Contacts of the helix formed by residues 143 - 153 (chain B) in PDB entry 2YTZ
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 PRO 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.6 10.5 - - + +
139B PRO* 3.7 12.8 - - + -
142B SER* 1.3 90.5 - - - +
144B MET* 1.3 66.7 + - - +
145B GLU 3.3 2.7 - - - -
146B PHE* 2.9 29.6 + - + +
147B LEU* 3.1 11.5 + - + -
162B VAL* 3.5 29.8 - - + -
163B THR 3.6 20.9 - - - +
164B ALA* 3.9 9.0 - - + -
182B TYR* 3.8 13.2 - - + +
200B LEU* 5.0 2.7 - - + -
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASP* 5.6 0.3 - - - +
210A LYS* 3.3 33.3 - - + -
142B SER* 3.1 19.5 + - - +
143B PRO* 1.3 82.6 - - - +
145B GLU* 1.3 57.6 + - - +
146B PHE 3.1 3.6 + - - -
147B LEU* 3.5 44.1 + - + +
148B ASP* 4.6 1.9 + - - +
181B LYS* 3.3 30.3 - - + +
182B TYR* 3.7 25.1 - - + -
200B LEU* 5.7 0.9 - - - -
203B VAL* 3.6 20.6 - - + -
207B TYR* 3.7 20.2 - - + +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A HIS* 5.2 4.0 - - - -
148A ASP* 5.6 1.8 - - - -
152A ARG* 4.0 13.5 + - - -
210A LYS* 4.6 3.3 - - + +
211A TYR* 3.8 31.4 - - + -
1004A SO4 4.9 8.3 + - - -
122B ASN* 2.8 35.2 + - - +
142B SER 5.3 2.9 - - - +
143B PRO 3.1 0.6 + - - -
144B MET* 1.3 76.8 - - - +
146B PHE* 1.3 96.7 + - + +
148B ASP 5.4 0.7 - - - -
1002B SAH 4.3 8.3 + - - -
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.0 21.1 - - + -
120B ASP* 4.1 0.7 - - - -
121B ALA* 4.1 18.2 - - + -
122B ASN* 3.6 26.2 - - - -
125B MET* 3.7 5.8 - - + +
137B LEU* 4.0 21.5 - - + -
139B PRO* 4.4 12.1 - - + -
142B SER 4.9 2.0 - - - -
143B PRO* 2.9 18.1 + - + +
145B GLU* 1.3 112.2 - - + +
147B LEU* 1.3 67.0 + - - +
148B ASP 3.4 2.2 - - - -
149B THR 3.7 2.5 + - - -
150B ALA* 3.2 24.8 + - - +
1002B SAH 3.4 41.5 - + - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.4 5.6 - - + -
143B PRO* 3.1 11.2 + - + +
144B MET* 3.5 44.8 + - + +
146B PHE* 1.3 79.2 - - - +
148B ASP* 1.3 62.6 + - - +
150B ALA* 3.5 1.7 + - - +
151B LEU* 3.1 42.0 + - + +
160B LEU* 4.4 15.9 - - + -
162B VAL* 4.6 11.7 - - + -
200B LEU* 6.2 0.2 - - + -
203B VAL* 4.1 12.3 - - + +
204B ILE* 4.1 23.1 - - + -
207B TYR* 3.8 23.1 - - + -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A MET 5.1 0.5 - - - +
145A GLU 4.9 1.9 - - - +
148A ASP* 3.2 42.1 + - - +
207A TYR* 5.0 0.2 - - - -
144B MET 4.6 2.0 + - - +
145B GLU 5.4 0.4 - - - -
146B PHE 3.4 0.8 - - - +
147B LEU* 1.3 77.3 - - - +
149B THR* 1.3 64.6 + - - +
151B LEU* 3.2 18.0 + - - +
152B ARG* 3.0 23.9 + - - -
207B TYR* 3.9 14.6 - - + -
210B LYS* 2.7 26.8 + - - -
211B TYR* 2.7 32.0 + - - -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A THR* 4.4 0.9 + - - +
152A ARG* 3.4 18.5 + - - -
122B ASN* 3.2 32.6 + - - +
125B MET* 3.4 13.5 - - + -
126B ALA* 3.4 36.1 - - + +
146B PHE 3.7 2.0 + - - -
147B LEU 3.5 0.2 - - - -
148B ASP* 1.3 75.0 - - - +
150B ALA* 1.3 60.6 + - - +
152B ARG* 3.0 24.7 + - - +
153B SER* 2.8 25.1 + - - -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B MET* 3.6 23.0 - - - -
135B ILE* 3.6 4.2 - - + +
137B LEU* 4.1 18.2 - - + -
146B PHE 3.2 19.0 + - - +
147B LEU 3.7 5.2 - - - +
148B ASP 3.2 0.2 - - - -
149B THR* 1.3 72.8 - - - +
151B LEU* 1.3 57.7 + - - +
152B ARG 3.0 5.2 - - - -
153B SER* 4.2 2.2 - - - +
154B ALA* 3.1 31.5 + - - +
160B LEU* 4.2 18.3 - - + +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 2.7 29.6 + - - -
147B LEU* 3.1 26.4 + - + +
148B ASP* 3.2 11.6 + - - +
150B ALA* 1.3 76.0 - - - +
152B ARG* 1.3 53.2 - - - +
154B ALA* 4.6 1.1 - - - -
160B LEU* 3.9 22.9 - - + -
204B ILE* 4.3 8.5 - - + +
207B TYR* 3.4 44.6 - - + +
208B ALA* 3.7 13.5 - - + +
211B TYR* 3.9 11.5 - - + -
213B LEU* 4.0 8.0 - - + +
233B LEU* 3.9 26.8 - - + +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASN* 3.8 32.0 + - - +
145A GLU* 3.5 26.9 + - - +
149A THR* 3.0 24.5 + - - +
152A ARG* 4.4 0.8 - - - +
125B MET 5.1 0.9 - - - +
126B ALA* 4.9 6.3 - - - +
129B HIS* 3.4 23.3 + - + +
130B ARG* 2.7 43.1 + - - +
148B ASP* 3.0 20.9 + - - +
149B THR* 3.0 41.6 + - - +
150B ALA 3.0 0.6 - - - -
151B LEU* 1.3 81.4 - - - +
153B SER* 1.3 52.2 + - - +
154B ALA 3.4 0.9 - - - -
211B TYR* 3.0 39.8 + - + -
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 3.4 27.6 + - - +
128B ARG 2.6 23.2 + - - -
131B TYR 2.5 30.8 + - - -
132B PHE* 3.2 25.5 + - - -
135B ILE* 3.6 15.2 - - - +
149B THR 2.8 12.3 + - - -
150B ALA* 3.3 0.4 + - - -
152B ARG* 1.3 78.2 - - - +
154B ALA* 1.3 58.1 + - - +
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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