Contacts of the helix formed by residues 175 - 181 (chain D) in PDB entry 3MX4
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 SER 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D ASP* 3.7 1.6 - - - -
159D GLY* 3.4 24.4 - - - -
162D ASN* 4.0 10.1 - - - -
173D ALA 3.5 3.2 + - - -
174D LYS* 1.3 77.0 - - - +
176D ASP* 1.3 58.8 + - - +
177D TRP 3.4 3.1 + - - -
178D ASP* 2.7 35.8 + - - +
179D VAL* 2.7 34.7 + - - +
186D TRP* 5.8 2.3 - - - -
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Residues in contact with ASP 176 (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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156D VAL 4.1 12.1 - - - +
157D VAL* 3.8 20.1 - - + +
158D ASP* 3.6 16.9 + - - +
175D SER* 1.3 74.3 - - - +
177D TRP* 1.3 64.8 + - - +
179D VAL* 3.3 8.1 + - - +
180D ILE* 3.3 15.9 + - - +
195D SER* 2.8 31.6 + - - -
200D ILE* 3.7 20.7 - - + +
203D ARG* 3.3 18.5 + - - -
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Residues in contact with TRP 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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111D ASN 4.2 9.4 - - - -
112D ILE* 4.9 1.6 - - + -
115D THR* 3.6 26.5 - - + -
118D LEU* 4.5 2.5 - - + -
153D TRP* 3.3 46.9 - + - -
157D VAL* 3.6 16.3 - - + +
158D ASP 3.0 19.5 + - - +
160D PHE* 3.4 46.6 - + + +
175D SER* 3.2 2.9 - - - +
176D ASP* 1.3 74.9 - - - +
178D ASP* 1.3 61.4 + - - +
180D ILE 3.2 2.3 + - - -
181D HIS* 2.9 63.4 + + + +
184D ARG* 3.5 44.9 - - + -
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Residues in contact with ASP 178 (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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159D GLY 4.4 0.3 - - - +
174D LYS* 3.5 28.8 + - + +
175D SER* 2.7 26.1 + - - +
177D TRP* 1.3 80.4 - - - +
179D VAL* 1.3 65.2 + - - +
181D HIS 3.5 3.0 - - - +
182D PRO* 3.2 25.9 - - + +
184D ARG* 2.8 50.8 + - - +
186D TRP* 3.7 8.9 - - - -
187D ALA* 3.4 19.2 - - + +
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Residues in contact with VAL 179 (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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174D LYS* 4.0 16.6 - - + +
175D SER 2.7 31.3 + - - +
176D ASP* 3.3 11.2 + - - +
178D ASP* 1.3 75.6 - - - +
180D ILE* 1.3 62.7 + - + +
182D PRO* 3.9 7.4 - - - +
194D HIS* 4.0 26.7 - - + +
195D SER 4.0 7.0 - - - +
197D PRO* 3.9 27.6 - - + +
200D ILE* 3.8 19.5 - - + -
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Residues in contact with ILE 180 (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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57D TYR* 3.7 9.8 + - + +
59D LEU* 3.7 30.3 - - + -
60D TYR* 3.6 10.1 - - + +
117D ASN* 2.8 23.6 + - - -
157D VAL* 4.8 6.3 - - + -
176D ASP 3.3 4.6 + - - +
177D TRP 3.2 6.1 + - - +
178D ASP 3.2 0.2 - - - -
179D VAL* 1.3 82.0 - - + +
181D HIS* 1.3 95.4 + - + +
182D PRO* 3.4 7.6 - - - +
197D PRO* 5.1 7.9 - - + +
200D ILE* 3.8 38.1 - - + -
201D GLU* 5.6 0.9 - - + +
204D ILE* 4.4 4.0 - - + -
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Residues in contact with HIS 181 (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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57D TYR* 4.0 7.0 - + - -
60D TYR* 2.5 38.3 + + - -
115D THR* 3.7 19.0 - - + +
117D ASN* 2.7 26.8 + - - -
118D LEU* 3.3 27.6 - - + +
157D VAL* 5.6 0.2 - - + -
177D TRP* 2.9 55.7 + + + +
178D ASP* 3.4 6.7 + - - +
180D ILE* 1.3 103.8 + - + +
182D PRO* 1.4 68.9 - - - +
183D GLY* 3.6 0.9 + - - -
184D ARG 4.8 1.2 + - - -
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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
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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