Contacts of the strand formed by residues 180 - 184 (chain A) in PDB entry 3MXW
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 HIS 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A THR* 4.7 3.1 - - - +
147A ASP* 3.4 35.0 - - + -
148A ILE 3.5 13.0 - - - +
149A THR* 4.4 3.8 - - + -
158A TYR* 4.1 4.6 - - - -
176A GLU* 2.7 35.8 + - + +
177A SER* 2.7 50.8 + - - +
178A LYS 3.6 0.6 - - - -
179A ALA* 1.3 82.6 - - - +
181A ILE* 1.3 72.2 + - - +
182A HIS 3.9 0.4 - - - -
97H GLU 4.1 12.0 + - - +
98H ARG* 3.4 17.1 + - - -
50L TYR* 3.1 27.1 - - - -
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Residues in contact with ILE 181 (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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147A ASP* 3.2 4.0 - - - -
148A ILE* 2.9 46.8 + - + +
158A TYR* 3.4 35.2 - - + +
161A LEU* 4.3 6.5 - - + -
162A ALA* 3.8 13.9 - - + +
173A VAL* 3.6 28.3 - - + -
174A TYR 3.5 9.0 - - - +
175A TYR* 3.4 42.0 - - + -
180A HIS* 1.3 77.4 - - - +
182A HIS* 1.3 62.0 + - - +
183A CYS* 3.9 9.6 - - - -
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Residues in contact with HIS 182 (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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3A SO4 3.4 25.6 + - - -
53A GLU* 2.7 30.5 + - - -
139A LEU* 5.4 0.7 - - + -
140A HIS* 3.3 0.2 + - - -
145A ALA* 3.5 22.4 - - + -
147A ASP* 3.3 5.3 + - - -
172A TRP* 3.7 22.4 - + - -
173A VAL* 3.4 1.9 - - - -
174A TYR* 2.8 45.1 + - + +
176A GLU* 3.4 24.7 - - + +
180A HIS* 3.9 1.6 - - - -
181A ILE* 1.3 72.5 - - - +
183A CYS* 1.3 64.3 + - - +
184A SER* 3.9 4.0 - - - -
400A ZN 2.1 32.6 - - - -
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Residues in contact with CYS 183 (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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145A ALA* 3.2 4.5 - - - +
146A VAL* 2.8 39.3 + - + +
148A ILE* 3.7 24.5 - - - -
165A ALA* 3.6 29.4 - - - -
170A PHE* 3.5 30.0 - - + -
172A TRP 3.4 5.6 - - - +
173A VAL* 4.1 3.4 - - - -
181A ILE* 3.9 8.7 - - - -
182A HIS* 1.3 81.3 - - - +
184A SER* 1.3 61.9 + - - +
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Residues in contact with SER 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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53A GLU* 2.7 29.5 + - - -
59A SER* 2.7 21.6 + - - -
139A LEU* 3.9 7.9 - - - -
144A ARG 3.1 14.4 - - - -
145A ALA* 3.9 5.4 - - - -
170A PHE* 3.6 3.7 - - - -
171A ASP 3.0 22.9 + - - -
172A TRP* 2.9 22.1 + - - +
182A HIS* 3.9 0.6 + - - -
183A CYS* 1.3 76.5 - - - +
185A VAL* 1.3 66.7 + - - +
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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