Contacts of the strand formed by residues 45 - 53 (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 TYR 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ASN* 3.3 42.0 + - - +
44A ASP* 1.3 94.2 - - - +
46A ILE* 1.3 82.8 + - - +
47A LYS* 4.0 14.6 - - + -
65A VAL* 4.2 7.0 - - + -
66A LEU 3.2 15.0 - - - +
68A LYS* 3.8 4.6 - - - +
93A SER 2.8 30.7 + - - -
94A PRO 3.5 13.0 - - - -
96A MSE 3.8 26.0 - - + -
99A LEU* 3.6 36.2 - - + +
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Residues in contact with ILE 46 (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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45A TYR* 1.3 84.3 - - - +
47A LYS* 1.3 70.4 + - - +
48A ARG* 4.8 4.5 - - + +
65A VAL* 3.6 0.7 - - - -
66A LEU* 2.9 53.9 + - + +
67A PRO 5.6 0.2 - - - +
68A LYS* 3.6 31.9 - - + -
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Residues in contact with LYS 47 (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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45A TYR* 4.0 14.9 - - + -
46A ILE* 1.3 77.8 - - - +
48A ARG* 1.3 63.5 + - - +
49A GLU* 5.2 7.9 - - + +
63A VAL* 3.8 20.2 - - + -
64A ILE 3.4 4.7 - - - +
65A VAL* 4.0 11.9 - - + +
85A SER* 4.5 2.4 + - - -
88A THR* 2.8 48.7 + - - +
89A GLU* 4.1 13.9 + - - +
99A LEU* 3.8 18.7 - - - +
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Residues in contact with ARG 48 (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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46A ILE* 5.0 5.2 - - + -
47A LYS* 1.3 76.0 - - - +
49A GLU* 1.3 68.9 + - - +
50A VAL* 3.4 17.0 - - + +
63A VAL* 3.8 0.4 - - - -
64A ILE* 2.8 53.6 + - + +
66A LEU* 4.3 16.8 - - + +
156A TRP* 3.6 26.1 - - - -
160A ASN* 3.3 26.7 + - - +
161A VAL* 4.3 14.1 - - - +
162A SER 5.3 0.2 - - - +
163A GLU* 5.0 5.7 + - - -
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Residues in contact with GLU 49 (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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47A LYS* 4.4 8.1 + - + +
48A ARG* 1.3 76.8 + - - +
50A VAL* 1.3 70.9 + - - +
61A HIS* 2.6 36.8 + - + +
62A THR 3.4 4.9 - - - +
63A VAL* 4.3 15.3 - - + -
85A SER* 4.2 7.1 + - - -
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Residues in contact with VAL 50 (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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48A ARG* 3.4 28.9 - - + +
49A GLU* 1.3 80.7 - - - +
51A MSE 1.3 62.7 + - - +
52A ILE* 3.7 15.3 - - + -
60A LEU 3.5 1.0 - - - +
61A HIS* 3.8 3.5 - - - -
62A THR* 2.9 54.3 + - - +
64A ILE* 4.0 13.2 - - + -
156A TRP* 3.7 31.2 - - + -
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Residues in contact with MSE 51 (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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50A VAL* 1.3 73.8 - - - +
52A ILE* 1.3 60.7 + - - +
53A PRO* 3.4 10.6 - - - +
59A LYS* 3.8 50.6 - - + +
60A LEU 3.7 1.6 - - - -
61A HIS* 3.7 36.3 - - + +
124A GLY 3.7 18.6 - - - +
126A GLU* 4.2 15.3 - - + +
156A TRP* 5.2 3.5 + - - -
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Residues in contact with ILE 52 (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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50A VAL* 3.7 14.6 - - + -
51A MSE 1.3 70.5 - - - +
53A PRO* 1.3 70.5 - - + +
54A MSE 3.3 26.1 - - + +
59A LYS* 3.3 1.9 - - - -
60A LEU 2.9 33.2 + - - +
62A THR* 3.4 33.4 - - + +
117A GLN* 4.0 8.3 - - - +
152A ASP 4.2 3.8 - - - +
153A THR* 4.1 14.8 - - + +
156A TRP* 3.5 52.3 - - + -
157A LEU* 4.4 2.5 - - + -
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Residues in contact with PRO 53 (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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51A MSE 3.4 9.4 - - - +
52A ILE* 1.3 90.3 - - + +
54A MSE 1.3 71.3 + - - +
57A GLY* 4.7 8.1 - - - +
58A VAL 3.7 5.8 - - - +
59A LYS* 4.0 17.7 - - + -
152A ASP* 4.6 4.5 - - - +
156A TRP* 4.3 15.0 - - + +
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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