Contacts of the helix formed by residues 146 - 160 (chain B) in PDB entry 4S0H
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 SER 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B LEU 3.9 1.6 + - - -
145B PHE* 1.3 77.5 - - - +
147B GLN* 1.3 66.8 + - - +
148B ALA* 3.5 10.5 - - - +
149B GLN* 2.8 47.9 + - - +
150B VAL* 3.2 11.9 + - - +
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Residues in contact with GLN 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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145B PHE 3.8 0.4 + - - -
146B SER* 1.3 73.8 - - - +
148B ALA* 1.3 64.3 + - - +
150B VAL* 4.2 3.8 - - - +
151B TYR* 3.4 19.1 + - - +
165E LEU* 3.5 38.1 - - + +
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Residues in contact with ALA 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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146B SER* 3.2 11.6 + - - +
147B GLN* 1.3 81.8 - - - +
149B GLN* 1.3 65.4 + - + +
151B TYR* 3.3 5.7 + - - +
152B GLU* 3.2 20.3 + - - +
175B LEU* 5.9 0.2 - - - -
165E LEU* 4.1 15.8 - - + +
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Residues in contact with GLN 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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145B PHE* 3.3 19.3 - - + +
146B SER* 2.8 38.4 + - - +
148B ALA* 1.3 78.8 - - + +
150B VAL* 1.3 62.1 + - - +
152B GLU* 3.0 8.2 + - - +
153B LEU* 2.8 33.5 + - + +
175B LEU* 3.0 41.4 + - + +
176B LYS* 4.1 4.2 + - - +
177B LEU* 3.8 25.7 - - + +
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Residues in contact with VAL 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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145B PHE* 3.6 31.2 - - + +
146B SER 3.2 16.5 + - - +
147B GLN* 4.2 3.8 - - - +
149B GLN* 1.3 74.1 - - - +
151B TYR* 1.3 57.1 + - - +
153B LEU* 3.4 8.7 + - - +
154B GLU* 2.8 51.4 + - + +
185B TRP* 5.0 9.6 - - + +
13C G 6.0 2.2 - - - +
14C A 5.1 5.6 - - - +
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Residues in contact with TYR 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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147B GLN* 3.4 10.3 + - - +
148B ALA 3.3 10.5 + - - +
149B GLN 3.2 0.2 - - - -
150B VAL* 1.3 81.2 - - - +
152B GLU* 1.3 63.7 + - + +
154B GLU* 3.4 6.6 + - - +
155B ARG* 3.1 40.2 + - - +
131E MET* 3.4 43.9 - - + +
132E PRO* 5.6 2.0 - - + -
164E HIS* 3.0 64.2 + + + +
165E LEU* 4.5 14.6 - - + -
172E ILE* 5.3 2.6 - - + +
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Residues in contact with GLU 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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148B ALA 3.2 8.6 + - - +
149B GLN 3.0 7.9 + - - +
151B TYR* 1.3 84.8 - - + +
153B LEU* 1.3 64.4 + - - +
155B ARG* 3.3 34.5 + - - +
156B ARG* 3.4 21.1 + - - +
171B LEU* 4.6 8.4 - - + +
174B VAL* 4.8 7.6 - - + +
175B LEU* 3.4 33.1 - - + +
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Residues in contact with LEU 153 (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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145B PHE* 4.4 14.1 - - + -
149B GLN 2.8 27.1 + - - +
150B VAL* 3.7 4.9 - - - +
152B GLU* 1.3 73.4 - - - +
154B GLU* 1.3 61.8 + - - +
156B ARG* 3.3 6.3 + - - +
157B PHE* 3.1 22.3 + - - +
171B LEU* 4.9 2.5 - - + -
175B LEU* 3.9 13.6 - - + +
177B LEU* 4.5 15.0 - - + -
182B VAL* 3.8 19.5 - - + -
185B TRP* 3.5 58.9 - - + +
186B PHE* 3.6 20.6 - - + -
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Residues in contact with GLU 154 (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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150B VAL* 2.8 35.2 + - + +
