Contacts of the strand formed by residues 45 - 53 (chain B) 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 TYR 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ASN* 3.3 41.1 + - - +
44B ASP* 1.3 95.1 - - - +
46B ILE* 1.3 77.2 + - - +
47B LYS* 4.0 21.5 - - + -
65B VAL* 4.1 13.2 - - + -
66B LEU 3.2 14.1 - - - +
68B LYS* 3.8 5.2 - - - +
93B SER 2.7 31.3 + - - -
94B PRO 3.4 13.7 - - - -
96B MSE 3.8 20.6 - - + -
99B LEU* 3.6 34.4 - - + +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 1.3 85.2 - - - +
47B LYS* 1.3 69.3 + - - +
48B ARG* 5.0 3.8 - - + -
64B ILE 3.5 0.2 - - - +
65B VAL* 3.6 0.2 - - - -
66B LEU* 2.8 54.9 + - + +
68B LYS* 3.6 31.9 - - + -
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 4.0 15.5 - - + -
46B ILE* 1.3 77.8 - - - +
48B ARG* 1.3 62.0 + - - +
49B GLU* 4.3 9.0 - - + +
63B VAL* 3.8 19.5 - - + -
64B ILE 3.5 4.5 - - - +
65B VAL* 3.9 16.6 - - + +
85B SER* 4.6 2.0 + - - -
88B THR* 2.8 43.4 + - - -
89B GLU* 4.3 11.9 + - - +
99B LEU* 3.9 18.6 - - - +
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.8 4.7 + - + -
47B LYS* 1.3 75.0 - - - +
49B GLU* 1.3 69.2 + - - +
50B VAL* 3.4 18.3 - - + +
64B ILE* 2.8 52.5 + - + +
66B LEU* 4.3 16.4 - - + -
156B TRP* 3.6 25.0 - - - -
160B ASN* 3.2 26.5 + - - +
161B VAL* 4.3 13.7 - - - +
162B SER 5.3 0.4 - - - +
163B GLU* 5.0 6.1 + - - -
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 4.3 9.1 + - + +
48B ARG* 1.3 78.3 - - - +
50B VAL* 1.3 70.3 + - - +
61B HIS* 2.6 36.4 + - + +
62B THR 3.4 4.7 - - - +
63B VAL* 4.3 17.0 - - + -
85B SER* 4.1 7.2 + - - -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG* 3.4 29.2 - - - +
49B GLU* 1.3 81.7 - - - +
51B MSE 1.3 63.3 + - - +
52B ILE* 3.7 15.9 - - + -
60B LEU 3.5 0.5 - - - +
61B HIS* 3.7 3.6 - - - -
62B THR* 2.9 54.9 + - - +
64B ILE* 4.0 14.1 - - + -
156B TRP* 3.7 30.7 - - + -
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Residues in contact with MSE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 1.3 75.6 - - - +
52B ILE* 1.3 59.9 + - - +
53B PRO* 3.4 10.4 - - - +
59B LYS* 3.8 47.7 - - + +
60B LEU 3.6 2.0 - - - -
61B HIS* 3.7 34.3 - - + +
124B GLY 3.6 18.2 - - - +
126B GLU* 4.3 14.6 - - + +
156B TRP* 5.2 3.5 + - - -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.7 14.4 - - + -
51B MSE 1.3 70.4 - - - +
53B PRO* 1.3 68.6 - - + +
54B MSE 3.3 26.5 - - + +
59B LYS* 3.3 1.2 - - - -
60B LEU 2.9 31.6 + - - +
62B THR* 3.5 32.8 - - + +
117B GLN* 4.0 8.3 - - - +
152B ASP 4.2 4.0 - - - +
153B THR* 4.2 14.6 - - + +
156B TRP* 3.5 52.0 - - + -
157B LEU* 4.5 3.4 - - + -
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Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B MSE 3.4 9.6 - - - +
52B ILE* 1.3 92.4 - - + +
54B MSE 1.3 70.8 + - - +
57B GLY* 4.6 8.1 - - - +
58B VAL 3.6 6.1 - - - +
59B LYS* 4.0 17.0 - - + -
152B ASP* 4.6 4.9 - - - +
156B TRP* 4.3 16.2 - - + +
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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