Contacts of the strand formed by residues 330 - 333 (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 GLU 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A SER* 2.6 25.3 + - - -
222A LEU* 3.0 41.0 + - + +
223A ILE* 3.8 12.9 + - - +
229A GLY* 3.7 4.5 - - - -
230A LEU 3.5 10.3 + - - +
231A PHE* 3.5 27.4 - - + -
296A ASN* 3.3 18.4 + - - +
302A ASN* 2.8 27.6 + - - -
328A ASP 3.9 0.4 + - - -
329A GLU* 1.3 76.5 - - - +
331A LEU* 1.3 65.3 + - - +
332A THR* 3.7 9.3 + - + +
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 3.7 29.8 - - + -
230A LEU* 2.7 38.9 + - + +
232A SER* 4.1 11.2 - - - +
242A MET* 3.9 24.9 - - + -
295A ALA* 3.8 17.3 - - + +
296A ASN 4.0 4.9 + - - -
302A ASN* 3.5 3.6 - - - +
303A CYS* 3.9 23.1 - - - -
319A ILE* 4.7 3.1 - - + -
321A THR* 5.1 0.9 - - + -
325A VAL* 3.9 28.9 - - + -
329A GLU 4.3 2.9 - - - +
330A GLU* 1.3 77.5 - - - +
332A THR* 1.3 63.7 + - - +
333A VAL* 5.4 0.2 - - - -
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 4.4 15.7 - - + -
295A ALA* 5.0 0.2 - - - -
296A ASN 3.4 13.2 - - - +
298A SER* 3.7 21.8 + - - -
300A THR 4.4 1.2 + - - -
301A PRO* 3.4 17.8 - - - +
302A ASN* 2.8 16.2 + - - +
303A CYS* 3.0 29.1 + - - +
323A ARG* 5.4 0.5 + - - -
330A GLU* 4.2 19.3 - - + +
331A LEU* 1.3 79.5 - - - +
333A VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 4.4 6.5 - - + -
296A ASN 3.1 7.3 + - - +
297A HIS* 3.2 10.4 - - - -
298A SER 3.1 16.9 + - - -
301A PRO* 3.6 9.2 - - - -
303A CYS* 3.6 20.6 - - + +
304A ILE* 3.9 2.5 - - + +
305A TYR* 3.6 52.5 - - + +
319A ILE* 3.6 30.5 - - + -
331A LEU 5.4 0.2 - - - -
332A THR* 1.3 82.2 - - - +
334A ALA* 1.3 69.4 + - - +
335A TYR* 3.3 2.4 + - + -
5K GLN* 5.8 0.2 - - - +
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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