Contacts of the strand formed by residues 239 - 246 (chain G) in PDB entry 1S9C
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 239 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G PRO* 3.5 38.1 - - + -
59G THR* 4.6 3.8 - - + -
94G LEU* 5.9 1.6 - - + -
96G LEU* 3.5 23.7 - - + +
224G ALA* 3.9 33.0 - - + -
228G LEU* 4.0 25.4 - - + -
235G ASP 3.9 0.6 + - - -
236G VAL 3.1 17.9 + - - +
237G SER 3.2 3.3 - - - +
238G ARG* 1.3 76.5 - - - +
240G LYS* 1.3 59.6 + - - +
241G ALA* 4.3 5.2 - - - -
242G VAL* 2.8 39.3 - - + -
286G VAL* 3.7 22.7 - - + -
288G LEU* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G GLU* 3.5 3.7 - - + +
96G LEU* 2.7 37.4 + - - +
237G SER 5.3 1.8 - - - +
238G ARG 3.2 8.0 + - - +
239G PHE* 1.3 76.8 - - - +
241G ALA* 1.3 62.2 + - + +
287G ASP* 3.0 26.4 + - + +
288G LEU 4.4 7.1 + - - +
289G ALA* 3.4 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G TYR* 4.0 12.8 - - + +
94G LEU 3.2 12.6 - - - +
95G GLU* 3.6 18.8 - - + +
96G LEU* 4.7 0.4 - - - +
239G PHE* 3.9 2.3 - - - -
240G LYS* 1.3 84.6 - - + +
242G VAL* 1.3 66.5 + - - +
285G TYR* 4.7 2.6 - - + -
286G VAL* 3.0 5.0 - - - +
287G ASP* 2.7 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G THR* 4.8 4.9 - - + -
93G TYR* 3.4 6.7 - - - -
94G LEU* 2.8 37.2 + - + +
220G PHE* 3.1 39.7 - - + -
224G ALA* 5.1 3.8 - - + -
239G PHE* 2.8 46.4 - - + -
241G ALA* 1.3 74.8 - - - +
243G LYS* 1.3 62.3 + - - +
269G PHE* 5.3 4.5 - - + -
285G TYR* 3.2 14.4 - - - +
286G VAL* 4.0 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLU* 3.3 34.4 + - - +
92G GLN 3.5 11.2 + - - +
93G TYR* 3.8 19.3 - - + +
141G GLN* 4.7 8.5 + - - -
143G SER* 5.5 1.2 - - - -
161G VAL* 4.9 1.2 - - - +
162G LYS 3.0 26.9 + - - +
163G VAL 3.6 15.0 - - - +
164G ALA* 3.7 28.9 - - + +
242G VAL* 1.3 76.5 - - - +
244G ALA* 1.3 73.5 + - - +
269G PHE* 4.4 0.3 - - - -
283G ASN 4.8 0.7 - - - +
284G ALA* 2.9 5.5 - - - +
285G TYR* 2.9 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLU* 3.4 5.9 - - - +
92G GLN 3.0 32.4 + - - +
220G PHE* 3.6 31.4 - - + -
243G LYS* 1.3 81.9 - - - +
245G ARG* 1.3 60.9 + - - +
246G PHE* 5.0 4.7 - - + -
269G PHE* 4.4 3.1 - - + -
281G ILE* 3.8 12.8 - - + -
283G ASN 5.2 0.9 - - - -
284G ALA* 3.6 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLY 4.2 0.7 - - - +
91G GLU* 2.5 38.2 + - + +
163G VAL* 5.8 2.0 - - - +
164G ALA* 3.6 26.9 - - + +
244G ALA* 1.3 74.5 - - - +
246G PHE* 1.3 73.5 + - - +
281G ILE* 3.3 5.5 - - - +
282G SER* 2.8 56.4 + - - +
283G ASN* 3.7 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G HIS* 3.2 52.9 - + + +
90G GLY* 2.8 30.9 + - - +
91G GLU* 3.7 2.7 - - - -
92G GLN* 3.8 21.8 - - + -
216G GLY* 3.2 41.7 - - - -
217G LEU* 3.9 9.9 - - + -
220G PHE* 4.1 16.6 - + + -
244G ALA* 5.0 4.0 - - + -
245G ARG* 1.3 82.2 - - - +
247G ALA* 1.3 63.7 + - - +
280G VAL 3.7 2.7 - - - +
281G ILE* 4.2 17.7 - - + -
----------------------------------------------------------
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