Contacts of the helix formed by residues 130 - 139 (chain A) in PDB entry 1YPN
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 LEU 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A SER 3.4 9.1 + - - +
129A SER* 1.3 71.7 + - - +
131A ARG* 1.3 57.8 + - - +
133A GLN* 3.4 28.2 - - - +
134A CYS* 2.9 33.6 + - - +
242A CYS 4.9 4.9 + - - -
243A GLN* 3.4 26.2 - - - +
244A VAL 4.4 2.0 - - - -
245A PRO* 3.9 29.7 - - + +
266A PRO* 4.7 15.4 - - + +
306A VAL* 4.7 15.9 - - + -
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Residues in contact with ARG 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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106A ASP* 3.0 24.5 + - - -
129A SER* 3.5 4.0 + - - +
130A LEU* 1.3 78.0 - - - +
132A ARG* 1.3 93.3 + - - +
134A CYS* 3.1 24.5 - - - -
135A GLN* 3.1 26.6 + - + +
193A LEU 2.9 25.9 + - - +
194A PRO* 3.6 2.2 - - - +
195A ALA* 3.4 26.3 - - - +
198A GLN* 3.8 4.2 - - - +
244A VAL 4.5 3.5 + - - +
245A PRO* 3.8 8.0 - - + +
246A ILE 3.0 37.9 - - - +
247A GLY* 3.9 2.2 - - - -
262A LEU* 5.4 1.3 - - + -
314A DPM 2.8 41.1 + - - +
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Residues in contact with ARG 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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106A ASP* 3.1 34.7 + - - +
127A THR* 3.6 18.8 - - + +
129A SER* 3.3 12.4 + - - +
131A ARG* 1.3 104.9 - - - +
133A GLN* 1.3 62.7 + - - +
135A GLN* 3.7 7.6 + - - +
136A LEU* 3.3 31.9 + - + +
155A ARG* 4.9 0.4 - - - +
168A ILE* 3.3 35.1 + - + +
169A LEU* 3.5 2.8 - - - +
170A ALA 3.3 14.6 - - - +
192A SER* 4.6 3.8 + - - +
198A GLN* 3.4 10.7 - - - +
314A DPM 2.7 62.1 + - - +
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Residues in contact with GLN 133 (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 THR* 4.5 7.5 + - + +
128A SER* 5.3 1.8 - - - +
129A SER 2.9 17.9 + - - +
130A LEU* 3.3 31.1 + - - +
132A ARG* 1.3 78.0 - - - +
134A CYS* 1.3 62.1 - - - +
136A LEU* 3.3 5.0 + - - +
137A ALA* 3.0 23.4 + - + +
145A ILE* 3.7 43.6 + - + +
266A PRO* 3.7 26.2 - - - +
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Residues in contact with CYS 134 (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 LEU 2.9 18.6 + - - +
131A ARG* 3.1 28.7 - - - -
133A GLN* 1.3 72.8 - - - +
135A GLN* 1.3 68.7 + - - +
137A ALA 3.5 0.2 + - - -
138A GLU* 3.1 28.1 + - - +
245A PRO* 4.3 9.4 - - + -
262A LEU* 4.2 16.2 - - - -
264A GLY* 4.1 11.4 - - - +
265A ALA 3.1 27.4 - - - +
266A PRO* 3.7 10.9 + - + -
268A GLY* 3.4 7.3 - - - -
271A ILE* 3.7 5.8 - - + +
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Residues in contact with GLN 135 (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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131A ARG* 3.1 27.3 + - - +
132A ARG* 4.0 4.4 - - - +
133A GLN 3.3 0.4 - - - -
134A CYS* 1.3 84.1 - - - +
136A LEU* 1.3 59.9 + - + +
138A GLU* 3.6 7.8 + - - +
139A ARG* 2.9 30.3 - - - +
190A GLU 5.1 3.2 + - - -
191A ILE 4.0 13.7 + - - +
192A SER* 3.6 15.2 + - - +
193A LEU* 3.1 42.6 + - - +
262A LEU* 3.4 30.7 - - + +
271A ILE* 4.3 8.7 - - + -
273A ARG* 5.0 4.2 - - - +
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Residues in contact with LEU 136 (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* 3.4 42.4 - - + -
125A VAL* 4.5 12.8 - - + -
127A THR* 5.2 2.2 - - + -
132A ARG* 3.3 23.2 + - + +
133A GLN* 3.3 3.6 + - - +
135A GLN* 1.3 74.9 - - + +
137A ALA* 1.3 57.1 + - - +
138A GLU 3.2 0.4 - - - -
139A ARG* 3.3 12.9 + - - +
140A ARG* 2.7 41.2 + - + +
143A LEU* 4.8 10.1 - - + -
145A ILE* 4.3 16.6 - - + -
168A ILE* 4.0 28.5 - - + -
187A LEU* 5.7 3.1 - - + -
192A SER* 6.2 0.2 - - - +
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Residues in contact with ALA 137 (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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133A GLN* 3.0 18.3 + - + +
134A CYS 3.8 1.6 - - - +
136A LEU* 1.3 77.5 - - - +
138A GLU* 1.3 61.4 + - - +
140A ARG 4.3 6.7 - - - -
141A PRO* 3.3 28.7 - - + +
145A ILE* 5.2 7.8 - - + +
266A PRO 3.8 6.5 - - - +
267A ASP* 3.5 32.7 - - - +
268A GLY 5.1 0.2 - - - -
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Residues in contact with GLU 138 (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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134A CYS 3.1 17.2 + - - +
135A GLN* 3.6 12.2 - - - +
136A LEU 3.2 0.4 - - - -
137A ALA* 1.3 79.7 - - - +
139A ARG* 1.3 65.6 + - + +
141A PRO* 4.6 2.4 - - - +
268A GLY* 3.6 22.6 - - - +
269A SER 5.9 0.2 - - - +
271A ILE* 3.5 16.1 - - + +
273A ARG* 2.9 44.6 + - - -
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Residues in contact with ARG 139 (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* 3.2 33.3 - - - +
135A GLN 2.9 26.5 + - - +
136A LEU* 3.3 17.6 + - - +
138A GLU* 1.3 90.7 - - + +
140A ARG* 1.3 74.0 + - + +
141A PRO* 3.4 9.2 - - - +
187A LEU* 5.8 0.6 - - - +
191A ILE* 3.1 51.6 + - - +
192A SER* 5.7 0.4 - - - -
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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