Contacts of the helix formed by residues 172 - 177 (chain D) in PDB entry 1MA1
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 TYR 172 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLN* 3.1 10.1 - - - -
167D VAL* 3.4 13.5 - - - -
168D TRP 3.3 26.9 - - - -
169D GLU* 3.6 17.7 + - - +
170D HIS 3.3 0.6 - - - -
171D ALA* 1.3 77.0 - - - +
173D TYR* 1.3 67.6 + + - +
175D ASP 3.2 2.3 + - - -
176D TYR* 2.7 41.7 + - + -
177D ARG 3.3 23.1 - - - -
178D ASN* 4.5 3.1 + - - -
180D ARG* 2.9 59.2 + - + +
183D TYR* 3.2 50.3 - + + -
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Residues in contact with TYR 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 3.1 17.9 - - + +
32C HIS 5.3 0.2 + - - -
36C HIS* 2.8 35.2 + + - -
170C HIS* 3.7 25.6 + - + +
173C TYR* 4.2 28.7 - + + -
174C ILE* 3.8 28.5 - - + -
28D GLN* 3.5 0.8 + - - -
169D GLU* 2.9 28.6 + - + +
170D HIS 4.5 0.8 - - - -
172D TYR* 1.3 87.1 - + - +
174D ILE* 1.3 59.7 + - - +
177D ARG* 2.8 74.8 + - - -
178D ASN* 3.6 4.5 - - - -
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TYR* 3.8 16.6 - - + -
177C ARG* 3.5 41.1 - - - +
27D GLU* 3.6 34.3 - - + +
28D GLN* 3.0 20.6 + - - +
31D ILE* 3.7 27.8 - - + -
173D TYR* 1.3 79.7 - - - +
175D ASP* 1.3 69.8 + - - +
177D ARG* 3.7 20.0 + - - +
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Residues in contact with ASP 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PRO 5.8 1.6 - - - -
23D HIS 4.2 0.9 - - - +
24D ILE* 3.6 6.1 - - - -
25D SER* 2.6 53.4 + - - -
28D GLN* 3.2 20.5 + - + +
172D TYR 4.1 0.7 - - - +
174D ILE* 1.3 83.7 - - - +
176D TYR* 1.3 87.6 + - + +
177D ARG* 3.7 0.9 - - - -
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Residues in contact with TYR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PRO 4.3 3.4 + - - -
23D HIS* 2.6 33.2 + - - -
24D ILE* 5.4 0.4 - - - -
28D GLN* 6.3 0.2 - - + -
172D TYR* 2.7 20.5 + - + +
175D ASP* 1.3 94.2 - - + +
177D ARG* 1.3 70.9 + - - +
178D ASN 3.1 0.7 + - - -
179D VAL* 2.8 38.6 + - + +
182D ASP* 3.5 35.0 - - + -
183D TYR* 3.6 38.8 - + + -
186D ALA* 3.2 15.4 - - + +
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Residues in contact with ARG 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU* 2.8 29.3 + - - -
31C ILE* 3.8 8.7 - - + -
174C ILE* 3.6 36.6 - - - +
177C ARG* 3.9 22.6 - - - +
172D TYR* 3.3 12.5 - - - -
173D TYR* 2.8 58.7 + - - -
174D ILE* 3.7 18.8 + - - +
175D ASP 5.6 0.7 - - - -
176D TYR* 1.3 80.5 - - - +
178D ASN* 1.3 72.2 + - - +
179D VAL* 3.2 0.6 + - + -
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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