Contacts of the helix formed by residues 135 - 148 (chain A) in PDB entry 1Y0P
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 3.4 4.4 - - - -
134A SER* 1.3 81.8 - - - +
136A GLY* 1.3 66.1 + - - -
137A ALA 3.3 2.7 - - - -
138A GLY 4.0 1.5 - - - +
139A PHE* 3.1 22.8 + - - -
162A GLY* 3.9 9.9 - - - -
165A ALA* 4.4 0.4 - - - -
258A VAL* 5.1 2.0 - - - -
312A ALA 4.9 0.2 + - - -
1805A FAD 3.3 34.5 + - - -
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Residues in contact with GLY 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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135A GLY* 1.3 71.9 - - - -
137A ALA* 1.3 61.2 + - - +
140A SER* 2.8 31.7 + - - -
165A ALA* 3.5 13.8 - - - +
257A VAL* 5.7 1.3 - - - -
258A VAL* 4.8 2.4 - - - +
261A LEU* 3.9 17.2 - - - +
553A ILE* 3.5 21.1 - - - -
554A ILE* 4.6 2.0 - - - -
1805A FAD 3.2 4.9 + - - -
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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
----------------------------------------------------------
136A GLY* 1.3 77.4 - - - +
138A GLY* 1.3 58.1 + - - +
141A ALA* 2.9 26.9 + - - +
312A ALA* 3.9 7.0 - - + -
532A ALA* 3.4 36.5 - - + +
533A GLY* 4.0 0.9 - - - -
553A ILE* 3.4 27.7 - - + +
557A GLY* 3.4 8.1 - - - -
1805A FAD 3.0 15.5 + - - +
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Residues in contact with GLY 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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131A VAL* 3.4 12.9 - - - +
133A GLY 3.2 24.7 + - - -
135A GLY 3.4 4.8 + - - +
136A GLY 3.3 0.4 - - - -
137A ALA* 1.3 75.7 - - - +
139A PHE* 1.3 59.8 + - - +
141A ALA 3.3 0.5 + - - -
142A ALA* 2.9 30.5 + - - +
154A LEU* 4.1 2.9 - - - -
312A ALA* 3.5 14.9 - - - +
1805A FAD 4.5 0.4 + - - -
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Residues in contact with PHE 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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133A GLY 4.3 0.8 + - - -
134A SER* 3.2 39.3 - - - -
135A GLY 3.1 15.8 + - - +
138A GLY* 1.3 75.5 - - - +
140A SER* 1.3 63.3 + - - +
142A ALA* 3.2 3.8 + - + +
143A ILE* 2.9 30.3 + - - +
154A LEU* 3.7 20.4 - - + +
161A ILE* 4.1 17.7 - - + -
258A VAL* 4.6 8.3 - - + -
261A LEU* 3.7 32.1 - - + -
262A TYR* 3.9 29.8 - + + -
265A ALA* 3.9 29.6 - - + -
272A LEU* 4.2 15.0 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 2.8 23.2 + - - -
137A ALA 3.8 3.6 - - - -
139A PHE* 1.3 77.3 - - - +
141A ALA* 1.3 58.2 + - - +
144A SER* 2.9 32.1 + - - -
222A TRP* 3.6 26.4 - - - -
261A LEU* 3.9 6.9 - - - +
553A ILE 4.3 0.4 - - - -
554A ILE* 3.3 26.5 - - - +
557A GLY* 4.0 4.0 - - - -
558A ARG 3.8 16.2 - - - -
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Residues in contact with ALA 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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131A VAL* 4.3 7.7 - - + +
137A ALA 2.9 17.2 + - - +
138A GLY 3.7 3.8 - - - +
140A SER* 1.3 75.9 - - - +
142A ALA* 1.3 58.4 + - - +
144A SER* 3.4 2.7 + - - -
145A ALA* 2.9 34.0 + - - +
310A ILE* 3.9 35.0 - - + -
557A GLY* 3.1 23.0 + - - +
561A GLY* 3.5 1.1 - - - -
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Residues in contact with ALA 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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131A VAL* 4.1 6.0 - - + +
138A GLY 2.9 17.6 + - - +
139A PHE* 3.7 4.0 - - + +
141A ALA* 1.3 78.6 - - - +
143A ILE* 1.3 57.1 - - + +
146A THR* 2.8 33.9 + - - -
152A VAL* 3.9 27.3 - - + +
154A LEU* 4.2 20.2 - - + -
270A ILE* 3.9 14.4 - - + -
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Residues in contact with ILE 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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139A PHE* 2.9 21.3 + - + +
140A SER 3.9 2.5 - - - +
142A ALA* 1.3 76.2 - - + +
144A SER* 1.3 58.7 + - - +
146A THR* 3.2 3.9 + - - -
147A ASP* 2.9 34.2 + - - +
222A TRP* 3.9 16.2 - - + -
226A MET* 4.1 5.2 - - - -
261A LEU* 3.4 46.2 - - + +
264A ASN* 3.9 11.2 - - + -
265A ALA* 4.3 9.0 - - + +
268A ARG* 3.6 29.2 - - - +
270A ILE* 4.0 19.1 - - + -
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Residues in contact with SER 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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140A SER 2.9 21.6 + - - -
143A ILE* 1.3 74.5 - - - +
145A ALA* 1.3 65.1 + - - +
147A ASP* 3.4 7.3 + - - +
148A SER* 3.0 27.5 + - - -
222A TRP* 4.2 7.9 - - - -
558A ARG* 2.8 44.9 + - - -
561A GLY* 3.2 13.5 - - - -
562A GLU* 4.0 10.1 - - - +
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Residues in contact with ALA 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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129A VAL* 4.7 10.8 - - + -
141A ALA 2.9 18.8 + - - +
142A ALA* 4.8 0.2 - - - -
144A SER* 1.3 79.4 + - - +
146A THR* 1.3 61.7 + - - +
148A SER* 3.1 9.9 + - - -
149A GLY 3.3 0.2 + - - -
150A ALA* 3.0 31.8 + - + +
152A VAL* 3.8 19.5 - - + -
561A GLY* 3.4 24.5 - - - +
565A ALA* 4.2 3.6 - - + -
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Residues in contact with THR 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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142A ALA 2.8 23.1 + - - -
143A ILE 3.5 3.6 - - - -
145A ALA* 1.3 75.2 - - - +
147A ASP* 1.3 63.1 + - - +
149A GLY* 3.1 14.9 + - - -
150A ALA 3.4 14.8 + - - +
152A VAL* 3.7 13.7 + - - +
268A ARG* 4.2 29.6 - - + +
270A ILE* 3.6 18.9 - - + +
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Residues in contact with ASP 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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143A ILE* 2.9 23.3 + - - +
144A SER* 3.9 6.8 - - - +
145A ALA 3.3 0.2 - - - -
146A THR* 1.3 77.2 - - - +
148A SER* 1.3 57.8 + - - +
149A GLY 3.3 1.8 + - - -
222A TRP* 5.1 6.8 + - - -
268A ARG* 2.8 45.6 + - - +
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Residues in contact with SER 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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144A SER 3.0 16.6 + - - -
145A ALA 3.1 1.2 + - - -
147A ASP* 1.3 75.6 - - - +
149A GLY* 1.3 58.5 + - - +
150A ALA 3.5 1.7 + - - -
562A GLU* 3.6 23.6 + - - +
565A ALA* 3.6 28.2 - - - +
566A LYS* 5.4 5.5 + - - -
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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