Contacts of the helix formed by residues 183 - 189 (chain V) in PDB entry 4MXW
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 LYS 183 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125V LEU* 3.6 42.2 + - + +
126V LYS* 5.5 3.0 + - - +
128V GLY* 3.0 30.0 + - - +
129V THR* 4.1 1.5 - - - +
130V ALA* 4.8 4.3 - - - +
182V SER* 1.3 70.7 - - - +
184V ALA* 1.3 66.0 + - - +
186V TYR* 3.2 7.0 + - + +
187V GLU* 3.0 53.6 + - + +
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Residues in contact with ALA 184 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182V SER* 3.3 9.5 + - - +
183V LYS* 1.3 78.9 - - - +
185V ASP* 1.3 65.1 + - - +
187V GLU* 3.4 5.6 + - - +
188V LYS* 3.0 25.0 + - - +
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Residues in contact with ASP 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181V LEU* 4.2 32.0 - - + +
182V SER* 3.5 18.4 + - - +
183V LYS 3.4 0.4 - - - -
184V ALA* 1.3 81.2 - - - +
186V TYR* 1.3 63.4 + - - +
188V LYS* 3.3 8.3 + - - +
189V HIS* 3.0 35.2 + - + -
192V TYR* 3.7 1.7 + - - -
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Residues in contact with TYR 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V PRO* 5.2 1.9 - - - +
120V PRO* 3.4 37.9 + - + +
125V LEU* 3.6 34.7 - - + +
130V ALA* 4.0 11.7 - - + -
132V VAL* 4.8 4.7 - - + -
181V LEU* 5.2 4.9 - - + +
182V SER 3.3 12.0 + - - +
183V LYS* 3.2 9.9 + - - +
185V ASP* 1.3 79.5 - - - +
187V GLU* 1.3 74.4 + - + +
189V HIS 3.4 9.2 + - - +
192V TYR* 2.4 68.5 + + - -
209V PHE* 4.1 7.6 - + - -
211V ARG* 3.9 22.7 + - - +
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Residues in contact with GLU 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125V LEU* 5.5 4.9 - - - +
183V LYS* 3.0 45.5 + - + +
184V ALA* 4.2 3.9 - - - +
186V TYR* 1.3 85.7 - - + +
188V LYS* 1.3 63.7 + - - +
189V HIS 3.2 8.6 + - - +
211V ARG* 5.7 4.5 - - - +
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Residues in contact with LYS 188 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184V ALA 3.0 17.7 + - - +
185V ASP* 3.6 12.3 - - - +
186V TYR 3.3 0.4 - - - -
187V GLU* 1.3 78.3 - - - +
189V HIS* 1.3 73.1 + - + +
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Residues in contact with HIS 189 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150V VAL* 3.5 42.0 - - + +
151V ASP* 4.7 10.3 - - + -
155V GLN* 5.9 0.8 + - - -
181V LEU* 6.6 0.2 - - + -
185V ASP* 3.0 28.2 + - + -
186V TYR 3.4 13.5 + - - +
187V GLU* 3.2 7.8 - - - +
188V LYS* 1.3 95.9 - - + +
190V LYS* 1.3 61.4 + - - +
191V VAL 5.2 0.2 - - - +
192V TYR* 3.9 7.6 - - + +
211V ARG 4.1 8.1 - - - +
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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