151B TYR* 3.7 7.2 - - - +
152B GLU 3.3 0.2 - - - -
153B LEU* 1.3 76.0 - - - +
155B ARG* 1.3 63.3 + - - +
157B PHE* 3.3 7.2 + - - +
158B LYS* 3.1 22.5 + - - +
185B TRP* 4.0 15.0 - - + -
189B ARG* 3.0 44.1 + - - -
192B LYS* 5.3 2.3 + - - -
131E MET* 4.9 12.0 - - + +
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Residues in contact with ARG 155 (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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151B TYR* 3.1 23.5 + - + +
152B GLU* 3.3 27.9 + - - +
153B LEU 3.3 0.2 - - - -
154B GLU* 1.3 77.4 - - - +
156B ARG* 1.3 61.9 + - - +
158B LYS* 3.3 11.0 + - - +
159B GLN 3.5 0.7 + - - -
128E GLU* 3.5 30.5 + - - +
129E PRO* 3.2 52.3 + - + +
131E MET* 3.7 35.2 - - + +
164E HIS* 3.3 37.2 + - - -
174E ASN* 3.5 21.0 + - - +
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Residues in contact with ARG 156 (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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152B GLU 3.4 10.1 + - - +
153B LEU 3.3 8.2 + - - +
154B GLU 3.3 0.4 - - - -
155B ARG* 1.3 81.6 - - - +
157B PHE* 1.3 57.3 + - - +
159B GLN* 3.0 19.5 + - - +
160B GLN* 3.0 66.7 + - - +
163B LEU* 4.4 7.0 - - + -
167B GLU* 3.2 19.8 + - - +
170B GLN* 3.4 26.0 - - - +
171B LEU* 3.7 39.6 - - + +
186B PHE* 4.1 10.1 - - + -
129E PRO* 5.1 1.3 - - - -
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Residues in contact with PHE 157 (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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153B LEU 3.1 13.7 + - - +
154B GLU* 3.6 10.1 - - - +
155B ARG 3.2 0.2 - - - -
156B ARG* 1.3 72.8 - - - +
158B LYS* 1.3 63.3 + - - +
159B GLN 3.0 6.7 + - - -
160B GLN 3.5 14.6 - - - +
161B ARG* 3.7 48.5 + - + +
185B TRP* 4.0 9.6 - + + -
186B PHE* 3.8 25.7 - + + -
189B ARG* 3.8 56.5 - - + -
190B ARG* 4.1 15.5 - - - -
193B SER* 4.2 6.3 - - - -
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Residues in contact with LYS 158 (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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99A LYS* 5.5 3.4 - - - +
139A PRO 5.0 1.6 + - - -
140A ASP* 3.3 14.1 + - - +
141A SER 3.0 21.4 + - - -
142A PRO 2.9 27.9 + - - -
143A ALA* 5.1 3.4 - - - +
147A HIS* 6.2 4.5 - - + +
154B GLU 3.1 12.3 + - - +
155B ARG* 3.4 13.7 - - - +
156B ARG 3.2 0.4 - - - -
157B PHE* 1.3 79.3 - - - +
159B GLN* 1.3 60.0 + - - +
129E PRO* 4.6 8.6 - - + +
130E ALA 2.8 29.5 + - - +
131E MET* 4.1 15.1 - - + +
132E PRO* 4.6 0.4 - - - +
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Residues in contact with GLN 159 (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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155B ARG 3.5 0.4 + - - +
156B ARG* 3.0 27.8 + - - +
157B PHE 3.0 2.4 - - - +
158B LYS* 1.3 83.2 - - - +
160B GLN* 1.3 71.4 + - + +
161B ARG* 4.0 2.6 + - - +
126E LYS* 3.3 39.8 - - - +
127E ALA 3.5 15.6 + - - -
128E GLU* 4.5 0.6 + - - +
129E PRO* 3.9 35.0 - - + +
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Residues in contact with GLN 160 (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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156B ARG* 3.0 48.3 + - - +
157B PHE* 3.5 8.7 - - - -
159B GLN* 1.3 87.9 + - + +
161B ARG* 1.3 58.8 + - - +
162B TYR 3.3 15.2 + - - +
163B LEU* 3.3 16.2 - - + +
167B GLU* 3.1 25.3 + - - +
186B PHE* 3.6 8.8 - - - -
126E LYS* 6.3 1.0 - - - +
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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