Contacts of the helix formed by residues 170 - 174 (chain A) in PDB entry 4M8J
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 ARG 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 4.4 16.6 + - - +
13A LYS* 5.2 8.5 - - - +
14A VAL* 3.8 25.5 - - - +
168A VAL* 4.0 5.4 - - - +
169A ILE* 1.3 104.9 - - + +
171A PRO* 1.3 73.1 - - + +
172A SER* 3.2 4.7 + - - +
173A SER* 2.9 27.9 + - - +
193A ASP* 3.6 28.7 + - + +
196A TYR* 6.4 0.2 - - + -
197A LEU* 5.2 4.3 - - + -
433A SER* 3.2 39.0 + - - +
435A CYS 3.4 20.6 + - - -
437A SER* 5.1 4.6 + - - +
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Residues in contact with PRO 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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157A PHE* 5.5 5.2 - - + -
168A VAL* 5.6 0.4 - - + -
169A ILE 4.2 2.0 - - - +
170A ARG* 1.3 87.8 - - + +
172A SER* 1.3 55.2 + - - +
173A SER 3.0 0.2 - - - -
174A THR* 2.3 40.9 + - + +
175A LEU* 3.2 6.2 - - + +
192A VAL* 5.4 1.8 - - + -
193A ASP* 3.6 12.6 - - - +
196A TYR* 3.6 45.1 - - + -
329A ILE* 4.0 29.2 - - + -
433A SER* 6.3 0.2 - - - -
486A VAL* 4.4 11.0 - - + -
490A VAL* 4.5 4.9 - - + -
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Residues in contact with SER 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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13A LYS* 5.6 2.1 + - - -
170A ARG* 4.1 6.4 + - - +
171A PRO* 1.3 77.5 - - - +
173A SER* 1.3 60.7 + - - +
174A THR 3.0 4.1 + - - -
175A LEU* 3.3 24.8 + - - +
184A VAL* 3.3 26.7 + - - +
189A GLY* 3.4 26.8 + - - -
192A VAL* 4.2 3.4 - - - -
193A ASP* 2.5 32.0 + - - -
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Residues in contact with SER 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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166A MET* 4.1 10.4 - - - +
167A GLU 4.9 2.9 - - - -
168A VAL* 3.7 25.9 - - - +
169A ILE* 4.6 3.8 + - - +
170A ARG* 2.9 25.6 + - - +
171A PRO 3.0 0.6 - - - -
172A SER* 1.3 80.2 + - - +
174A THR* 1.3 58.0 + - - +
175A LEU 3.6 0.2 - - - -
176A VAL* 3.4 19.5 - - - +
184A VAL* 4.9 3.4 - - - -
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Residues in contact with THR 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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157A PHE* 4.3 15.0 - - + -
160A PHE* 4.1 28.3 - - + -
168A VAL* 3.6 33.2 - - + -
171A PRO 2.3 29.3 + - - +
173A SER* 1.3 79.0 - - - +
175A LEU* 1.3 63.4 + - - +
176A VAL 3.1 9.2 + - - -
177A PRO* 3.2 11.5 - - - +
490A VAL* 3.7 21.7 - - + +
493A SER* 3.1 17.6 + - - -
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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