Contacts of the strand formed by residues 323 - 329 (chain C) in PDB entry 1BPO
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 GLN 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B GLU* 3.7 28.4 + - - +
332B GLU* 4.2 17.2 - - + +
333B ASN* 5.8 0.2 + - - -
9C PHE* 6.1 0.2 - - - -
11C GLU* 3.2 15.6 - - - +
13C LEU 3.7 6.1 - - - -
14C GLN* 3.4 20.6 - - - +
298C ILE 5.7 2.0 + - - -
299C SER* 5.3 1.8 + - - +
318C VAL* 3.2 4.5 - - - -
319C ASN* 3.1 46.2 + - - +
321C LYS* 4.4 10.0 - - + +
322C GLY* 1.3 78.9 - - - +
324C VAL* 1.3 60.6 + - - +
325C LEU* 2.8 40.6 + - + +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU* 3.5 2.0 - - - -
12C HIS* 2.7 41.6 + - + +
13C LEU* 3.1 34.6 + - + -
15C LEU* 4.2 13.7 - - + -
32C MET* 5.3 1.1 - - - -
38C ILE* 3.6 27.6 - - + -
55C MET* 4.1 10.8 - - + -
316C ILE* 3.9 27.1 - - + -
317C GLY 3.3 8.7 - - - +
318C VAL* 4.1 8.5 - - + +
323C GLN* 1.3 73.6 - - - +
325C LEU* 1.3 54.9 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B GLU* 5.1 0.4 - - - +
9C PHE* 3.7 32.8 - - + -
10C GLN 3.2 12.3 - - - +
11C GLU* 4.8 5.4 - - + -
298C ILE* 4.8 5.6 - - + +
299C SER* 4.2 8.3 - - - -
303C ILE* 4.1 27.4 - - + -
316C ILE* 3.0 7.3 - - - +
317C GLY 2.8 31.1 + - - +
319C ASN* 3.7 23.3 - - - +
323C GLN* 2.8 41.3 - - + +
324C VAL* 1.3 74.5 - - - +
326C SER* 1.3 64.4 + - - +
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Residues in contact with SER 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ARG 4.0 0.3 - - - +
9C PHE* 3.5 1.6 - - - -
10C GLN* 2.9 40.8 + - - +
12C HIS* 2.9 34.1 + - - -
309C HIS* 4.2 11.3 - - - -
312C THR* 4.9 1.2 + - - +
315C ILE 3.0 13.2 + - - -
316C ILE* 3.9 7.6 - - - -
325C LEU* 1.3 78.3 - - - +
327C VAL* 1.3 71.0 + - - +
328C CYS* 5.4 0.9 - - - +
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.9 26.0 - - + -
8C ARG 3.5 12.8 - - - +
9C PHE* 4.1 10.5 - - + -
274C PHE* 4.2 7.6 - - + -
282C ILE* 4.1 25.1 - - + -
284C LEU* 4.7 0.2 - - + -
298C ILE* 3.6 36.1 - - + -
312C THR* 4.6 0.3 + - - -
314C GLY* 3.4 0.9 - - - -
315C ILE* 2.9 36.6 + - + +
325C LEU* 5.9 0.2 - - + -
326C SER* 1.3 81.4 + - - +
328C CYS* 1.3 68.8 + - - +
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Residues in contact with CYS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.1 29.7 - - - +
8C ARG* 3.1 52.8 + - - -
10C GLN* 4.5 4.0 - - - -
274C PHE* 4.1 11.0 - - - -
312C THR* 3.3 33.0 - - - +
314C GLY* 4.0 5.6 - - - -
326C SER* 5.4 1.3 - - - +
327C VAL* 1.3 79.7 - - - +
329C VAL* 1.3 69.9 + - - +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PRO 3.7 3.8 - - - -
7C ILE* 4.5 0.9 - - - +
8C ARG* 4.0 4.3 + - - -
270C HIS* 4.2 34.2 + - + +
272C VAL* 4.3 14.8 - - + -
274C PHE* 4.3 9.6 - - + -
284C LEU* 3.7 26.7 - - + -
312C THR 5.4 0.7 - - - +
313C ALA 5.2 1.6 + - - -
328C CYS* 1.3 86.6 - - - +
330C GLU* 1.3 66.4 + - - +
331C GLU* 3.2 15.1 + - - +
334C ILE* 3.5 42.6 - - + -
357C LEU* 5.0 1.1 - - + -
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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