Contacts of the strand formed by residues 20 - 28 (chain G) in PDB entry 3AOI
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 20 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ARG 5.0 0.4 - - - -
15G THR* 3.4 16.5 + - - -
16G GLN* 3.4 30.8 + - + +
17G GLY 4.4 0.3 - - - +
19G GLU* 1.3 79.5 - - + +
21G GLY* 1.3 80.2 + - - +
22G GLU* 3.0 28.5 + - + -
198G ARG* 2.8 53.7 + - + +
199G ILE 3.5 7.0 - - - -
200G TRP* 3.8 29.4 - + + +
207G PRO* 3.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ARG 3.7 6.7 - - - -
15G THR* 4.4 3.8 - - - -
20G TYR* 1.3 85.0 - - - +
22G GLU* 1.3 60.8 + - - -
23G PHE* 3.1 20.4 - - - -
198G ARG* 3.5 0.2 - - - -
199G ILE 3.0 30.3 + - - -
207G PRO* 3.6 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G VAL* 3.8 0.5 - - - -
14G ARG* 2.9 68.2 + - + +
20G TYR* 3.0 35.1 + - + +
21G GLY* 1.3 72.9 - - - -
23G PHE* 1.3 68.7 + - - +
24G VAL* 4.3 1.5 - - + +
196G THR* 5.1 9.0 + - - -
197G LEU 4.1 1.8 - - - -
198G ARG* 3.4 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F PHE* 6.1 0.4 - - + -
11G PHE* 3.8 29.6 - + + -
12G THR 3.6 2.5 - - - -
13G VAL* 3.5 20.2 - - + -
15G THR* 5.4 2.2 - - - -
21G GLY* 3.1 24.5 - - - -
22G GLU* 1.3 84.2 + - - +
24G VAL* 1.3 61.9 + - - +
25G LEU* 5.4 0.2 - - - -
195G LEU 3.4 2.3 - - - +
196G THR* 2.9 3.7 - - - -
197G LEU* 2.8 59.6 + - + +
199G ILE* 4.1 7.6 - - + -
207G PRO* 3.7 18.4 - - + -
208G LEU* 3.4 44.0 - - + -
211G LEU* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G VAL 3.3 0.8 - - - +
11G PHE* 3.5 4.0 - - - -
12G THR* 3.0 51.7 + - + +
14G ARG* 3.8 27.6 - - - +
22G GLU* 5.5 1.1 - - + +
23G PHE* 1.3 76.0 - - - +
25G LEU* 1.3 66.6 + - - +
26G GLU* 2.9 25.8 - - - +
194G LYS* 4.1 11.0 - - + +
195G LEU 3.4 3.1 - - - -
196G THR* 3.2 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F HIS 5.8 0.4 - - - +
224F TYR* 3.8 20.2 - - + +
225F PHE* 3.8 29.6 - - + -
9G PRO* 3.7 24.9 - - + +
10G VAL 3.4 5.4 - - - -
11G PHE* 4.1 11.7 - - + -
23G PHE 5.3 0.2 - - - +
24G VAL* 1.3 80.8 - - - +
26G GLU* 1.3 59.7 + - - +
28G LEU* 2.9 39.3 - - + +
36G LEU* 4.1 19.3 - - + -
195G LEU* 2.7 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G PRO* 4.1 1.1 - - - -
10G VAL* 2.9 44.0 + - - +
12G THR* 5.2 3.7 - - - +
24G VAL* 2.9 33.2 - - - +
25G LEU* 1.3 74.6 - - - +
27G PRO* 1.3 84.3 - - + +
28G LEU* 3.6 0.4 - - - -
184G THR* 4.3 12.8 - - + +
193G ASP 4.0 0.2 - - - +
194G LYS* 3.6 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LYS* 4.2 20.4 - - + +
8G ALA 4.1 13.7 - - - +
9G PRO* 4.2 11.1 - - - +
10G VAL* 5.2 3.1 - - + -
26G GLU* 1.3 92.8 - - + +
28G LEU* 1.3 75.1 + - - +
184G THR* 4.5 9.0 - - + +
185G ARG 5.5 1.3 - - - +
186G LEU* 3.7 27.8 - - + -
192G LEU* 4.1 19.5 - - + -
193G ASP 3.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F HIS* 6.5 1.1 - - + -
9G PRO* 4.5 6.5 - - + -
25G LEU* 2.9 47.1 - - + +
26G GLU* 3.6 2.2 - - - -
27G PRO* 1.3 94.1 - - - +
29G GLU* 1.3 66.4 - - - +
32G PHE* 4.0 10.5 - - + -
33G GLY* 3.5 31.6 - - - +
36G LEU* 4.6 5.2 - - + -
192G LEU* 3.2 20.7 - - - +
193G ASP* 3.0 27.8 + - + +
195G LEU* 3.7 15.5 - - + +
----------------------------------------------------------
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