Contacts of the helix formed by residues 170 - 178 (chain A) in PDB entry 1IZC
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 4.4 1.7 + - - -
21A MET* 4.4 0.2 - - - +
24A TYR* 3.4 41.6 + - + -
141A TYR* 4.6 0.4 - - - -
154A PHE* 5.8 0.6 - - - +
160A ASP* 3.5 18.2 + - - +
161A ALA 3.1 23.0 + - - +
162A SER* 3.3 12.7 - - - -
167A ASP* 3.0 18.8 + - - -
168A PRO 4.6 0.8 + - - -
169A TYR* 1.3 80.7 - - - +
171A VAL* 1.3 63.2 + - - +
172A ALA 3.2 1.8 - - - -
173A THR* 2.6 27.3 + - - +
174A SER* 3.1 25.3 + - - -
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Residues in contact with VAL 171 (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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141A TYR* 4.0 37.5 - - + -
142A GLY 4.8 5.6 - - - +
149A PHE* 4.1 23.3 - - + -
167A ASP* 3.1 5.6 + - - +
169A TYR* 4.1 9.2 - - + +
170A ASN* 1.3 79.3 - - - +
172A ALA* 1.3 59.6 + - - +
174A SER* 3.5 1.4 + - - -
175A ASN* 3.0 35.3 + - - +
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Residues in contact with ALA 172 (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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164A PHE* 3.7 21.5 - - + -
167A ASP* 2.9 22.9 + - + +
171A VAL* 1.3 77.5 - - - +
173A THR* 1.3 65.9 + - - +
175A ASN* 4.9 2.7 - - - -
176A ASN* 2.9 41.0 + - - +
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Residues in contact with THR 173 (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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19A SER* 3.6 22.8 + - - +
24A TYR* 4.3 10.5 - - + -
25A PRO* 4.0 11.4 - - + +
162A SER* 3.0 15.8 + - - -
163A LEU* 4.5 0.7 + - - +
164A PHE* 3.6 14.1 - - - -
167A ASP* 3.3 1.4 + - - -
170A ASN* 2.6 32.9 + - - +
172A ALA* 1.3 78.9 - - - +
174A SER* 1.3 57.9 + - - +
177A HIS* 2.9 52.4 + - + +
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Residues in contact with SER 174 (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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24A TYR* 4.6 13.5 - - - -
25A PRO* 4.7 6.7 - - - +
139A MET 5.9 0.4 - - - -
140A TYR* 4.3 2.1 - - - -
141A TYR* 3.5 29.4 + - - -
147A ARG* 3.6 21.1 + - - -
170A ASN 3.1 12.5 + - - -
171A VAL 3.8 0.7 - - - -
173A THR* 1.3 80.1 - - - +
175A ASN* 1.3 63.6 + - - +
178A VAL* 3.2 37.1 + - - +
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Residues in contact with ASN 175 (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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29A ARG* 2.8 22.4 + - - -
139A MET 4.7 0.2 - - - +
140A TYR* 3.5 17.2 - - - -
141A TYR* 3.0 56.2 + - - +
142A GLY 4.2 5.1 + - - -
143A PRO* 5.0 2.2 - - - +
144A ILE* 3.7 31.7 - - + +
171A VAL* 3.0 22.5 + - + +
172A ALA* 4.3 2.9 - - - +
174A SER* 1.3 79.1 - - - +
176A ASN* 1.3 64.2 + - - +
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Residues in contact with ASN 176 (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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27A ASN* 3.8 4.6 + - - +
29A ARG* 3.4 32.9 + - - +
164A PHE* 3.1 42.1 - - + -
172A ALA* 2.9 29.7 + - - +
175A ASN* 1.3 83.2 - - - +
177A HIS* 1.3 61.3 + - + +
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Residues in contact with HIS 177 (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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17A TYR 4.7 0.2 - - - -
19A SER* 4.3 6.1 - - - -
25A PRO* 2.8 30.3 + - + +
26A GLY 3.4 13.6 - - - +
27A ASN* 3.3 42.8 + - + +
28A LEU* 3.5 5.5 + - - +
29A ARG* 3.3 21.9 + - - +
119A ALA 3.7 4.9 - - - +
163A LEU* 4.0 24.4 - - + +
164A PHE* 3.6 24.0 - + - -
173A THR* 2.9 31.5 + - + +
176A ASN* 1.3 84.0 - - - +
178A VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 178 (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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25A PRO* 4.0 19.3 - - + -
29A ARG* 2.8 22.2 + - - -
114A LEU* 4.0 18.8 - - + -
118A ALA 3.9 16.6 - - - +
119A ALA 3.3 10.1 - - - +
120A GLY 5.0 0.7 - - - +
121A ILE* 5.0 0.4 - - + -
139A MET* 3.6 30.7 - - + +
140A TYR* 2.7 25.7 + - + +
147A ARG* 5.2 3.8 - - - +
174A SER* 3.2 26.2 + - - +
176A ASN 3.7 0.2 - - - -
177A HIS* 1.3 76.3 - - - +
179A CYS* 1.3 59.2 + - - +
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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