Contacts of the helix formed by residues 153 - 161 (chain A) in PDB entry 4CSC
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ARG* 5.6 0.2 - - - +
151A GLU 3.0 15.1 + - - +
152A SER* 1.3 73.9 + - - +
154A PHE* 1.3 58.4 + - - +
156A ARG* 3.5 5.0 + - - +
157A ALA* 3.0 30.0 + - - +
170A MET* 3.9 12.3 - - + +
173A GLU* 4.1 26.0 + - + +
174A SER* 4.4 6.8 - - - -
177A ASP* 3.5 22.2 + - - -
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Residues in contact with PHE 154 (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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152A SER* 3.2 5.3 + - - +
153A ASN* 1.3 77.4 - - - +
155A ALA* 1.3 58.4 + - - +
157A ALA* 3.2 2.8 + - - +
158A TYR* 2.8 54.3 + + + +
162A ILE* 4.8 3.1 - - + -
167A TYR* 3.5 44.2 - + + -
170A MET* 3.7 31.1 + - + +
171A VAL* 3.8 20.6 - - + +
174A SER* 4.6 1.2 - - - -
255A LEU* 3.4 39.9 - - + -
256A SER 4.9 0.9 - - - -
257A ASP* 4.0 17.5 - - + -
258A PRO* 4.1 13.9 - - + -
413A ARG* 5.4 0.9 - - - -
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Residues in contact with ALA 155 (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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149A ASN* 4.8 6.7 - - - +
152A SER* 2.9 26.9 + - - +
154A PHE* 1.3 82.7 - - - +
156A ARG* 1.3 60.9 + - - +
158A TYR* 4.0 5.1 - - - +
159A ALA* 3.2 21.7 + - - +
257A ASP* 4.0 14.1 - - + +
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Residues in contact with ARG 156 (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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152A SER 3.3 17.3 + - - +
153A ASN* 3.8 5.6 - - - +
154A PHE 3.1 0.2 - - - -
155A ALA* 1.3 76.9 - - - +
157A ALA* 1.3 67.6 + - - +
159A ALA* 3.1 9.6 + - + +
160A GLU* 3.0 46.4 + - + +
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Residues in contact with ALA 157 (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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153A ASN 3.0 19.5 + - - +
154A PHE 3.5 4.5 - - - +
156A ARG* 1.3 77.6 - - - +
158A TYR* 1.3 60.0 + - - +
160A GLU* 3.2 12.8 + - - +
161A GLY 3.2 11.8 + - - -
162A ILE* 3.1 28.2 + - + +
170A MET* 3.5 37.2 - - + -
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Residues in contact with TYR 158 (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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154A PHE* 2.8 40.5 + + + +
155A ALA* 4.0 6.1 - - - +
157A ALA* 1.3 68.6 - - - +
159A ALA* 1.3 59.8 + - - +
161A GLY* 2.7 25.8 + - - -
162A ILE* 3.9 8.0 - - + +
167A TYR* 3.3 36.3 - + - -
255A LEU* 3.9 22.4 - - + +
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Residues in contact with ALA 159 (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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155A ALA 3.2 13.7 + - - +
156A ARG* 3.1 15.4 + - + +
158A TYR* 1.3 82.0 - - - +
160A GLU* 1.3 64.9 + - + +
161A GLY* 3.5 0.5 + - - -
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Residues in contact with GLU 160 (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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156A ARG* 3.0 37.9 + - + +
157A ALA* 3.5 12.7 - - - +
158A TYR 3.0 0.4 - - - -
159A ALA* 1.3 81.5 - - + +
161A GLY* 1.3 58.3 + - - +
162A ILE* 5.1 1.6 - - + +
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Residues in contact with GLY 161 (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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157A ALA 3.2 0.2 + - - -
158A TYR 2.7 21.8 + - - -
159A ALA 3.3 1.5 - - - -
160A GLU* 1.3 73.3 - - - +
162A ILE* 1.3 67.4 + - - +
163A LEU* 3.5 0.9 + - - -
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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