Contacts of the helix formed by residues 119 - 132 (chain A) in PDB entry 1YNU
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A THR* 2.7 33.0 + - - -
118A ALA* 1.3 74.4 - - - +
120A ALA* 1.3 60.2 + - - -
121A THR 3.2 2.7 - - - -
123A ALA 3.2 8.8 + - - -
281A ARG* 3.1 26.8 + - - -
282A VAL 4.0 3.6 - - - -
283A GLY* 3.3 13.8 - - - +
600A PY4 3.5 6.1 - - - -
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Residues in contact with ALA 120 (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 GLY* 1.3 68.1 - - - -
121A THR* 1.3 58.5 + - - +
122A SER 3.2 1.6 - - - -
123A ALA* 3.5 9.6 - - - +
124A ASN* 2.8 38.2 + - - +
230A ASP* 5.0 0.7 - - - +
232A ILE* 4.2 3.4 - - + -
268A VAL* 4.2 11.2 - - + -
269A TYR 3.9 8.3 - - - +
270A SER* 3.7 17.3 - - - -
283A GLY* 4.1 1.6 - - - -
600A PY4 2.6 39.9 + - + +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 5.2 0.2 - - - -
120A ALA* 1.3 80.9 - - - +
122A SER* 1.3 61.7 + - - +
124A ASN* 3.5 3.0 + - - +
125A GLU* 3.3 21.8 + - - +
145A TYR* 5.2 0.9 + - - -
150A ARG* 3.5 16.6 + - - +
151A ASP* 3.3 35.8 + - + +
281A ARG* 4.0 8.1 + - - -
600A PY4 2.6 39.0 + - - -
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 3.8 5.2 - - - +
118A ALA* 3.3 36.7 + - - -
119A GLY 3.4 3.7 + - - -
120A ALA 3.2 0.4 - - - -
121A THR* 1.3 81.5 - - - +
123A ALA* 1.3 58.9 + - - +
125A GLU* 3.8 7.3 + - - +
126A THR* 2.8 33.3 + - - -
302A PHE 5.7 0.3 - - - -
303A GLY* 4.3 12.0 + - - -
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Residues in contact with ALA 123 (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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117A THR* 3.2 25.3 + - + +
119A GLY 3.2 9.6 + - - +
120A ALA* 3.2 10.0 + - - +
122A SER* 1.3 77.0 - - - +
124A ASN* 1.3 61.8 + - - +
126A THR* 4.3 0.2 - - - -
127A PHE* 3.1 24.8 + - - +
268A VAL* 4.3 6.6 - - + +
284A ALA 3.8 12.1 - - - +
285A ILE* 3.4 31.3 - - + +
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Residues in contact with ASN 124 (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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120A ALA 2.8 22.1 + - - +
121A THR* 4.1 3.8 - - - +
123A ALA* 1.3 74.7 - - - +
125A GLU* 1.3 67.3 + - - +
127A PHE* 3.3 6.6 + - - +
128A ILE* 3.1 26.9 + - - +
148A PHE* 4.0 12.5 - - + -
151A ASP* 5.1 3.0 + - + -
152A LEU* 3.5 20.2 - - + -
196A LEU* 4.3 14.3 - - + +
228A ILE* 4.8 1.9 - - - +
230A ASP* 2.9 27.8 + - - +
268A VAL* 3.7 22.4 - - - +
600A PY4 3.7 14.1 + - - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR 3.3 13.9 + - - +
122A SER* 4.2 7.7 - - - +
124A ASN* 1.3 78.8 - - - +
126A THR* 1.3 63.9 + - - +
128A ILE* 3.0 10.3 + - - +
129A PHE* 2.9 41.7 + - + -
151A ASP* 3.5 27.1 + - - +
152A LEU* 4.4 1.0 - - - +
155A ARG* 2.7 59.8 + - - +
156A THR* 4.0 5.2 - - + -
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 4.9 6.4 - - + +
122A SER* 2.8 24.7 + - - -
123A ALA* 3.7 4.9 - - - -
125A GLU* 1.3 81.3 + - - +
127A PHE* 1.3 63.5 + - - +
129A PHE* 3.2 4.4 + - - -
130A CYS* 3.1 7.8 + - - -
285A ILE* 3.9 17.5 - - + -
