Contacts of the helix formed by residues 142 - 153 (chain A) in PDB entry 4YXK
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 ASN 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PHE 3.4 1.2 + - - -
141A GLY* 1.3 77.9 - - - +
143A ASP* 1.3 64.7 + - - +
144A TYR* 3.8 1.2 - - - +
145A GLU* 2.8 44.7 + - - +
146A ASP* 3.1 25.1 + - - +
104H TYR* 3.6 10.4 - - - -
91L SER 3.1 20.9 - - - +
92L ASN 3.1 14.3 - - - +
93L THR* 3.8 7.1 - - - +
94L TRP* 3.3 46.0 - - + +
96L TYR* 4.3 5.2 - - + -
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Residues in contact with ASP 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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142A ASN* 1.3 73.5 - - - +
144A TYR* 1.3 59.2 + - - +
146A ASP* 3.1 7.2 + - - +
147A ARG* 2.9 29.8 + - - +
102H GLY 4.6 3.3 - - - +
103H TYR* 5.0 0.9 - - - -
104H TYR* 3.6 10.9 - - - -
32L SER* 2.2 42.0 + - - +
50L TYR* 2.4 34.2 + - - -
91L SER* 3.2 14.8 + - - +
92L ASN* 4.2 7.2 - - - +
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Residues in contact with TYR 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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142A ASN* 3.8 0.4 - - - +
143A ASP* 1.3 75.1 - - - +
145A GLU* 1.3 72.9 + - + +
147A ARG* 3.2 6.8 + - + +
148A TYR* 2.7 59.6 + + + +
200A THR* 5.6 7.0 - - + -
92L ASN* 3.1 30.6 + - - +
93L THR* 3.7 21.5 - - + -
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Residues in contact with GLU 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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140A PHE* 3.6 25.3 - - + +
142A ASN* 2.8 27.6 + - - +
144A TYR* 1.3 83.5 - - + +
146A ASP* 1.3 59.8 + - - +
148A TYR* 4.0 2.7 - - - -
149A TYR* 2.7 33.3 + - - +
200A THR* 5.1 5.6 - - + -
203A LYS* 3.2 38.4 + - - -
204A MET* 3.5 24.1 - - + +
57H TYR* 4.7 0.2 + - - -
93L THR* 6.1 0.7 - - + -
94L TRP* 3.3 22.5 + - - -
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Residues in contact with ASP 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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138A ILE 4.2 3.9 - - - +
139A HIS* 3.3 19.8 + - - -
140A PHE* 2.8 28.8 + - - +
142A ASN 3.1 19.8 + - - +
143A ASP* 3.5 5.6 - - - +
145A GLU* 1.3 77.5 - - - +
147A ARG* 1.3 62.2 + - - +
149A TYR* 3.8 4.8 - - - +
150A ARG* 3.1 32.7 + - - +
102H GLY* 3.8 7.9 - - - +
104H TYR* 3.0 25.5 + - + -
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Residues in contact with ARG 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 ASP 2.9 17.1 + - - +
144A TYR* 3.8 7.0 - - + +
146A ASP* 1.3 75.0 - - - +
148A TYR* 1.3 58.2 + - - +
150A ARG* 3.1 31.0 + - - +
151A GLU* 2.9 54.0 + - - +
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Residues in contact with TYR 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 TYR* 2.7 49.0 + + + +
145A GLU* 3.7 6.5 - - - +
147A ARG* 1.3 72.7 - - - +
149A TYR* 1.3 56.7 + - - +
151A GLU* 3.3 4.9 + - - +
152A ASN* 2.9 57.0 + - - +
155A ARG* 4.2 5.5 + - - -
156A TYR* 3.3 9.6 - - - -
198A THR* 4.4 9.9 + - + -
200A THR* 3.8 22.9 - - + -
201A ASP* 2.6 41.2 + - - -
204A MET* 3.5 18.6 - - + -
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Residues in contact with TYR 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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135A ARG* 5.5 0.5 - - - +
136A PRO* 4.0 6.1 + - - +
137A LEU* 5.3 3.8 - - + -
138A ILE* 3.8 43.5 - - + +
140A PHE* 3.7 23.1 - + + -
145A GLU 2.7 23.3 + - - +
146A ASP* 3.8 4.7 - - - +
148A TYR* 1.3 74.7 - - - +
150A ARG* 1.3 67.1 + - + +
152A ASN* 5.2 0.4 - - - +
153A MET* 3.0 73.1 + - + +
156A TYR* 4.1 14.5 - + - -
204A MET* 4.1 16.6 - - + -
208A VAL* 3.5 34.9 - - + +
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Residues in contact with ARG 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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137A LEU* 5.5 12.3 - - + -
146A ASP* 3.1 19.0 + - - +
147A ARG* 3.1 33.3 + - - +
149A TYR* 1.3 79.5 - - + +
151A GLU* 1.3 70.7 + - - +
153A MET* 3.6 21.9 - - - +
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Residues in contact with GLU 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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147A ARG* 2.9 52.6 + - + +
148A TYR* 4.0 2.8 - - - +
150A ARG* 1.3 87.7 - - + +
152A ASN* 1.3 73.7 + - - +
154A TYR* 3.6 20.1 - - - -
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Residues in contact with ASN 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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148A TYR* 2.9 54.9 + - + +
151A GLU* 1.3 92.2 + - - +
153A MET* 1.3 65.9 + - - +
154A TYR* 3.0 9.6 + - - -
155A ARG* 3.1 45.0 + - - +
156A TYR* 3.8 23.9 - - + +
201A ASP* 4.4 1.3 - - - +
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Residues in contact with MET 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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135A ARG* 2.3 63.9 + - + +
136A PRO 4.3 5.8 - - - +
137A LEU* 6.0 1.3 - - - -
149A TYR* 3.0 59.1 + - + +
150A ARG* 3.6 19.1 - - - +
151A GLU 3.5 0.6 - - - -
152A ASN* 1.3 76.8 - - - +
154A TYR* 1.3 57.2 + - - +
155A ARG 3.1 0.2 - - - -
156A TYR* 3.1 24.8 + - + +
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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