Contacts of the helix formed by residues 172 - 177 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A HIS* 6.1 0.3 - - - -
28B GLN* 3.2 6.7 - - - -
167B VAL* 3.4 14.1 - - + -
168B TRP 3.3 26.9 - - - -
169B GLU* 3.1 17.9 + - - +
170B HIS 3.3 0.8 + - - -
171B ALA* 1.3 78.1 - - + +
173B TYR* 1.3 70.9 + + - +
174B ILE 3.1 3.7 + - - -
175B ASP* 3.1 1.6 + - - -
176B TYR* 2.7 37.4 + - + -
177B ARG 3.3 23.1 - - - -
178B ASN* 4.5 4.0 + - - -
180B ARG* 2.9 57.4 + - + +
183B TYR* 3.2 49.6 - + + -
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.1 20.0 - - + +
36A HIS* 2.8 35.2 + + - -
170A HIS* 3.8 24.5 + - + +
173A TYR* 4.0 29.6 - + + -
174A ILE* 3.7 31.4 - - + -
28B GLN* 3.5 1.0 + - - -
169B GLU* 2.9 29.5 + - + +
170B HIS 4.5 0.8 - - - -
172B TYR* 1.3 88.2 - + - +
174B ILE* 1.3 58.9 + - - +
177B ARG* 2.8 73.4 + - - -
178B ASN* 3.6 3.8 - - - -
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 3.6 17.7 - - + -
177A ARG* 3.3 41.7 - - - +
27B GLU* 3.5 32.3 - - + +
28B GLN* 2.9 21.8 + - - +
31B ILE* 3.7 27.6 - - + -
173B TYR* 1.3 80.7 - - - +
175B ASP* 1.3 68.8 + - - +
177B ARG* 3.8 19.1 + - - +
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Residues in contact with ASP 175 (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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22B PRO 5.9 1.1 - - - -
23B HIS 4.3 0.6 - - - +
24B ILE* 3.7 5.5 - - - -
25B SER* 2.7 52.2 + - - -
28B GLN* 3.0 20.5 + - - +
172B TYR 3.1 2.3 + - - +
174B ILE* 1.3 87.0 - - - +
176B TYR* 1.3 86.3 + - + +
177B ARG* 3.7 1.1 - - - +
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO 4.3 3.3 + - - -
23B HIS* 2.5 33.3 + - - -
24B ILE* 5.4 0.4 - - + -
28B GLN* 6.4 0.2 - - + -
172B TYR* 2.7 20.2 + - + +
175B ASP* 1.3 97.2 - - + +
177B ARG* 1.3 71.2 - - - +
178B ASN 3.1 0.5 + - - -
179B VAL* 2.8 38.6 + - + +
182B ASP* 3.5 36.1 - - + -
183B TYR* 3.7 38.1 - + + -
186B ALA* 3.2 14.8 - - + +
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 2.6 31.7 + - - -
31A ILE* 3.7 12.1 - - + -
174A ILE* 3.4 37.3 - - - +
177A ARG* 3.7 23.8 - - - +
172B TYR* 3.3 12.1 - - - -
173B TYR* 2.8 57.3 + - - -
174B ILE* 3.8 16.8 + - - +
175B ASP 5.6 0.4 - - - -
176B TYR* 1.3 81.4 - - - +
178B ASN* 1.3 68.9 + - - +
179B VAL* 3.2 1.0 + - + -
4C GLU* 5.8 2.2 - - - +
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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
------------------------------------------------------------
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