Contacts of the strand formed by residues 327 - 338 (chain A) in PDB entry 1NSX
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 LYS 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLU* 2.8 40.1 + - + +
157A ALA 3.5 5.6 - - - +
158A ILE* 4.2 24.8 - - + +
322A LEU* 4.7 2.0 - - - -
325A GLY 3.8 1.8 + - - +
326A GLU* 1.3 79.3 + - - +
328A TYR* 1.3 72.3 + - - +
329A GLN* 3.9 21.4 + - + +
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Residues in contact with TYR 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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155A TYR* 4.0 17.0 - - + -
156A GLU* 3.2 6.2 - - - -
157A ALA* 2.8 38.5 + - + +
165A PHE* 3.7 46.0 - + + -
166A ASN* 4.3 4.5 + - - -
167A PRO* 3.4 23.9 + - + +
273A GLN* 4.1 12.8 + - - -
322A LEU* 3.9 24.8 - - + +
326A GLU 3.7 1.8 + - - -
327A LYS* 1.3 75.5 - - - +
329A GLN* 1.4 70.0 + - - +
330A ALA* 3.4 32.9 - - + +
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Residues in contact with GLN 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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154A HIS* 3.6 13.2 + - + -
155A TYR 3.2 6.5 - - - +
156A GLU* 3.4 28.2 - - + +
272A ASP* 4.4 4.3 - - - +
273A GLN* 4.6 2.9 + - - -
327A LYS* 3.9 24.5 + - + +
328A TYR* 1.4 85.0 - - - +
330A ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 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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154A HIS* 2.9 7.8 + - - -
155A TYR* 2.8 44.1 + - + -
272A ASP* 3.8 8.1 - - - +
273A GLN* 3.4 25.6 - - + +
328A TYR* 3.4 23.3 - - + +
329A GLN* 1.3 76.6 - - - +
331A THR* 1.3 63.8 + - - +
332A THR* 5.9 0.2 - - - +
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Residues in contact with THR 331 (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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152A LYS* 4.0 26.2 - - + -
153A ILE 3.2 9.6 - - - +
154A HIS* 2.9 24.8 + - - +
155A TYR* 5.4 0.2 - - - -
253A LEU* 3.6 30.9 - - + +
271A THR* 3.4 1.7 - - - -
272A ASP* 3.1 38.6 + - - +
273A GLN* 5.4 0.2 - - - +
330A ALA* 1.3 72.4 + - - +
332A THR* 1.3 69.6 + - - +
333A ILE* 4.4 4.3 - - + -
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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
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152A LYS* 3.5 0.5 - - - +
153A ILE* 2.9 45.6 + - + +
155A TYR* 4.9 8.8 - - - -
269A VAL* 4.8 0.9 - - + -
270A PHE 3.5 8.1 - - - +
271A THR* 3.0 17.8 + - - -
273A GLN* 4.7 2.9 - - - +
305A CYS* 3.4 33.0 + - + +
330A ALA* 5.9 0.3 - - - +
331A THR* 1.3 74.2 + - - +
333A ILE* 1.3 68.1 + - - +
334A TYR* 3.8 29.2 - - + +
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Residues in contact with ILE 333 (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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150A LYS* 4.6 22.0 - - + -
151A TRP 3.4 7.2 - - - +
152A LYS* 3.5 26.7 - - + -
253A LEU* 4.4 25.6 - - + +
268A SER 3.5 0.7 - - - +
269A VAL* 3.4 6.6 - - - +
270A PHE* 2.8 59.8 + - + +
331A THR* 4.4 4.5 - - + -
332A THR* 1.3 81.0 - - - +
334A TYR* 1.3 76.3 + - - +
335A SER* 4.2 3.6 - - - +
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Residues in contact with TYR 334 (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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37A TRP* 3.5 16.4 - - + -
151A TRP* 2.7 79.8 + + + -
153A ILE* 4.0 18.1 - - + +
169A GLY* 4.4 6.6 + - - -
171A VAL* 4.0 11.9 - - + +
173A PHE* 3.8 25.6 - + - -
267A ILE* 4.3 4.5 - - + -
268A SER 3.4 2.5 - - - -
269A VAL* 3.9 29.4 - - + -
303A PHE* 2.6 32.4 + - + -
305A CYS* 4.5 1.2 + - - -
332A THR* 3.8 25.7 - - + +
333A ILE* 1.3 76.6 - - - +
335A SER* 1.3 60.5 + - - +
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Residues in contact with SER 335 (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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37A TRP* 4.6 1.6 - - - -
148A ASP 4.8 2.1 + - - -
149A ASN 3.9 3.7 + - - -
150A LYS* 3.9 24.3 - - - +
267A ILE* 3.3 6.4 - - - -
268A SER* 2.9 42.0 + - - +
270A PHE* 4.2 13.2 - - - -
333A ILE* 4.0 3.1 - - - -
334A TYR* 1.3 73.8 - - - +
336A LEU* 1.3 60.8 + - - +
337A HIS* 3.2 26.8 + - - -
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Residues in contact with LEU 336 (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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23A VAL* 4.2 23.3 - - + -
37A TRP* 3.7 21.3 - - + +
39A LYS* 4.4 18.2 - - + +
44A LEU* 4.1 21.5 - - + -
148A ASP 4.4 2.1 - - - +
149A ASN* 3.1 39.4 + - + +
265A THR* 4.1 16.6 - - + -
266A SER 3.7 10.3 - - - +
267A ILE* 3.9 13.7 - - + -
334A TYR 4.1 0.8 + - - -
335A SER* 1.3 73.5 + - - +
337A HIS* 1.3 82.6 + - - +
338A THR* 4.5 4.5 - - - +
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Residues in contact with HIS 337 (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 ASP 6.0 1.1 - - - -
264A ASP 3.8 0.3 - - - +
265A THR* 3.6 1.6 - - - -
266A SER* 2.9 50.7 + - - +
268A SER* 3.6 25.3 + - - -
270A PHE* 5.7 1.2 - - - -
335A SER* 3.2 30.2 + - - -
336A LEU* 1.3 80.0 + - - +
338A THR* 1.3 67.0 + - - +
339A LYS 4.3 0.2 - - - -
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Residues in contact with THR 338 (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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39A LYS* 3.1 39.8 + - - +
264A ASP* 3.2 15.3 - - + +
265A THR* 4.1 4.8 + - - +
336A LEU* 4.5 5.0 - - - +
337A HIS* 1.3 80.0 + - - +
339A LYS* 1.3 73.7 + - - +
340A LEU* 3.5 20.4 + - + +
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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