Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 3MR3
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 GLU 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.1 18.7 - - + +
12A VAL 3.0 18.6 - - - +
13A ASP* 3.2 12.0 - - + +
100A MET* 3.7 7.3 - - - +
103A MET* 5.8 0.2 - - - -
112A ALA* 2.9 35.9 + - + +
113A SER* 2.7 31.5 + - - +
114A ILE 3.8 0.2 - - - -
115A ASP* 1.3 78.5 - - - +
117A ALA* 1.3 60.3 + - - +
118A TYR* 5.1 1.2 + - - -
224A LYS* 4.4 13.7 + - - +
435A MG 2.1 30.6 - - - -
9P T 2.8 20.3 - - - +
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Residues in contact with ALA 117 (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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11A LEU* 3.2 6.7 - - - +
12A VAL 3.0 29.3 + - - +
100A MET* 3.9 20.6 - - - -
103A MET* 3.7 27.0 - - + +
109A ILE* 4.3 6.7 - - + -
110A GLU 3.2 17.3 - - - +
112A ALA 4.1 1.1 - - - +
116A GLU* 1.3 76.3 - - - +
118A TYR* 1.3 64.7 - - - +
119A VAL* 4.1 0.2 - - - +
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Residues in contact with TYR 118 (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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9A VAL* 4.3 2.9 - - + -
10A ALA 3.2 11.9 - - - +
11A LEU* 3.6 26.2 - - + +
109A ILE* 3.1 9.5 - - - +
110A GLU* 2.9 40.2 + - + +
112A ALA* 3.6 28.9 - - + -
116A GLU* 5.1 1.3 + - - -
117A ALA* 1.3 73.0 - - - +
119A VAL* 1.3 61.6 - - - +
220A LYS* 3.4 51.4 - - + -
224A LYS* 3.6 15.6 - - - +
256A ARG* 2.8 39.8 + - - -
310A VAL* 3.9 21.2 - - + +
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Residues in contact with VAL 119 (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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9A VAL* 3.3 6.9 - - - +
10A ALA* 2.7 46.5 + - + +
12A VAL* 4.4 6.7 - - + -
103A MET* 3.2 34.8 - - + -
107A ALA* 3.7 16.4 - - + +
108A VAL 3.7 5.2 - - - +
109A ILE* 4.2 5.2 - - + -
117A ALA 4.1 1.8 - - - +
118A TYR* 1.3 76.6 - - - +
120A ASP* 1.3 61.9 + - - +
121A LEU* 3.6 28.6 + - + -
200A MET* 4.1 17.9 - - + -
310A VAL* 4.3 3.1 - - - -
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Residues in contact with ASP 120 (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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7A ARG* 4.6 11.5 - - - -
8A VAL 3.9 4.0 - - - +
9A VAL* 4.8 4.5 - - - +
107A ALA* 3.7 15.1 - - - +
108A VAL* 3.3 21.2 + - + +
119A VAL* 1.3 70.1 - - - +
121A LEU* 1.3 59.8 + - - +
122A THR* 3.0 28.6 + - - -
123A SER* 4.8 7.1 + - - -
124A ALA 5.4 0.2 + - - -
310A VAL* 3.9 33.7 + - + +
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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