Contacts of the strand formed by residues 59 - 67 (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 LYS 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A MSE 3.8 42.0 - - + +
52A ILE 3.3 5.4 - - - +
53A PRO* 4.0 18.6 - - + -
57A GLY 4.0 9.4 - - - +
58A VAL* 1.3 73.3 - - - +
60A LEU* 1.3 62.5 + - - +
61A HIS 4.1 0.2 - - - -
125A SER* 3.9 0.9 - - - -
126A GLU* 3.0 55.6 + - - +
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Residues in contact with LEU 60 (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 3.5 0.9 - - - +
51A MSE 4.3 1.8 - - - -
52A ILE* 2.9 26.1 + - - +
54A MSE 3.7 29.6 - - + -
58A VAL* 4.1 13.5 - - + -
59A LYS* 1.3 80.3 - - - +
61A HIS* 1.3 60.0 + - - +
62A THR* 3.1 14.7 + - - -
79A ARG* 3.4 29.8 - - - +
117A GLN* 3.4 25.6 - - - +
118A ASP 4.0 4.3 - - - +
120A ARG* 3.7 30.3 - - + +
125A SER* 3.2 11.4 - - - +
149A ASP* 4.0 6.3 - - - +
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Residues in contact with HIS 61 (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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49A GLU* 2.6 32.1 + - + +
50A VAL 4.6 3.1 - - - -
51A MSE 3.7 21.1 - - + -
60A LEU* 1.3 69.1 - - - +
62A THR* 1.3 62.7 + - - +
63A VAL* 3.7 14.8 - - + +
83A ASP* 5.8 0.4 - - - -
84A ALA* 4.6 0.9 - - - +
85A SER* 3.3 28.7 - - - -
116A PHE 4.4 0.2 - - - +
117A GLN* 3.5 2.1 - - - +
118A ASP* 2.8 50.5 + - - +
124A GLY* 3.4 33.5 - - - +
125A SER* 2.8 11.2 + - - +
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Residues in contact with THR 62 (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 4.0 0.2 - - - +
49A GLU* 3.4 5.7 - - - +
50A VAL* 2.9 51.3 + - + +
52A ILE* 3.4 17.4 - - + +
60A LEU 3.1 8.8 + - - -
61A HIS* 1.3 73.3 - - - +
63A VAL* 1.3 62.7 + - - +
64A ILE* 4.1 3.6 - - + -
115A VAL* 3.4 32.1 - - + -
116A PHE 3.6 5.4 - - - +
117A GLN* 3.0 31.3 + - + +
153A THR* 5.2 1.1 - - + -
157A LEU* 4.7 2.2 - - + -
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Residues in contact with VAL 63 (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* 3.8 28.3 - - + -
48A ARG 3.8 2.9 - - - +
49A GLU* 4.3 7.4 - - + +
61A HIS* 3.7 26.2 - - + +
62A THR* 1.3 75.9 - - - +
64A ILE* 1.3 63.2 + - - +
65A VAL* 4.3 2.2 - - + -
84A ALA* 4.0 4.9 - - + +
85A SER* 3.9 22.9 - - - +
88A THR* 3.4 30.4 - - + +
114A ARG 3.7 1.4 - - - +
115A VAL* 3.3 5.6 - - - +
116A PHE 2.8 34.6 + - - +
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Residues in contact with ILE 64 (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 3.5 1.9 - - - +
47A LYS* 3.4 3.1 - - - +
48A ARG* 2.8 54.7 + - + +
50A VAL* 4.0 33.9 - - + -
62A THR* 4.6 4.3 - - + -
63A VAL* 1.3 76.8 - - - +
65A VAL* 1.3 62.5 + - - +
66A LEU* 3.7 18.4 - - + +
113A ILE* 3.6 26.0 - - + -
114A ARG 3.6 2.7 - - - -
115A VAL* 4.1 18.6 - - + -
156A TRP* 4.4 1.6 - - + -
157A LEU* 4.1 15.7 - - + -
161A VAL* 4.1 18.2 - - + -
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Residues in contact with VAL 65 (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* 4.2 13.7 - - + -
46A ILE 3.6 2.7 - - - +
47A LYS* 4.0 24.9 - - + -
63A VAL* 4.3 2.0 - - + -
64A ILE* 1.3 75.6 - - - +
66A LEU* 1.3 63.3 + - - +
88A THR* 4.1 21.3 - - + -
96A MSE 3.6 30.8 - - + +
99A LEU* 4.1 20.2 - - + -
100A LEU* 4.2 8.1 - - + -
113A ILE* 3.5 3.9 - - - -
114A ARG* 2.8 43.7 + - + +
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Residues in contact with LEU 66 (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* 3.2 5.8 - - - +
46A ILE* 2.9 55.2 + - + +
48A ARG* 4.3 17.3 - - + +
64A ILE* 3.7 24.2 - - + +
65A VAL* 1.3 74.5 - - - +
67A PRO* 1.3 74.1 - - + +
70A ALA* 4.6 1.3 - - + -
96A MSE 4.4 0.9 - - - -
113A ILE* 4.0 16.8 - - + -
161A VAL* 4.1 9.0 - - + -
163A GLU* 3.5 45.8 - - + +
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Residues in contact with PRO 67 (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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44A ASP 3.9 8.1 - - - +
46A ILE* 5.6 0.3 - - - +
65A VAL 4.1 0.9 - - - +
66A LEU* 1.3 90.0 - - + +
68A LYS* 1.3 67.7 + - - +
69A GLY 3.4 0.2 + - - -
70A ALA* 3.1 30.7 + - + +
96A MSE 3.9 17.5 - - + -
108A VAL 5.7 1.1 - - - +
111A GLY* 3.9 21.3 - - - +
112A TYR 3.5 26.9 - - - +
113A ILE* 4.2 5.6 - - + -
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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