Contacts of the strand formed by residues 279 - 288 (chain I) 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 ILE 279 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I ALA* 3.1 20.6 - - + +
248I LYS* 3.2 19.7 + - - +
270I GLN* 3.3 29.8 - - + +
271I THR 3.5 5.2 - - - +
272I LYS* 3.9 22.4 - - + -
277I GLY 4.5 2.7 - - - +
278I ASP* 1.3 71.4 - - - +
280I VAL* 1.3 62.3 + - - +
281I ILE 3.6 24.7 - - - +
282I SER* 4.0 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I THR* 3.9 9.2 - - + -
246I PHE* 3.7 4.3 - - - +
247I ALA* 2.8 23.0 + - - -
248I LYS* 3.3 22.9 - - + +
249I PRO 3.6 5.2 - - - +
250I VAL* 3.3 36.3 - - + -
256I LEU* 4.7 0.2 - - + -
271I THR* 2.8 39.6 + - + +
272I LYS* 4.2 3.1 - - - +
273I VAL* 3.5 17.9 - - + -
278I ASP* 4.1 5.2 - - + +
279I ILE* 1.3 76.8 - - - +
281I ILE* 1.3 65.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I THR* 3.6 17.3 - - + +
220I PHE* 3.6 39.3 - - + +
223I SER* 4.7 1.3 - - - +
244I ALA* 3.8 22.7 - - + -
245I ARG 3.3 11.0 - - - +
246I PHE* 4.2 14.6 - - + -
269I PHE* 4.0 17.9 - - + -
270I GLN* 3.5 8.2 - - - +
271I THR* 2.9 38.1 + - - +
279I ILE* 3.6 2.9 - - - +
280I VAL* 1.3 93.5 - - + +
282I SER* 1.3 63.5 + - - +
284I ALA* 4.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I ARG* 2.8 43.7 + - - +
247I ALA* 4.9 7.6 - - - +
269I PHE 4.9 0.2 - - - -
270I GLN* 4.4 9.4 - - - -
279I ILE* 4.0 15.5 - - - -
281I ILE* 1.3 75.8 - - - +
283I ASN* 1.3 90.2 + - - +
284I ALA* 2.9 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ALA* 3.6 18.0 - - + +
165I VAL 2.8 44.2 + - - +
166I ALA* 3.4 22.2 - - - +
167I ILE* 4.4 13.8 + - - +
243I LYS* 4.3 2.1 - - - +
244I ALA* 4.8 0.7 - - - -
245I ARG* 3.8 21.0 - - + +
269I PHE 4.4 2.4 + - - -
270I GLN* 5.0 0.2 - - - +
282I SER* 1.3 98.0 + - - +
284I ALA* 1.3 58.3 + - - +
285I TYR* 4.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I VAL 4.5 1.2 - - - +
167I ILE* 5.2 0.9 - - - +
243I LYS 3.0 16.8 - - - +
244I ALA* 3.6 13.5 - - + -
268I HIS* 3.5 7.3 + - - +
269I PHE* 3.0 58.4 + - + +
281I ILE* 4.1 4.0 - - + -
282I SER 3.8 3.6 - - - +
283I ASN* 1.3 80.4 - - - +
285I TYR* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 285 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I TYR* 3.9 15.7 - + - -
162I LYS* 5.7 1.6 - - - +
163I VAL 4.1 6.1 + - - -
165I VAL* 3.6 35.9 - - + -
241I ALA* 4.7 4.4 - - + +
242I VAL* 3.2 5.6 - - - +
243I LYS* 2.9 62.6 + - + +
266I ARG* 3.3 49.2 + - + -
267I ILE 3.2 14.4 - - - +
268I HIS* 4.1 5.8 - - - +
269I PHE* 3.7 5.2 - - - -
284I ALA* 1.3 79.3 - - - +
286I VAL* 1.3 70.9 + - - +
287I ASP* 3.3 16.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I ALA* 6.0 1.1 - - - -
227I VAL* 3.2 37.2 - - + -
239I PHE* 3.8 27.1 - - + -
241I ALA 3.0 14.4 - - - +
242I VAL* 4.0 8.3 - - + -
265I ASN 3.8 0.3 - - - +
266I ARG* 3.7 0.3 - - - -
267I ILE* 3.0 36.4 + - + +
269I PHE* 4.3 5.2 - - + -
285I TYR* 1.3 79.2 - - - +
287I ASP* 1.3 67.2 + - - +
288I LEU* 3.7 20.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I LYS* 3.0 34.2 + - + +
241I ALA* 2.7 25.3 + - + +
265I ASN* 3.6 4.3 - - + +
266I ARG* 2.8 54.0 + - - +
285I TYR* 3.3 11.4 + - - -
286I VAL* 1.3 73.5 - - - +
288I LEU* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I VAL* 5.2 4.9 - - + -
228I LEU* 5.7 0.4 - - - -
231I PHE* 3.2 33.9 - - + +
232I ALA* 3.9 16.4 - - + -
238I ARG* 3.1 29.4 - - + +
239I PHE* 4.2 9.0 - - + -
240I LYS* 4.5 7.9 + - - +
265I ASN* 2.8 37.6 + - + +
267I ILE* 3.8 28.0 - - + -
286I VAL* 3.9 17.0 - - + +
287I ASP* 1.3 82.1 - - - +
289I ALA* 1.3 62.3 + - - +
----------------------------------------------------------
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