Contacts of the strand formed by residues 121 - 126 (chain D) in PDB entry 3MGO
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 121 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D TYR* 5.8 2.8 + - - -
117D ALA* 3.2 6.3 - - - +
118D TYR* 2.9 31.4 + - - +
119D ASP* 4.4 2.7 - - - +
120D GLY* 1.3 81.6 - - - +
122D ASP* 1.3 73.6 + - - +
123D TYR* 4.1 0.3 - - - +
136D ALA* 6.3 0.6 - - - +
137D ASP* 5.1 8.3 + - - -
1E ILE* 3.5 31.4 - - + -
60E TRP* 4.8 0.4 - - - -
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Residues in contact with ASP 122 (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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115D GLN* 5.4 2.3 + - - +
116D TYR 4.0 3.9 - - - +
121D LYS* 1.3 79.0 + - - +
123D TYR* 1.3 59.7 + - - +
124D ILE 6.4 0.2 - - - -
136D ALA* 3.3 22.2 - - + +
60E TRP* 2.8 33.1 + - - +
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Residues in contact with TYR 123 (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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81D LEU* 3.6 22.4 - - + -
84D TYR* 3.4 15.4 - - - -
85D TYR* 3.2 29.8 - + - -
116D TYR* 3.0 22.6 + - + +
117D ALA 4.3 0.7 - - - +
118D TYR* 4.1 20.2 - - + +
121D LYS 3.2 0.6 + - - +
122D ASP* 1.3 74.5 - - - +
124D ILE* 1.3 74.9 + - + +
134D THR 3.9 0.3 - - - +
136D ALA* 3.2 16.8 + - - +
137D ASP* 4.5 1.1 - - - -
139D ALA* 3.1 14.1 + - + -
140D ALA* 3.2 41.5 - - + +
143D THR* 2.8 33.3 + - - -
9F ILE* 3.8 17.9 - - + -
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Residues in contact with ILE 124 (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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115D GLN* 3.6 0.7 - - - -
116D TYR* 2.8 40.3 + - + +
122D ASP* 6.4 0.4 - - - -
123D TYR* 1.3 100.4 - - + +
125D ALA* 1.3 66.7 + - - +
133D TRP* 3.8 22.9 - - + -
134D THR 3.5 12.3 - - - +
135D ALA* 4.9 2.7 - - - -
140D ALA* 4.4 3.8 - - + +
143D THR* 4.3 4.0 - - + -
144D LYS* 3.9 32.5 - - + +
147D TRP* 3.7 42.2 - - + -
9F ILE* 4.7 0.4 - - + -
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Residues in contact with ALA 125 (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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114D HIS 3.5 5.6 - - - -
115D GLN* 3.6 23.1 - - + -
122D ASP* 5.9 5.6 - - + +
124D ILE* 1.3 80.1 - - - +
126D LEU* 1.3 65.6 + - - +
127D LYS 3.5 0.2 + - - -
133D TRP* 3.4 8.2 - - - -
134D THR* 2.8 43.9 + - - +
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Residues in contact with LEU 126 (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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112D GLY 5.1 4.2 - - - +
113D TYR* 5.4 1.1 - - - -
114D HIS* 2.8 35.6 + - + +
115D GLN* 5.2 2.9 - - - +
125D ALA* 1.3 75.3 - - - +
127D LYS* 1.3 68.5 + - - +
130D LEU* 3.6 48.7 - - + +
131D ARG 3.9 0.7 - - - +
132D SER 3.6 16.6 - - - +
133D TRP* 3.5 22.4 - - + -
153D ALA* 4.1 16.6 - - + +
156D LEU* 4.4 14.4 - - + -
157D ARG 5.2 0.2 - - - +
160D LEU* 3.8 17.7 - - + -
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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