Contacts of the helix formed by residues 143 - 153 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.5 8.9 - - + +
139A PRO* 3.7 19.5 - - + -
141A GLY 3.8 6.1 - - - +
142A SER* 1.3 86.4 - - - +
144A MET* 1.3 69.3 + - - +
145A GLU 3.2 3.1 - - - -
146A PHE* 2.9 13.9 + - + +
147A LEU* 2.9 27.2 + - + -
162A VAL* 3.4 34.5 - - + -
163A THR 4.0 5.6 - - - +
164A ALA* 4.1 4.0 - - + -
182A TYR* 3.7 13.2 - - + +
200A LEU* 4.6 7.9 - - + -
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Residues in contact with MET 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 SER* 3.2 18.5 + - - +
143A PRO* 1.3 82.5 - - - +
145A GLU* 1.3 60.7 + - - +
146A PHE 3.2 0.9 + - - -
147A LEU* 3.6 38.7 + - + +
148A ASP 4.7 1.9 + - - -
181A LYS* 3.1 32.3 - - + +
182A TYR* 3.9 24.9 - - + -
203A VAL* 4.0 9.0 - - + -
207A TYR* 3.7 30.3 - - + +
148B ASP* 5.1 0.9 - - - +
210B LYS* 3.4 37.6 - - + -
211B TYR* 4.6 0.2 + - - -
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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
----------------------------------------------------------
122A ASN* 3.1 31.1 + - - +
142A SER* 4.9 4.4 + - - +
143A PRO 3.1 1.2 + - - -
144A MET* 1.3 76.8 - - - +
146A PHE* 1.3 78.1 + - + +
148A ASP 5.5 0.2 - - - -
129B HIS* 4.5 10.0 - - - -
130B ARG* 5.2 1.2 + - - -
148B ASP* 4.9 1.3 - - - +
152B ARG* 3.5 31.4 + - - +
210B LYS* 4.8 4.4 - - - +
211B TYR* 3.5 31.8 + - - -
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Residues in contact with PHE 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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55A LEU* 3.7 28.9 - - + -
120A ASP* 4.3 0.2 - - - -
121A ALA* 3.7 22.2 - - + -
122A ASN* 3.5 30.3 - - - -
125A MET* 3.8 11.3 - - + +
137A LEU* 4.2 14.8 - - + -
139A PRO* 4.2 17.5 - - + -
142A SER 5.1 2.0 - - - -
143A PRO* 2.9 11.3 + - + +
145A GLU* 1.3 94.7 - - + +
147A LEU* 1.3 65.7 + - - +
148A ASP 3.3 2.9 - - - -
149A THR* 3.1 6.8 + - - -
150A ALA* 2.9 20.6 + - - +
1001A SAH 3.4 35.2 - + - -
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Residues in contact with LEU 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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137A LEU* 4.2 6.9 - - + +
143A PRO* 2.9 17.2 + - + +
144A MET* 3.6 38.0 + - + +
146A PHE* 1.3 75.0 - - - +
148A ASP* 1.3 62.9 + - - +
150A ALA* 3.2 3.1 + - - +
151A LEU* 3.0 30.0 + - + +
160A LEU* 4.1 22.2 - - + -
162A VAL* 4.3 18.8 - - + -
200A LEU* 6.3 0.2 - - + -
203A VAL* 4.1 6.7 - - + +
204A ILE* 4.1 29.6 - - + -
207A TYR* 4.1 18.2 - - + -
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Residues in contact with ASP 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 MET 4.7 2.8 + - - +
145A GLU 5.5 0.2 - - - -
146A PHE 3.3 1.0 - - - -
147A LEU* 1.3 79.2 - - - +
149A THR* 1.3 62.3 + - - +
151A LEU* 3.3 16.1 + - - +
152A ARG* 2.7 37.1 + - - -
207A TYR* 3.8 15.6 - - + -
210A LYS* 3.0 25.3 + - - -
211A TYR* 3.0 21.6 + - - -
144B MET 5.6 0.2 - - - +
145B GLU 5.1 2.6 - - - +
148B ASP* 3.2 41.6 + - - +
149B THR 4.8 0.2 + - - -
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Residues in contact with THR 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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122A ASN* 3.3 35.3 + - - +
125A MET* 3.6 23.7 - - + +
126A ALA* 3.6 13.9 - - + +
146A PHE 3.1 4.1 + - - -
148A ASP* 1.3 75.1 - - - +
150A ALA* 1.3 60.2 + - - +
152A ARG* 3.2 22.5 + - - +
153A SER* 3.0 24.8 + - - -
126B ALA* 6.2 0.2 - - - +
149B THR* 4.4 1.1 + - - +
152B ARG* 3.0 26.9 + - - +
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Residues in contact with ALA 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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125A MET* 3.7 22.8 - - - -
135A ILE* 3.8 4.5 - - + +
137A LEU* 3.9 21.8 - - + -
146A PHE 2.9 15.3 + - - +
147A LEU* 3.5 5.4 - - - +
149A THR* 1.3 73.3 - - - +
151A LEU* 1.3 57.3 + - - +
152A ARG 3.0 5.4 - - - -
153A SER* 4.3 1.3 - - - -
154A ALA* 3.1 32.7 + - - +
160A LEU* 4.0 18.4 - - + +
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Residues in contact with LEU 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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130A ARG* 2.9 25.9 + - - -
147A LEU* 3.0 24.4 + - + +
148A ASP* 3.6 9.2 - - - +
149A THR 3.3 0.4 - - - -
150A ALA* 1.3 75.6 - - - +
152A ARG* 1.3 57.9 + - - +
154A ALA* 4.5 1.3 - - - -
160A LEU* 3.5 24.9 - - + -
204A ILE* 4.2 8.7 - - + +
207A TYR* 3.5 35.9 - - + +
208A ALA* 3.6 22.4 - - + +
211A TYR* 4.1 12.8 - - + -
213A LEU* 4.3 6.3 - - + +
233A LEU* 4.0 29.6 - - + +
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Residues in contact with ARG 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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125A MET 5.3 0.4 - - - -
126A ALA* 5.0 6.3 - - - +
129A HIS* 3.6 25.6 + - + +
130A ARG* 2.8 33.9 + - - +
148A ASP* 2.7 23.4 + - - -
149A THR* 3.2 37.1 + - - +
150A ALA 3.0 0.4 - - - -
151A LEU* 1.3 79.7 - - - +
153A SER* 1.3 58.8 + - - +
154A ALA 3.5 1.6 - - - -
211A TYR* 2.8 47.9 + - + -
1004A SO4 4.5 0.2 - - - +
122B ASN* 3.7 40.8 + - - +
145B GLU* 4.0 8.3 + - - -
149B THR* 3.4 19.2 + - - -
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Residues in contact with SER 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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125A MET* 3.1 29.3 + - - +
128A ARG 2.8 21.5 + - - -
130A ARG 3.8 0.2 - - - -
131A TYR 2.7 28.2 + - - -
132A PHE* 3.1 21.1 + - - -
135A ILE* 3.6 17.4 - - - +
149A THR 3.0 15.5 + - - -
150A ALA 3.2 0.2 + - - -
152A ARG* 1.3 77.9 - - - +
154A ALA* 1.3 57.4 + - - +
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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