Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 1MPX
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 ILE 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.6 31.2 - - + -
65A VAL 3.5 8.1 - - - +
66A LEU* 4.0 23.3 - - + -
67A PRO* 4.2 12.3 - - + -
70A ALA* 4.6 1.6 - - + -
73A ALA* 3.8 33.9 - - + +
74A PRO 3.0 11.0 + - - +
75A ILE* 3.3 15.2 - - + +
76A VAL* 3.0 25.6 + - - -
112A TYR* 1.3 74.1 - - - +
114A ARG* 1.3 61.2 + - - +
115A VAL* 4.0 4.0 + - + -
161A VAL* 4.4 3.4 - - + -
163A GLU* 3.9 18.6 - - + +
164A SER* 4.2 8.3 - - - +
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Residues in contact with ARG 114 (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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63A VAL 3.7 1.4 - - - +
64A ILE* 3.6 1.6 - - - -
65A VAL* 2.8 44.2 + - + +
76A VAL* 3.2 42.2 + - - +
78A THR* 3.0 31.5 + - - +
87A ARG* 5.4 1.6 - - - +
88A THR* 5.4 0.4 - - + +
96A MSE 4.6 2.7 - - + -
100A LEU* 4.0 24.2 - - + -
104A ASP* 3.0 39.0 + - - +
107A PHE* 3.9 12.2 - - + -
112A TYR 3.8 2.5 + - - +
113A ILE* 1.3 71.9 - - - +
115A VAL* 1.3 73.2 + - - +
116A PHE* 3.3 28.2 - - + -
171A ILE* 3.8 11.3 - - - +
172A GLY* 6.0 0.4 - - - -
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Residues in contact with VAL 115 (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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62A THR* 3.4 31.0 - - + -
63A VAL 3.3 5.6 - - - +
64A ILE* 4.1 25.1 - - + -
75A ILE* 3.7 24.9 - - + -
76A VAL 2.9 10.5 + - - +
77A LEU* 3.4 20.5 - - + -
78A THR 2.9 25.6 + - - -
113A ILE* 4.2 4.5 - - + -
114A ARG* 1.3 85.3 + - - +
116A PHE* 1.3 65.7 + - - +
157A LEU* 4.3 12.3 - - + -
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Residues in contact with PHE 116 (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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62A THR* 3.6 0.7 - - - +
63A VAL 2.8 31.4 + - - +
78A THR* 3.3 31.4 - - + -
80A THR* 4.2 10.8 - - + -
84A ALA* 3.5 18.9 - - + +
87A ARG* 3.7 53.8 - - + -
88A THR* 3.5 31.4 - - + -
100A LEU* 5.6 0.4 - - + -
101A SER* 5.5 0.7 - - - -
104A ASP* 3.7 14.1 - - - -
114A ARG* 3.3 38.4 - - + -
115A VAL* 1.3 77.7 - - - +
117A GLN* 1.3 60.6 + - - +
176A GLU* 4.1 0.4 - - - -
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Residues in contact with GLN 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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52A ILE* 4.0 5.5 - - - +
54A MSE 4.5 1.2 - - - +
60A LEU* 3.6 21.0 - - + +
61A HIS 3.5 5.4 - - - +
62A THR* 3.0 29.6 + - + +
77A LEU* 4.6 6.7 - - + -
78A THR 2.9 11.2 + - - +
79A ARG* 2.9 42.8 + - - -
80A THR* 2.8 27.9 + - - +
84A ALA* 4.0 3.6 - - - -
116A PHE* 1.3 77.1 - - - +
118A ASP* 1.3 71.7 - - - +
119A VAL 3.4 0.2 + - - -
153A THR* 2.9 33.2 + - - +
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Residues in contact with ASP 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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60A LEU* 3.8 3.6 - - - +
61A HIS* 2.8 37.2 + - - +
80A THR 3.4 4.6 - - - +
83A ASP* 3.6 10.9 + - - +
84A ALA* 2.8 30.5 + - - +
117A GLN* 1.3 80.3 - - - +
119A VAL* 1.3 60.2 + - - +
120A ARG 3.8 0.2 + - - -
122A LYS* 3.4 18.8 - - + +
123A TYR* 3.6 7.6 - - - +
124A GLY 3.1 13.9 + - - -
125A SER* 2.7 32.7 + - - +
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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