296A ALA* 4.2 14.8 - - + +
299A MET* 2.8 63.1 + - + +
300A SER* 5.7 1.1 - - - -
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Residues in contact with PHE 127 (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 ALA 3.1 15.1 + - - +
124A ASN* 3.7 6.7 - - - +
125A GLU 3.2 0.4 - - - -
126A THR* 1.3 77.5 - - - +
128A ILE* 1.3 63.0 + - + +
130A CYS* 3.2 6.0 + - + +
131A LEU* 3.0 34.4 + - + +
226A HIS* 5.6 0.9 - + - -
228A ILE* 3.7 28.0 - - + -
266A HIS* 3.0 56.5 - + + -
267A VAL 5.2 0.9 - - - -
268A VAL* 4.6 10.3 - - + -
285A ILE* 3.2 44.6 - - + -
292A VAL* 3.6 23.3 - - + -
296A ALA* 5.9 0.7 - - + -
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Residues in contact with ILE 128 (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 ASN 3.1 17.0 + - - +
125A GLU* 3.0 8.7 + - - +
127A PHE* 1.3 78.1 - - - +
129A PHE* 1.3 56.6 + - - +
131A LEU* 3.1 14.5 - - + +
132A ALA 2.8 32.2 + - - +
138A VAL* 4.8 16.8 - - + -
152A LEU* 3.8 34.1 - - + +
156A THR* 3.6 19.1 - - + +
158A VAL* 3.6 32.1 - - + -
196A LEU* 4.8 11.4 - - + -
228A ILE* 4.9 8.7 - - + -
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Residues in contact with PHE 129 (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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125A GLU* 2.9 53.2 + - + -
126A THR* 3.6 3.6 - - - +
128A ILE* 1.3 77.5 - - - +
130A CYS* 1.3 60.4 + - - +
132A ALA 4.3 10.3 + - - +
133A ASP* 5.5 1.6 - - - +
134A PRO* 6.4 1.1 - - + -
155A ARG* 3.3 42.8 - - + -
156A THR* 3.6 16.6 - - + -
299A MET* 3.5 28.5 - - + -
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Residues in contact with CYS 130 (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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126A THR* 3.1 9.0 + - - +
127A PHE* 3.7 11.4 - - + +
128A ILE 3.1 0.4 - - - -
129A PHE* 1.3 79.0 - - - +
131A LEU* 1.3 58.0 + - + +
292A VAL* 4.5 15.7 - - + -
295A ALA* 4.0 14.6 - - + -
296A ALA* 3.8 31.9 - - - -
299A MET* 3.0 31.2 - - - -
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Residues in contact with LEU 131 (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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127A PHE* 3.0 36.0 + - + +
128A ILE* 3.1 22.7 - - + +
130A CYS* 1.3 80.7 - - - +
132A ALA* 1.3 84.0 + - + +
133A ASP* 4.2 1.3 + - - +
138A VAL* 5.8 4.3 - - + -
193A LYS* 2.9 44.1 + - + +
194A GLY* 4.8 3.1 - - - +
226A HIS* 4.2 35.8 - - + +
228A ILE* 3.7 25.4 - - + -
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Residues in contact with ALA 132 (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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128A ILE* 2.8 16.9 + - + +
129A PHE* 4.3 9.6 - - - +
130A CYS 3.8 0.2 - - - -
131A LEU* 1.3 93.0 - - + +
133A ASP* 1.3 64.3 + - - +
134A PRO* 3.9 1.4 - - - +
136A GLU* 3.7 5.4 - - + -
137A ALA 5.0 1.1 - - - +
138A VAL* 6.2 1.1 - - + -
156A THR* 4.9 1.0 - - - +
158A VAL* 3.5 36.1 - - + +
193A LYS* 3.8 18.4 - - + -
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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