Contacts of the strand formed by residues 140 - 153 (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 TRP 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.5 51.6 - - + +
125A SER* 3.5 4.3 - - - -
126A LYS* 3.5 40.2 - - + +
139A GLY* 1.3 75.6 - - - -
141A ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 141 (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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124A GLU* 3.3 8.0 - - - -
125A SER 2.9 31.5 + - - +
137A PRO* 3.9 11.7 - - - +
138A ASP 2.9 26.5 + - - +
139A GLY 3.3 5.7 - - - +
140A TRP* 1.3 77.2 + - - +
142A ASP* 1.4 62.9 + - - +
143A TYR* 3.4 14.3 - - + -
340A PHE* 3.5 39.5 - - + -
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Residues in contact with ASP 142 (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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123A THR 3.3 6.5 - - - +
124A GLU* 3.3 16.7 + - - +
141A ASN* 1.4 77.7 + - - +
143A TYR* 1.3 60.5 + - - +
340A PHE* 3.7 3.3 - - - -
341A GLY* 2.7 35.8 + - - -
342A LEU* 2.9 42.2 + - + +
343A ASP* 4.6 2.8 - - - +
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Residues in contact with TYR 143 (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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122A ALA* 3.3 3.6 - - - -
123A THR* 2.8 42.5 + - - +
125A SER* 3.8 26.4 + - - -
127A VAL* 4.5 9.3 - - + +
137A PRO* 3.4 27.7 - - - +
141A ASN* 3.4 26.8 - - + +
142A ASP* 1.3 76.7 - - - +
144A GLY* 1.3 59.4 + - - +
145A THR* 6.1 1.3 - - + -
339A ALA 3.2 9.6 - - - +
340A PHE* 3.5 37.9 - + + -
341A GLY 4.3 0.2 - - - +
342A LEU* 3.4 7.7 - - - +
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Residues in contact with GLY 144 (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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121A SER* 3.3 10.5 - - - -
143A TYR* 1.3 76.5 - - - +
145A THR* 1.3 70.0 + - - +
338A GLN* 3.3 0.5 - - - -
339A ALA 2.9 32.3 + - - +
342A LEU* 3.4 18.1 - - - +
345A LEU* 3.5 12.0 - - - +
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Residues in contact with THR 145 (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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119A ALA* 5.0 1.6 + - - +
120A ALA* 3.2 6.4 - - - +
121A SER* 2.6 55.8 + - - +
143A TYR* 5.8 1.6 - - + -
144A GLY* 1.3 80.9 - - - +
146A LEU* 1.4 64.6 + - - +
147A THR* 4.9 6.9 + - - +
337A TYR 3.2 9.9 - - - -
338A GLN* 3.8 24.7 - - + +
345A LEU* 4.0 5.7 - - - +
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Residues in contact with LEU 146 (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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118A LEU* 4.2 22.2 - - + -
119A ALA 3.4 7.6 - - - +
120A ALA* 3.7 20.2 - - + -
145A THR* 1.4 77.5 - - - +
147A THR* 1.3 60.8 + - - +
336A GLY* 3.2 3.6 - - - -
337A TYR* 2.8 43.3 + - + -
345A LEU* 4.3 12.5 - - + +
346A PHE* 4.0 29.4 - - + -
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Residues in contact with THR 147 (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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118A LEU* 3.4 7.9 - - - +
119A ALA* 2.8 46.8 + - - +
145A THR* 4.9 5.4 + - - -
146A LEU* 1.3 86.3 - - - +
148A LEU* 1.3 59.8 + - - +
149A ASN* 2.8 22.7 + - - +
334A PHE* 3.7 30.1 - - + -
335A ILE 3.3 7.6 - - - -
336A GLY* 4.1 6.1 - - - -
337A TYR 4.3 6.1 - - - +
338A GLN* 4.8 8.5 - - - +
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Residues in contact with LEU 148 (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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116A LEU* 4.7 18.6 - - + -
117A GLY 3.5 21.3 - - - +
118A LEU* 4.6 5.8 - - + +
147A THR* 1.3 71.8 - - - +
149A ASN* 1.3 67.6 + - - +
334A PHE* 3.1 5.7 - - - -
335A ILE* 2.8 45.4 + - + +
1001A BOG 3.8 35.9 - - + -
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Residues in contact with ASN 149 (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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115A ASP 3.8 0.2 - - - +
116A LEU* 3.2 9.4 - - - +
117A GLY* 2.9 40.5 + - - +
119A ALA* 3.9 19.8 - - - +
147A THR* 2.8 26.4 + - - -
148A LEU* 1.3 77.2 - - - +
150A PHE* 1.3 61.5 + - - +
333A ALA 3.5 5.4 - - - +
334A PHE* 3.7 9.0 - - - +
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Residues in contact with PHE 150 (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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114A PHE* 3.4 44.9 - + + -
115A ASP 3.2 10.1 - - - -
116A LEU* 3.6 22.7 - - + -
149A ASN* 1.3 77.6 - - - +
151A GLN* 1.3 62.2 + - - +
152A TYR* 3.7 24.2 - - + -
331A LEU* 4.0 22.0 - - + -
332A SER* 3.4 5.2 - - - -
333A ALA* 2.9 54.7 + - + +
355A ILE* 6.2 0.7 - - + -
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Residues in contact with GLN 151 (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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113A SER 4.7 0.5 - - - +
114A PHE* 3.4 4.0 - - - +
115A ASP* 2.9 41.9 + - + +
150A PHE* 1.3 78.3 - - - +
152A TYR* 1.3 67.2 + - - +
153A ASP 5.3 0.2 - - - +
330A THR* 5.5 8.5 - - + -
331A LEU 3.4 9.4 - - - +
332A SER* 3.3 15.8 + - - +
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Residues in contact with TYR 152 (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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111A ILE 5.7 0.2 - - - -
112A ARG 3.7 23.7 + - - -
113A SER 3.9 5.4 - - - -
114A PHE* 3.8 24.0 - + + +
150A PHE* 3.7 23.3 - + + -
151A GLN* 1.3 80.2 - - - +
153A ASP* 1.3 82.7 + - - +
154A PHE* 3.8 42.8 + + - -
155A ASP* 5.4 1.2 - - - +
330A THR* 3.3 3.2 - - - -
331A LEU* 2.6 47.8 + - + +
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Residues in contact with ASP 153 (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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111A ILE* 4.7 9.3 - - + +
112A ARG* 6.0 0.7 - - - -
113A SER 5.2 1.2 + - - -
151A GLN* 5.3 0.4 - - - +
152A TYR* 1.3 92.4 + - - +
154A PHE* 1.3 64.9 + - - +
155A ASP* 3.4 8.9 + - - +
159A LYS* 5.1 2.9 - - - -
160A ASN* 2.8 32.8 + - - +
328A ASP* 3.0 30.2 - - - +
329A VAL 3.3 7.6 - - - +
330A THR* 3.7 10.0 - - + +
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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