 145 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G VAL* 4.1 4.9 - - - -
142G ASP* 2.9 29.6 + - - +
143G GLU 3.7 1.4 - - - -
144G LEU* 1.3 77.2 - - - +
146G PRO* 1.3 79.7 - - - +
147G SER* 3.0 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ARG* 3.4 35.7 + - + -
42G GLY 3.9 5.4 - - - +
43G LYS 3.8 18.6 - - - +
44G ASP* 3.9 4.7 - - - -
45G CYS* 3.1 41.7 - - - +
46G THR* 3.3 4.3 - - - +
140G SER 3.4 8.5 - - - +
141G VAL* 3.9 8.5 - - + -
144G LEU 4.3 3.0 - - - +
145G GLY* 1.3 85.2 - - - +
147G SER* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 6.2 0.7 - - - -
41G ARG* 4.3 4.0 - - - +
46G THR* 3.3 4.6 + - - +
109G CYS* 4.3 7.0 - - - -
110G ASP* 5.5 0.5 + - - -
138G PHE 4.3 0.7 - - - -
139G VAL* 3.2 25.3 - - - +
140G SER* 2.7 25.8 + - - -
142G ASP* 4.1 8.1 - - - +
144G LEU* 4.3 8.8 - - - +
145G GLY 3.0 16.5 + - - -
146G PRO* 1.3 72.6 + - - +
148G ILE* 1.3 66.7 + - - +
149G TYR* 4.0 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 4.9 1.2 - - - +
39G ALA* 3.6 33.0 - - + +
40G VAL 4.0 2.9 - - - -
41G ARG* 3.5 25.1 - - + +
46G THR* 3.7 12.6 - - + -
137G THR* 3.7 26.9 - - + -
138G PHE 3.3 4.5 - - - +
139G VAL* 3.8 4.3 - - + -
147G SER* 1.3 79.3 - - - +
149G TYR* 1.3 76.3 + - - +
159G GLY* 3.3 1.0 - - - -
160G TYR* 3.0 39.8 + - + +
161G LYS 3.8 8.5 - - - +
162G ALA* 3.9 4.9 - - - -
163G THR* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 5.0 5.4 - - + +
63A THR* 3.4 26.5 - - - +
109G CYS* 4.3 2.7 - - - +
110G ASP* 3.5 37.4 - - + +
113G ALA* 3.7 20.0 - - + -
137G THR* 3.6 0.5 - - - -
138G PHE* 2.7 47.4 + - + +
144G LEU* 3.9 19.0 - - + +
147G SER* 4.0 24.7 - - - -
148G ILE* 1.3 92.4 - - - +
150G LYS* 1.3 59.6 + - - +
157G TYR* 4.1 17.0 - + + -
158G VAL 3.3 16.4 - - - -
159G GLY* 3.6 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G ILE* 3.5 22.7 - - + -
136G LEU 3.1 13.5 - - - +
137G THR* 3.4 15.7 - - + +
149G TYR* 1.3 75.6 - - - +
151G THR* 1.3 62.1 + - - +
156G TYR* 3.8 3.6 - - - +
157G TYR* 3.2 21.3 - - - +
158G VAL 3.2 10.6 + - - +
160G TYR* 3.5 29.7 + - + -
163G THR* 2.7 32.6 + - + +
164G ALA 3.1 20.2 + - - -
165G THR* 3.1 20.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
113G ALA* 3.4 32.8 - - + +
116G MET* 4.6 2.4 - - + +
117G ALA* 3.9 13.9 - - + +
120G SER* 5.6 1.9 + - - -
134G VAL 4.3 0.3 - - - +
135G ILE* 3.4 7.2 - - - +
136G LEU* 2.8 62.6 + - - +
138G PHE* 4.1 4.3 - - + -
150G LYS* 1.3 75.2 - - - +
152G ASP* 1.3 61.3 + - - +
156G TYR 3.2 7.0 - - - -
157G TYR* 3.4 23.8 - - + -
----------------------------------------------------------
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