Contacts of the helix formed by residues 136 - 146 (chain A) in PDB entry 1Y88
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ILE* 1.3 74.6 - - - +
137A LYS* 1.3 54.2 + - - +
138A GLU* 2.9 17.3 + - - +
139A VAL* 2.9 43.4 + - - +
140A LEU* 2.8 36.6 + - - +
171A LYS* 5.0 5.5 + - - +
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Residues in contact with LYS 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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3A ASN* 3.3 40.0 - - + +
136A ASP* 1.3 74.8 - - - +
138A GLU* 1.3 57.3 + - - +
140A LEU* 3.7 23.3 - - + +
141A ASP* 2.8 77.6 + - - +
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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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136A ASP* 2.9 10.8 + - - +
137A LYS* 1.3 76.3 - - - +
139A VAL* 1.3 68.0 + - + +
141A ASP* 3.2 5.6 + - - +
142A GLU* 2.9 55.5 + - - +
145A ARG* 3.8 14.5 + - - -
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Residues in contact with VAL 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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135A ILE* 4.0 25.8 - - + -
136A ASP* 2.9 35.3 + - - +
138A GLU* 1.3 73.4 - - + +
140A LEU* 1.3 64.4 + - - +
142A GLU* 3.3 14.4 + - - +
143A LEU* 2.9 38.5 + - + +
167A LEU* 4.1 25.6 - - + -
171A LYS* 4.1 21.5 - - + -
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Residues in contact with LEU 140 (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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3A ASN* 6.0 1.6 - - + -
6A PHE* 4.2 21.3 - - + -
130A ILE* 4.2 4.9 - - + +
131A THR* 4.4 21.5 - - + -
135A ILE* 3.6 28.6 - - + +
136A ASP 2.8 22.9 + - - +
137A LYS* 3.7 25.4 - - + +
139A VAL* 1.3 74.1 - - - +
141A ASP* 1.3 64.8 + - - +
143A LEU* 3.2 3.5 + - - +
144A VAL* 2.9 49.2 + - + +
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Residues in contact with ASP 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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3A ASN* 4.8 2.3 + - - -
5A TYR* 4.4 16.6 - - + +
6A PHE 5.4 0.9 + - - -
137A LYS* 2.8 57.9 + - - +
138A GLU* 3.2 6.2 + - - +
140A LEU* 1.3 76.4 - - - +
142A GLU* 1.3 60.7 + - - +
144A VAL* 3.2 5.7 + - - +
145A ARG* 2.8 60.6 + - + +
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Residues in contact with GLU 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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138A GLU* 2.9 41.3 + - - +
139A VAL* 3.4 22.9 - - - +
141A ASP* 1.3 77.7 - - - +
143A LEU* 1.3 64.5 + - - +
145A ARG* 3.5 19.2 + - - +
146A ALA* 3.3 18.0 + - - +
165A ILE* 3.6 35.6 - - + +
166A GLY* 4.2 13.1 - - - +
167A LEU* 3.7 18.1 - - + +
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Residues in contact with LEU 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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130A ILE* 3.6 17.7 - - + -
133A LEU* 5.3 0.4 - - + -
135A ILE* 3.8 28.3 - - + -
139A VAL* 2.9 24.9 + - + +
140A LEU 3.6 5.6 - - - +
142A GLU* 1.3 75.7 - - - +
144A VAL* 1.3 61.5 + - - +
146A ALA* 3.0 9.9 + - - +
148A LEU* 2.9 38.9 + - + +
154A VAL* 4.4 14.6 - - + -
162A LEU* 3.7 31.0 - - + -
165A ILE* 4.0 7.9 - - + -
167A LEU* 4.2 14.8 - - + -
175A VAL* 4.5 10.5 - - + -
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Residues in contact with VAL 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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5A TYR* 3.5 32.1 - - + +
6A PHE* 3.5 32.3 - - + -
9A HIS* 3.6 32.7 - - + -
130A ILE* 4.3 1.8 - - + -
140A LEU* 2.9 30.1 + - + +
141A ASP* 3.2 5.6 + - - +
143A LEU* 1.3 74.4 - - - +
145A ARG* 1.3 53.9 + - - +
147A GLY* 2.5 28.4 + - - -
148A LEU 3.4 15.5 - - - +
149A VAL* 4.4 2.0 - - + -
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Residues in contact with ARG 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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5A TYR* 3.6 32.8 + - + +
9A HIS* 5.6 1.0 + - - -
138A GLU* 3.8 23.0 + - - -
141A ASP* 2.8 53.1 + - - +
142A GLU* 3.8 22.5 - - - +
144A VAL* 1.3 71.5 - - - +
146A ALA* 1.3 56.7 + - - +
147A GLY* 3.2 3.5 + - - -
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Residues in contact with ALA 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 GLU 3.3 10.6 + - - +
143A LEU 3.0 11.7 + - - +
145A ARG* 1.3 74.8 - - - +
147A GLY* 1.3 59.5 + - - +
148A LEU* 3.3 20.4 + - + +
161A LYS* 4.4 10.0 - - - +
165A ILE* 3.9 28.0 - - + -
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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