Contacts of the strand formed by residues 303 - 310 (chain A) in PDB entry 1O9S
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 CYS 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A MET* 5.2 0.4 - - - -
301A PRO* 3.4 19.5 - - - +
302A ASN* 1.3 97.9 - - - +
304A ILE* 1.3 61.3 + - - +
319A ILE* 3.5 30.1 - - + -
320A ARG 3.3 8.3 - - - +
321A THR* 3.9 17.7 - - - -
322A LEU* 3.6 10.0 - - - +
331A LEU* 3.9 23.6 - - - -
332A THR 3.0 14.6 + - - +
333A VAL* 3.6 9.4 - - + +
334A ALA 4.3 0.2 + - - -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A CYS* 1.3 72.1 - - - +
305A TYR* 1.3 85.5 + - - +
306A ASP* 3.7 7.4 + - + -
319A ILE* 3.5 4.3 - - - -
320A ARG* 2.9 48.5 + - + +
322A LEU* 3.3 26.9 - - + -
333A VAL* 3.9 10.1 - - + -
5K GLN* 4.3 10.5 - - - +
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A TYR* 3.7 23.2 - + + -
267A LEU* 3.8 17.3 - - + -
292A GLY 4.6 0.7 + - - -
295A ALA 4.3 4.0 + - - -
304A ILE* 1.3 90.0 - - - +
306A ASP* 1.3 58.8 + - - +
317A LYS* 4.2 10.0 - - + +
318A CYS 3.3 7.2 - - - +
319A ILE* 3.3 33.4 - - + -
333A VAL* 3.6 26.5 - - + +
334A ALA 4.1 8.3 - - - -
335A TYR* 3.4 16.7 - + - -
4K MLZ 3.2 45.3 + - + -
5K GLN* 3.5 36.4 + - + +
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE* 3.7 6.9 + - + +
305A TYR* 1.3 74.1 - - - +
307A MET* 1.3 74.3 + - - +
317A LYS* 3.1 10.8 - - - +
318A CYS* 2.6 51.5 + - - -
320A ARG* 3.0 38.5 + - + +
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Residues in contact with MET 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 3.8 14.8 - - - +
269A LEU* 4.1 23.8 - - + +
270A ASP* 5.7 3.1 - - + -
306A ASP* 1.3 89.2 + - - +
308A PHE* 1.3 62.1 + - - +
315A PRO* 6.3 3.4 - - + -
316A ILE 3.9 4.7 - - - +
317A LYS* 3.8 29.4 - - - -
318A CYS* 4.0 4.7 - - - -
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 3.4 33.0 - - + -
146A TYR* 3.2 27.1 - - - -
148A TYR* 5.0 0.4 - + - -
149A PRO* 3.7 24.5 - - + -
241A VAL* 4.2 5.8 - - + -
244A PHE* 3.4 35.2 - + - -
307A MET* 1.3 74.7 - - - +
309A VAL* 1.3 87.0 + - - +
310A HIS* 3.8 15.7 - + + -
315A PRO* 3.6 2.3 - - - +
316A ILE* 2.9 37.3 + - + +
317A LYS 4.2 3.6 - - - -
318A CYS* 3.8 31.6 - - + +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TYR* 3.8 48.6 - - + +
124A PRO* 5.5 4.0 - - + -
125A ASP* 2.8 15.2 + - - +
146A TYR* 4.1 12.0 + - - -
308A PHE* 1.3 86.7 - - - +
310A HIS* 1.3 65.5 + - - +
311A PRO* 4.1 1.7 - - - +
314A GLY* 4.0 7.2 - - - +
315A PRO* 4.4 13.7 - - + -
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Residues in contact with HIS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 3.9 8.8 + + - -
155A LEU* 5.5 1.1 - - + -
193A PHE* 4.9 1.0 - - - -
209A ASP* 2.8 29.3 + - - -
244A PHE* 3.8 32.7 - + - -
308A PHE* 3.8 6.5 - + + -
309A VAL* 1.3 76.7 - - - +
311A PRO* 1.3 72.8 - - + +
312A ARG* 3.0 37.4 + - + -
313A PHE* 3.3 35.5 + + - +
314A GLY* 2.7 44.4 + - - +
316A ILE* 3.9 13.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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