Contacts of the strand formed by residues 328 - 340 (chain A) in PDB entry 1YC9
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 ASP 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ASP* 3.0 28.5 - - - +
157A TRP* 5.5 0.7 - - - -
159A LYS* 2.7 32.6 + - - +
326A TYR 3.4 3.9 + - - +
327A PRO* 1.3 71.9 - - - +
329A VAL* 1.4 60.6 + - - +
330A THR* 3.9 11.1 + - + +
358A ALA 3.7 0.7 - - - +
359A ILE* 3.2 3.5 - - - -
360A TYR* 2.7 45.6 + - + +
362A PRO* 6.4 0.2 - - + -
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Residues in contact with VAL 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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153A ASP* 3.3 6.1 - - - +
154A PHE* 2.9 44.4 + - + +
155A ASP 4.4 2.1 + - - +
156A PHE* 3.8 34.0 - - + +
157A TRP* 5.7 0.9 - - + +
327A PRO* 4.0 7.0 + - + +
328A ASP* 1.4 76.9 + - - +
330A THR* 1.3 66.3 + - - +
357A PRO* 4.6 7.9 - - + -
358A ALA 3.3 11.4 - - - +
359A ILE* 3.7 28.5 - - + -
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Residues in contact with THR 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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151A GLN* 5.5 9.2 - - + -
152A TYR 3.3 8.5 - - - -
153A ASP* 3.7 21.1 - - - +
154A PHE* 3.7 4.4 - - - -
328A ASP* 3.9 12.5 + - - +
329A VAL* 1.3 79.0 - - - +
331A LEU* 1.3 64.6 + - - +
332A SER* 5.3 3.9 + - - -
357A PRO* 3.1 9.5 - - - +
358A ALA* 2.9 42.9 + - - +
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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
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150A PHE* 4.0 23.1 - - + -
151A GLN* 3.4 4.9 - - - +
152A TYR* 2.6 46.6 + - + +
154A PHE* 3.6 28.7 - - + -
330A THR* 1.3 75.8 - - - +
332A SER* 1.3 66.1 + - - +
355A ILE* 4.1 20.4 - - + -
356A GLY* 3.6 28.9 - - - +
357A PRO* 3.8 8.3 - - + -
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Residues in contact with SER 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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150A PHE* 3.4 11.0 - - - -
151A GLN* 3.3 23.7 + - - +
330A THR* 5.3 3.5 + - - -
331A LEU* 1.3 74.5 + - - +
333A ALA* 1.3 65.2 + - - +
354A ALA 4.6 0.2 - - - -
355A ILE* 3.4 2.1 - - - +
356A GLY 3.0 34.3 + - - -
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Residues in contact with ALA 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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149A ASN* 3.5 1.4 - - - +
150A PHE* 2.9 48.4 + - + +
332A SER* 1.3 79.8 - - - +
334A PHE* 1.3 66.9 + - - +
354A ALA 3.0 14.4 - - - +
355A ILE* 4.0 19.1 - - + -
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Residues in contact with PHE 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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147A THR* 3.7 25.8 - - + -
148A LEU 3.1 13.7 - - - +
149A ASN* 3.7 12.8 - - - +
333A ALA* 1.3 78.0 - - - +
335A ILE* 1.3 67.3 + - - +
338A GLN* 4.1 13.7 - - - -
352A ALA* 3.5 29.8 - - + -
353A GLY* 3.1 14.2 - - - -
354A ALA* 2.9 54.7 + - + +
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Residues in contact with ILE 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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147A THR* 3.3 0.5 - - - -
148A LEU* 2.8 49.0 + - + +
334A PHE* 1.3 80.3 - - - +
336A GLY* 1.3 61.4 + - - +
351A ASP* 5.3 4.5 - - + +
352A ALA 3.5 20.0 - - - +
353A GLY* 4.1 9.4 - - - -
1001A BOG 4.1 45.0 - - + +
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Residues in contact with GLY 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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146A LEU 3.2 12.1 - - - -
147A THR* 4.1 4.7 - - - -
334A PHE* 4.4 0.2 - - - -
335A ILE* 1.3 79.8 - - - +
337A TYR* 1.3 69.1 + - - -
351A ASP* 3.2 10.9 - - - +
352A ALA* 2.9 30.3 + - - -
1001A BOG 4.0 10.1 - - - +
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Residues in contact with TYR 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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145A THR* 3.2 2.9 - - - -
146A LEU* 2.8 50.0 + - + +
147A THR* 4.3 0.9 - - - +
336A GLY* 1.3 78.0 - - - -
338A GLN* 1.3 68.0 - - - +
345A LEU* 3.3 36.1 - - + +
346A PHE* 3.7 35.3 - + + -
350A ASN 3.4 6.5 - - - -
352A ALA 4.5 0.4 - - - +
1001A BOG 3.5 69.7 + - + +
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Residues in contact with GLN 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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144A GLY 3.3 7.4 - - - +
145A THR* 3.8 20.7 - - + +
147A THR* 4.8 6.6 - - + +
334A PHE* 4.1 19.7 - - - -
337A TYR* 1.3 80.2 - - - +
339A ALA* 1.4 63.7 + - - +
345A LEU* 4.3 0.2 - - - -
350A ASN* 3.0 26.1 + - - +
352A ALA* 3.4 25.9 - - + +
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Residues in contact with ALA 339 (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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143A TYR* 3.2 10.7 - - - +
144A GLY 2.9 32.5 + - - +
338A GLN* 1.4 75.3 - - - +
340A PHE* 1.3 61.9 + - - +
341A GLY 3.5 7.2 + - - +
344A HIS 3.5 15.7 - - - +
345A LEU* 3.6 17.0 - - + +
350A ASN* 3.5 23.1 - - - +
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Residues in contact with PHE 340 (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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137A PRO* 3.9 18.2 - - + -
141A ASN* 3.5 44.0 - - + -
142A ASP* 3.8 4.7 - - - -
143A TYR* 3.5 34.0 - + + -
339A ALA* 1.3 70.0 - - - +
341A GLY* 1.3 63.7 + - - +
344A HIS* 3.9 16.1 - + - +
350A ASN* 5.3 0.9 + - - +
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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