Contacts of the strand formed by residues 323 - 330 (chain A) in PDB entry 1N0W
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 ALA 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LEU* 3.5 23.7 - - + +
313A LYS* 3.4 2.9 - - - +
314A ILE* 3.0 34.1 + - + +
317A SER* 6.6 0.2 - - - -
320A LEU* 4.3 21.3 - - + +
322A GLU* 1.3 77.5 - - - +
324A GLU* 1.3 64.2 + - - +
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Residues in contact with GLU 324 (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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112A LEU* 4.2 6.5 - - - +
303A ARG* 2.8 40.9 + - - -
311A ILE* 4.2 1.1 - - + -
312A CYS 3.2 7.4 - - - +
313A LYS* 3.4 30.7 + - + +
322A GLU* 5.9 0.4 - - + -
323A ALA* 1.3 80.6 - - - +
325A ALA* 1.3 64.4 + - - +
504A EDO 3.3 32.8 + - - -
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Residues in contact with ALA 325 (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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108A GLU* 3.6 35.7 - - + +
109A LEU* 4.3 6.1 - - + +
112A LEU* 3.7 19.7 - - + -
311A ILE* 3.5 1.7 - - - +
312A CYS* 2.9 33.1 + - - +
324A GLU* 1.3 77.7 - - - +
326A MSE 1.3 60.0 + - - +
327A PHE* 4.2 1.4 + - - -
504A EDO 3.9 8.1 - - - -
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Residues in contact with MSE 326 (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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106A SER* 4.1 0.9 + - - -
108A GLU* 3.7 24.2 - - + +
109A LEU 4.7 0.2 + - - -
309A THR* 4.1 18.8 - - - -
310A ARG 3.3 14.6 - - - +
311A ILE* 4.4 11.0 - - + +
325A ALA* 1.3 76.6 - - - +
327A PHE* 1.3 68.8 + - - +
337A ALA* 3.6 29.1 + - + +
504A EDO 3.8 32.2 + - - +
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Residues in contact with PHE 327 (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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106A SER* 3.7 16.2 - - - +
109A LEU* 4.3 15.5 - - + -
131A THR 4.1 6.3 - - - -
132A GLY* 4.5 2.0 - - - -
136A ILE* 4.0 28.0 - - + -
302A LEU* 4.0 8.5 - - + -
309A THR* 3.3 7.3 - - - -
310A ARG* 2.7 64.8 + - + +
311A ILE 4.0 1.8 - - - -
312A CYS* 3.9 23.8 - - + -
325A ALA 4.3 5.6 - - - -
326A MSE 1.3 77.2 - - - +
328A ALA* 1.3 67.3 + - - +
329A ILE* 4.2 14.1 - - + -
334A VAL* 3.8 16.6 - - + -
335A GLY 3.5 12.6 - - - +
337A ALA* 4.0 8.7 - - - +
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Residues in contact with ALA 328 (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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308A GLU* 3.3 29.6 - - + +
309A THR* 4.5 1.1 - - - -
310A ARG 4.6 0.2 - - - +
327A PHE* 1.3 76.7 - - - +
329A ILE* 1.3 65.5 + - - +
330A ASN* 4.3 9.6 - - - +
334A VAL* 3.3 6.6 - - - +
335A GLY 2.8 32.5 + - - +
336A ASP 3.8 19.3 - - - +
337A ALA* 4.0 7.0 - - - -
338A LYS 5.2 0.7 - - - +
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Residues in contact with ILE 329 (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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130A ARG* 4.2 7.2 - - - +
132A GLY* 4.2 3.4 - - - -
135A GLN* 3.9 40.6 - - + +
308A GLU* 3.0 28.8 + - + +
310A ARG* 3.3 47.3 - - + +
327A PHE* 4.2 12.3 - - + -
328A ALA* 1.3 76.6 - - - +
330A ASN* 1.3 66.0 - - - +
333A GLY 4.1 3.1 - - - -
334A VAL* 4.5 3.4 - - + +
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Residues in contact with ASN 330 (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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135A GLN* 5.0 5.0 + - - -
170A ARG* 4.5 6.9 + - - -
177A ARG* 5.8 0.8 - - - +
308A GLU* 4.2 13.2 - - - +
328A ALA* 4.2 8.3 + - - +
329A ILE* 1.3 79.9 - - - +
331A ALA* 1.3 67.3 + - - +
332A ASP* 3.1 15.5 + - - +
333A GLY* 3.0 29.0 + - - +
334A VAL 4.7 0.2 - - - -
335A GLY* 4.0 19.4 - - - +
336A ASP 5.2 2.0 + - - -
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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