Contacts of the helix formed by residues 183 - 193 (chain A) in PDB entry 4MYF
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 GLY 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLN 4.3 0.2 - - - -
182A CYS* 1.3 75.7 - - - +
184A ALA* 1.3 65.4 + - - -
185A LEU* 3.2 3.1 - - - -
186A HIS* 3.2 24.0 + - - +
187A ALA* 3.1 21.8 + - - +
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Residues in contact with ALA 184 (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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182A CYS 3.7 1.2 + - - -
183A GLY* 1.3 71.3 - - - -
185A LEU* 1.3 60.3 + - + +
187A ALA* 3.5 6.6 + - - +
188A GLN* 2.9 31.3 + - - +
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Residues in contact with LEU 185 (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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183A GLY* 3.2 1.0 - - - -
184A ALA* 1.3 79.7 - - + +
186A HIS* 1.3 63.9 + - + +
188A GLN* 3.6 26.4 + - - +
189A TYR* 3.0 28.1 + - - +
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Residues in contact with HIS 186 (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 LEU* 3.4 21.5 - - + +
143A VAL* 3.6 20.9 - - + +
144A ARG* 3.3 65.7 + - - +
145A PRO* 4.4 5.2 - - + +
159A ARG* 5.4 0.7 - - - -
182A CYS* 5.9 0.2 - - - -
183A GLY* 3.2 27.2 + - - +
185A LEU* 1.3 81.1 - - + +
187A ALA* 1.3 65.8 + - - +
189A TYR* 3.3 3.5 + - - +
190A VAL* 3.2 26.9 + - - +
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Residues in contact with ALA 187 (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 LEU* 3.4 12.8 - - + +
183A GLY 3.1 12.7 + - - +
184A ALA* 3.8 9.0 - - - +
186A HIS* 1.3 73.9 - - - +
188A GLN* 1.3 64.0 + - - +
190A VAL* 3.2 3.4 + - - +
191A ARG* 2.9 38.7 + - - +
197A LEU* 3.7 24.2 - - + +
199A TRP* 5.0 8.7 - - + -
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Residues in contact with GLN 188 (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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184A ALA 2.9 18.6 + - - +
185A LEU* 3.6 27.0 + - - +
187A ALA* 1.3 77.3 - - - +
189A TYR* 1.3 56.9 + - - +
191A ARG* 4.8 4.7 - - - +
192A ASP* 2.9 54.4 + - - +
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Residues in contact with TYR 189 (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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143A VAL* 3.6 22.7 - - + -
159A ARG* 3.4 50.7 + - + +
162A LEU* 3.6 30.0 - - + +
163A GLU* 3.3 29.8 - - - +
185A LEU 3.0 18.0 + - - +
186A HIS 3.6 5.4 - - - +
187A ALA 3.3 0.4 - - - -
188A GLN* 1.3 78.1 - - - +
190A VAL* 1.3 62.7 + - - +
192A ASP* 3.4 4.0 + - - +
193A HIS* 2.8 60.1 + + - -
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Residues in contact with VAL 190 (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 LEU* 4.3 9.0 - - + -
143A VAL* 4.0 17.5 - - + -
162A LEU* 4.4 4.9 - - + -
172A PHE* 4.1 19.1 - - + -
174A GLU* 3.8 21.8 - - + +
186A HIS 3.2 12.9 + - - +
187A ALA 3.7 5.8 - - - +
189A TYR* 1.3 80.2 - - - +
191A ARG* 1.3 57.6 + - - +
193A HIS* 3.0 14.6 + - - +
195A GLY* 3.0 45.6 + - - +
196A HIS 4.1 0.4 - - - +
197A LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ALA* 2.9 27.0 + - - +
188A GLN* 4.1 4.3 - - - +
190A VAL* 1.3 77.5 - - - +
192A ASP* 1.3 61.0 + - - +
194A GLN* 2.9 20.8 + - - +
195A GLY 3.9 17.0 - - - +
197A LEU* 3.5 44.0 + - + +
199A TRP* 3.6 21.2 - - - +
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Residues in contact with ASP 192 (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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188A GLN* 2.9 40.6 + - - +
189A TYR* 3.8 5.8 - - - +
191A ARG* 1.3 78.2 - - - +
193A HIS* 1.3 61.3 + - + +
194A GLN* 3.2 7.9 + - - +
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Residues in contact with HIS 193 (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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162A LEU* 3.7 37.8 + - + -
163A GLU* 5.4 2.4 - - - +
169A GLY* 3.2 22.2 + - - -
189A TYR* 2.8 64.5 + + - +
190A VAL* 3.0 11.0 + - - +
192A ASP* 1.3 80.4 - - + +
194A GLN* 1.3 68.3 + - - +
195A GLY 3.2 3.6 - - - -
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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